Starting phenix.real_space_refine on Tue Jul 7 00:33:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fi8_50448/07_2026/9fi8_50448.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fi8_50448/07_2026/9fi8_50448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fi8_50448/07_2026/9fi8_50448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fi8_50448/07_2026/9fi8_50448.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fi8_50448/07_2026/9fi8_50448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fi8_50448/07_2026/9fi8_50448.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 283 5.49 5 S 141 5.16 5 C 24891 2.51 5 N 7403 2.21 5 O 8251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 422 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40969 Number of models: 1 Model: "" Number of chains: 28 Chain: "HA" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3287 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 382} Chain breaks: 3 Chain: "HB" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1234 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "HC" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1432 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 16, 'TRANS': 164} Chain breaks: 2 Chain: "HD" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 844 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "HE" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "HF" Number of atoms: 2739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2739 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "HG" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 726 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "HH" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 761 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 9, 'TRANS': 80} Chain: "HI" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1203 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 15, 'TRANS': 128} Chain: "HJ" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3448 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 29, 'TRANS': 400} Chain breaks: 2 Chain: "HK" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1045 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "HL" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "HM" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4037 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 493} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "HN" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 232 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "HO" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1391 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 158} Chain: "HP" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1608 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 14, 'TRANS': 182} Chain breaks: 1 Chain: "HQ" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4753 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 31, 'TRANS': 575} Chain breaks: 9 Chain: "HR" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1361 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain breaks: 1 Chain: "HS" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1001 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "HT" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2313 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 19, 'TRANS': 261} Chain breaks: 1 Chain: "bN" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1220 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain: "hB" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1203 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 28, 'rna3p_pyr': 17} Link IDs: {'rna2p': 10, 'rna3p': 45} Chain: "hD" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 5, 'rna3p': 9} Chain: "hG" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1436 Classifications: {'RNA': 68} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 21, 'rna3p_pyr': 28} Link IDs: {'rna2p': 18, 'rna3p': 49} Chain: "hL" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 706 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 13, 'rna3p_pyr': 9} Link IDs: {'rna2p': 10, 'rna3p': 22} Chain: "hM" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 6, 'rna3p_pyr': 4} Link IDs: {'rna2p': 6, 'rna3p': 3} Chain: "hR" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 575 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 7, 'rna3p_pyr': 8} Link IDs: {'rna2p': 11, 'rna3p': 15} Chain: "hS" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pyr': 9, 'rna3p_pyr': 8} Link IDs: {'rna2p': 9, 'rna3p': 7} Time building chain proxies: 8.35, per 1000 atoms: 0.20 Number of scatterers: 40969 At special positions: 0 Unit cell: (150.57, 183.695, 162.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 141 16.00 P 283 15.00 O 8251 8.00 N 7403 7.00 C 24891 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.3 seconds 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8284 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 20 sheets defined 49.2% alpha, 3.9% beta 14 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'HA' and resid 13 through 21 Processing helix chain 'HA' and resid 28 through 34 removed outlier: 4.107A pdb=" N ASPHA 32 " --> pdb=" O GLUHA 28 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLUHA 34 " --> pdb=" O SERHA 30 " (cutoff:3.500A) Processing helix chain 'HA' and resid 48 through 65 removed outlier: 3.832A pdb=" N LEUHA 52 " --> pdb=" O ARGHA 48 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLUHA 53 " --> pdb=" O LYSHA 49 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEUHA 54 " --> pdb=" O ALAHA 50 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLNHA 57 " --> pdb=" O GLUHA 53 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEUHA 58 " --> pdb=" O LEUHA 54 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HISHA 65 " --> pdb=" O PHEHA 61 " (cutoff:3.500A) Processing helix chain 'HA' and resid 159 through 169 Proline residue: HA 165 - end of helix Processing helix chain 'HA' and resid 179 through 184 removed outlier: 3.659A pdb=" N TYRHA 183 " --> pdb=" O PROHA 180 " (cutoff:3.500A) Processing helix chain 'HA' and resid 200 through 212 removed outlier: 3.783A pdb=" N GLNHA 205 " --> pdb=" O SERHA 201 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLUHA 206 " --> pdb=" O SERHA 202 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHEHA 207 " --> pdb=" O PHEHA 203 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEUHA 208 " --> pdb=" O SERHA 204 " (cutoff:3.500A) Processing helix chain 'HA' and resid 238 through 244 removed outlier: 3.739A pdb=" N ARGHA 244 " --> pdb=" O LEUHA 240 " (cutoff:3.500A) Processing helix chain 'HA' and resid 246 through 258 removed outlier: 3.518A pdb=" N LYSHA 252 " --> pdb=" O SERHA 248 " (cutoff:3.500A) Processing helix chain 'HA' and resid 258 through 263 Processing helix chain 'HA' and resid 287 through 305 removed outlier: 3.686A pdb=" N GLUHA 296 " --> pdb=" O LEUHA 292 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARGHA 297 " --> pdb=" O LEUHA 293 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEUHA 298 " --> pdb=" O ALAHA 294 " (cutoff:3.500A) Processing helix chain 'HA' and resid 327 through 332 Processing helix chain 'HA' and resid 338 through 351 removed outlier: 3.593A pdb=" N TRPHA 345 " --> pdb=" O LEUHA 341 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYSHA 349 " --> pdb=" O TRPHA 345 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYSHA 350 " --> pdb=" O GLUHA 346 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLNHA 351 " --> pdb=" O GLNHA 347 " (cutoff:3.500A) Processing helix chain 'HA' and resid 363 through 366 removed outlier: 3.823A pdb=" N CYSHA 366 " --> pdb=" O TRPHA 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'HA' and resid 363 through 366' Processing helix chain 'HA' and resid 391 through 397 removed outlier: 3.612A pdb=" N ARGHA 395 " --> pdb=" O LEUHA 391 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEUHA 397 " --> pdb=" O THRHA 393 " (cutoff:3.500A) Processing helix chain 'HA' and resid 400 through 406 removed outlier: 4.206A pdb=" N GLNHA 404 " --> pdb=" O ASPHA 401 " (cutoff:3.500A) Processing helix chain 'HA' and resid 444 through 458 removed outlier: 3.694A pdb=" N ASNHA 450 " --> pdb=" O LEUHA 446 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYSHA 457 " --> pdb=" O ALAHA 453 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYSHA 458 " --> pdb=" O TYRHA 454 " (cutoff:3.500A) Processing helix chain 'HA' and resid 465 through 469 removed outlier: 3.540A pdb=" N LYSHA 468 " --> pdb=" O PROHA 465 " (cutoff:3.500A) Processing helix chain 'HA' and resid 470 through 477 removed outlier: 4.113A pdb=" N METHA 474 " --> pdb=" O ASPHA 470 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEUHA 475 " --> pdb=" O TYRHA 471 " (cutoff:3.500A) Processing helix chain 'HA' and resid 479 through 490 Processing helix chain 'HB' and resid 2 through 12 removed outlier: 3.758A pdb=" N LEUHB 6 " --> pdb=" O SERHB 2 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VALHB 12 " --> pdb=" O SERHB 8 " (cutoff:3.500A) Processing helix chain 'HB' and resid 70 through 77 removed outlier: 3.513A pdb=" N ARGHB 74 " --> pdb=" O PHEHB 70 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VALHB 77 " --> pdb=" O ASNHB 73 " (cutoff:3.500A) Processing helix chain 'HB' and resid 78 through 85 removed outlier: 3.542A pdb=" N PHEHB 82 " --> pdb=" O LEUHB 78 " (cutoff:3.500A) Processing helix chain 'HB' and resid 100 through 120 removed outlier: 3.982A pdb=" N GLNHB 104 " --> pdb=" O GLYHB 100 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALAHB 105 " --> pdb=" O SERHB 101 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLYHB 106 " --> pdb=" O SERHB 102 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALAHB 107 " --> pdb=" O GLYHB 103 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARGHB 109 " --> pdb=" O ALAHB 105 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VALHB 117 " --> pdb=" O GLYHB 113 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SERHB 118 " --> pdb=" O ARGHB 114 " (cutoff:3.500A) Processing helix chain 'HB' and resid 125 through 129 removed outlier: 3.856A pdb=" N GLUHB 129 " --> pdb=" O LEUHB 126 " (cutoff:3.500A) Processing helix chain 'HC' and resid 1 through 3 No H-bonds generated for 'chain 'HC' and resid 1 through 3' Processing helix chain 'HC' and resid 18 through 33 removed outlier: 3.581A pdb=" N LEUHC 33 " --> pdb=" O LEUHC 29 " (cutoff:3.500A) Processing helix chain 'HC' and resid 110 through 120 removed outlier: 4.383A pdb=" N ALAHC 116 " --> pdb=" O GLUHC 112 " (cutoff:3.500A) Processing helix chain 'HC' and resid 201 through 226 removed outlier: 3.668A pdb=" N ILEHC 205 " --> pdb=" O ASPHC 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLUHC 211 " --> pdb=" O ARGHC 207 " (cutoff:3.500A) Processing helix chain 'HD' and resid 12 through 43 removed outlier: 3.678A pdb=" N TRPHD 19 " --> pdb=" O CYSHD 15 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALAHD 21 " --> pdb=" O LYSHD 17 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARGHD 22 " --> pdb=" O ASPHD 18 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARGHD 23 " --> pdb=" O TRPHD 19 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VALHD 30 " --> pdb=" O ALAHD 26 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ASNHD 31 " --> pdb=" O GLUHD 27 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARGHD 33 " --> pdb=" O GLUHD 29 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILEHD 34 " --> pdb=" O VALHD 30 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYSHD 36 " --> pdb=" O GLYHD 32 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYRHD 39 " --> pdb=" O TYRHD 35 " (cutoff:3.500A) Processing helix chain 'HD' and resid 48 through 52 Processing helix chain 'HD' and resid 55 through 59 removed outlier: 3.510A pdb=" N ARGHD 58 " --> pdb=" O GLYHD 55 " (cutoff:3.500A) Processing helix chain 'HD' and resid 79 through 89 Processing helix chain 'HE' and resid 26 through 36 removed outlier: 3.896A pdb=" N ILEHE 30 " --> pdb=" O THRHE 26 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYSHE 31 " --> pdb=" O SERHE 27 " (cutoff:3.500A) Processing helix chain 'HE' and resid 36 through 45 removed outlier: 3.853A pdb=" N ILEHE 40 " --> pdb=" O GLNHE 36 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYSHE 44 " --> pdb=" O ILEHE 40 " (cutoff:3.500A) Processing helix chain 'HE' and resid 110 through 113 Processing helix chain 'HE' and resid 114 through 119 removed outlier: 3.790A pdb=" N LEUHE 118 " --> pdb=" O ASPHE 114 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEUHE 119 " --> pdb=" O ALAHE 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'HE' and resid 114 through 119' Processing helix chain 'HE' and resid 120 through 131 Processing helix chain 'HE' and resid 150 through 161 removed outlier: 3.607A pdb=" N METHE 154 " --> pdb=" O PROHE 150 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYSHE 156 " --> pdb=" O ALAHE 152 " (cutoff:3.500A) Processing helix chain 'HF' and resid 7 through 15 removed outlier: 3.739A pdb=" N VALHF 11 " --> pdb=" O PHEHF 7 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLUHF 12 " --> pdb=" O SERHF 8 " (cutoff:3.500A) Processing helix chain 'HF' and resid 19 through 37 removed outlier: 3.555A pdb=" N ILEHF 25 " --> pdb=" O HISHF 21 " (cutoff:3.500A) Processing helix chain 'HF' and resid 42 through 50 removed outlier: 3.821A pdb=" N ILEHF 47 " --> pdb=" O VALHF 43 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLNHF 48 " --> pdb=" O ALAHF 44 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASPHF 50 " --> pdb=" O GLYHF 46 " (cutoff:3.500A) Processing helix chain 'HF' and resid 54 through 68 Processing helix chain 'HF' and resid 81 through 98 removed outlier: 3.570A pdb=" N LEUHF 90 " --> pdb=" O LYSHF 86 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARGHF 91 " --> pdb=" O ARGHF 87 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALAHF 97 " --> pdb=" O LEUHF 93 " (cutoff:3.500A) Processing helix chain 'HF' and resid 101 through 107 removed outlier: 3.589A pdb=" N GLUHF 105 " --> pdb=" O ASNHF 101 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THRHF 106 " --> pdb=" O CYSHF 102 " (cutoff:3.500A) Processing helix chain 'HF' and resid 107 through 115 removed outlier: 3.598A pdb=" N LEUHF 112 " --> pdb=" O THRHF 108 " (cutoff:3.500A) Processing helix chain 'HF' and resid 115 through 121 removed outlier: 3.967A pdb=" N GLNHF 119 " --> pdb=" O ARGHF 115 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARGHF 120 " --> pdb=" O ALAHF 116 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEUHF 121 " --> pdb=" O ASPHF 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'HF' and resid 115 through 121' Processing helix chain 'HF' and resid 132 through 140 removed outlier: 3.748A pdb=" N VALHF 139 " --> pdb=" O LEUHF 135 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLYHF 140 " --> pdb=" O ALAHF 136 " (cutoff:3.500A) Processing helix chain 'HF' and resid 147 through 163 removed outlier: 3.766A pdb=" N ALAHF 158 " --> pdb=" O GLNHF 154 " (cutoff:3.500A) Processing helix chain 'HF' and resid 164 through 166 No H-bonds generated for 'chain 'HF' and resid 164 through 166' Processing helix chain 'HF' and resid 189 through 194 removed outlier: 4.506A pdb=" N VALHF 193 " --> pdb=" O LYSHF 189 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEUHF 194 " --> pdb=" O VALHF 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'HF' and resid 189 through 194' Processing helix chain 'HF' and resid 231 through 235 removed outlier: 3.603A pdb=" N LYSHF 234 " --> pdb=" O SERHF 231 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLYHF 235 " --> pdb=" O METHF 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'HF' and resid 231 through 235' Processing helix chain 'HF' and resid 237 through 245 removed outlier: 4.233A pdb=" N GLUHF 242 " --> pdb=" O LYSHF 238 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEUHF 243 " --> pdb=" O ILEHF 239 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARGHF 245 " --> pdb=" O LYSHF 241 " (cutoff:3.500A) Processing helix chain 'HF' and resid 261 through 276 removed outlier: 3.861A pdb=" N ALAHF 271 " --> pdb=" O SERHF 267 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILEHF 272 " --> pdb=" O VALHF 268 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARGHF 273 " --> pdb=" O ALAHF 269 " (cutoff:3.500A) Processing helix chain 'HF' and resid 282 through 299 removed outlier: 3.518A pdb=" N VALHF 287 " --> pdb=" O PHEHF 283 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEUHF 293 " --> pdb=" O ALAHF 289 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLUHF 295 " --> pdb=" O ASNHF 291 " (cutoff:3.500A) Processing helix chain 'HF' and resid 302 through 314 removed outlier: 4.125A pdb=" N LYSHF 308 " --> pdb=" O ARGHF 304 " (cutoff:3.500A) Processing helix chain 'HF' and resid 349 through 354 Processing helix chain 'HG' and resid 11 through 18 removed outlier: 3.782A pdb=" N LEUHG 15 " --> pdb=" O ARGHG 11 " (cutoff:3.500A) Processing helix chain 'HG' and resid 19 through 25 removed outlier: 3.816A pdb=" N LEUHG 25 " --> pdb=" O SERHG 21 " (cutoff:3.500A) Processing helix chain 'HG' and resid 32 through 37 removed outlier: 4.650A pdb=" N ALAHG 36 " --> pdb=" O SERHG 33 " (cutoff:3.500A) Processing helix chain 'HG' and resid 41 through 46 removed outlier: 3.593A pdb=" N SERHG 46 " --> pdb=" O ASNHG 42 " (cutoff:3.500A) Processing helix chain 'HG' and resid 61 through 83 removed outlier: 4.528A pdb=" N GLUHG 65 " --> pdb=" O TRPHG 61 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THRHG 74 " --> pdb=" O LEUHG 70 " (cutoff:3.500A) Proline residue: HG 75 - end of helix Processing helix chain 'HG' and resid 83 through 94 removed outlier: 3.733A pdb=" N ALAHG 90 " --> pdb=" O PHEHG 86 " (cutoff:3.500A) Processing helix chain 'HH' and resid 13 through 21 removed outlier: 3.934A pdb=" N LEUHH 17 " --> pdb=" O SERHH 13 " (cutoff:3.500A) Processing helix chain 'HH' and resid 26 through 40 removed outlier: 3.729A pdb=" N ALAHH 34 " --> pdb=" O GLNHH 30 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALAHH 38 " --> pdb=" O ALAHH 34 " (cutoff:3.500A) Processing helix chain 'HH' and resid 42 through 46 Processing helix chain 'HH' and resid 47 through 64 removed outlier: 3.772A pdb=" N GLUHH 52 " --> pdb=" O ILEHH 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASPHH 53 " --> pdb=" O ARGHH 49 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRPHH 57 " --> pdb=" O ASPHH 53 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYRHH 64 " --> pdb=" O METHH 60 " (cutoff:3.500A) Processing helix chain 'HH' and resid 76 through 88 removed outlier: 4.000A pdb=" N LYSHH 80 " --> pdb=" O THRHH 76 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILEHH 81 " --> pdb=" O PHEHH 77 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYSHH 87 " --> pdb=" O ALAHH 83 " (cutoff:3.500A) Processing helix chain 'HI' and resid 9 through 14 removed outlier: 3.657A pdb=" N PHEHI 13 " --> pdb=" O GLNHI 9 " (cutoff:3.500A) Processing helix chain 'HI' and resid 16 through 20 removed outlier: 3.956A pdb=" N SERHI 20 " --> pdb=" O PHEHI 17 " (cutoff:3.500A) Processing helix chain 'HI' and resid 25 through 51 removed outlier: 4.067A pdb=" N TRPHI 31 " --> pdb=" O ASPHI 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N METHI 34 " --> pdb=" O LYSHI 30 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASPHI 35 " --> pdb=" O TRPHI 31 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRPHI 36 " --> pdb=" O GLUHI 32 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HISHI 37 " --> pdb=" O ILEHI 33 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYRHI 38 " --> pdb=" O METHI 34 " (cutoff:3.500A) Proline residue: HI 44 - end of helix Processing helix chain 'HI' and resid 56 through 69 removed outlier: 4.545A pdb=" N LEUHI 60 " --> pdb=" O GLYHI 56 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLNHI 61 " --> pdb=" O SERHI 57 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEUHI 66 " --> pdb=" O TYRHI 62 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILEHI 67 " --> pdb=" O METHI 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALAHI 68 " --> pdb=" O HISHI 64 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEUHI 69 " --> pdb=" O ASPHI 65 " (cutoff:3.500A) Processing helix chain 'HJ' and resid 150 through 166 removed outlier: 3.711A pdb=" N ARGHJ 161 " --> pdb=" O GLYHJ 157 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THRHJ 162 " --> pdb=" O SERHJ 158 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEUHJ 166 " --> pdb=" O THRHJ 162 " (cutoff:3.500A) Processing helix chain 'HJ' and resid 172 through 191 removed outlier: 3.642A pdb=" N ASPHJ 177 " --> pdb=" O PHEHJ 173 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SERHJ 178 " --> pdb=" O TYRHJ 174 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SERHJ 181 " --> pdb=" O ASPHJ 177 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLUHJ 188 " --> pdb=" O SERHJ 184 " (cutoff:3.500A) Processing helix chain 'HJ' and resid 194 through 206 removed outlier: 3.730A pdb=" N VALHJ 201 " --> pdb=" O VALHJ 197 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYSHJ 205 " --> pdb=" O VALHJ 201 " (cutoff:3.500A) Processing helix chain 'HJ' and resid 230 through 244 removed outlier: 3.698A pdb=" N LEUHJ 235 " --> pdb=" O ALAHJ 231 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEUHJ 236 " --> pdb=" O ARGHJ 232 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERHJ 244 " --> pdb=" O ALAHJ 240 " (cutoff:3.500A) Processing helix chain 'HJ' and resid 245 through 250 removed outlier: 3.563A pdb=" N ASPHJ 248 " --> pdb=" O VALHJ 245 " (cutoff:3.500A) Processing helix chain 'HJ' and resid 272 through 279 Processing helix chain 'HJ' and resid 280 through 282 No H-bonds generated for 'chain 'HJ' and resid 280 through 282' Processing helix chain 'HJ' and resid 286 through 288 No H-bonds generated for 'chain 'HJ' and resid 286 through 288' Processing helix chain 'HJ' and resid 289 through 298 removed outlier: 3.827A pdb=" N GLNHJ 295 " --> pdb=" O HISHJ 291 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARGHJ 296 " --> pdb=" O ASPHJ 292 " (cutoff:3.500A) Processing helix chain 'HJ' and resid 299 through 302 removed outlier: 3.534A pdb=" N GLNHJ 302 " --> pdb=" O PROHJ 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'HJ' and resid 299 through 302' Processing helix chain 'HJ' and resid 313 through 333 removed outlier: 3.660A pdb=" N VALHJ 317 " --> pdb=" O SERHJ 313 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRPHJ 320 " --> pdb=" O SERHJ 316 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALAHJ 323 " --> pdb=" O LEUHJ 319 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLUHJ 326 " --> pdb=" O LYSHJ 322 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARGHJ 327 " --> pdb=" O ALAHJ 323 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARGHJ 333 " --> pdb=" O ILEHJ 329 " (cutoff:3.500A) Processing helix chain 'HJ' and resid 373 through 378 removed outlier: 4.146A pdb=" N ASPHJ 377 " --> pdb=" O GLUHJ 373 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLUHJ 378 " --> pdb=" O GLNHJ 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'HJ' and resid 373 through 378' Processing helix chain 'HJ' and resid 387 through 400 removed outlier: 3.584A pdb=" N ASPHJ 397 " --> pdb=" O ARGHJ 393 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHEHJ 398 " --> pdb=" O ARGHJ 394 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHEHJ 399 " --> pdb=" O VALHJ 395 " (cutoff:3.500A) Processing helix chain 'HJ' and resid 412 through 428 removed outlier: 4.170A pdb=" N ASNHJ 419 " --> pdb=" O ALAHJ 415 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEUHJ 420 " --> pdb=" O GLNHJ 416 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VALHJ 421 " --> pdb=" O PHEHJ 417 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLUHJ 426 " --> pdb=" O TYRHJ 422 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILEHJ 427 " --> pdb=" O THRHJ 423 " (cutoff:3.500A) Processing helix chain 'HJ' and resid 428 through 435 removed outlier: 3.560A pdb=" N TRPHJ 432 " --> pdb=" O GLYHJ 428 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N METHJ 433 " --> pdb=" O LEUHJ 429 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYSHJ 434 " --> pdb=" O SERHJ 430 " (cutoff:3.500A) Processing helix chain 'HJ' and resid 438 through 443 Processing helix chain 'HJ' and resid 455 through 469 removed outlier: 4.063A pdb=" N ARGHJ 463 " --> pdb=" O LEUHJ 459 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEUHJ 464 " --> pdb=" O ASPHJ 460 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEUHJ 465 " --> pdb=" O ALAHJ 461 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALAHJ 468 " --> pdb=" O LEUHJ 464 " (cutoff:3.500A) Processing helix chain 'HJ' and resid 483 through 488 removed outlier: 3.599A pdb=" N LEUHJ 487 " --> pdb=" O ASPHJ 483 " (cutoff:3.500A) Processing helix chain 'HJ' and resid 495 through 499 removed outlier: 4.446A pdb=" N GLUHJ 498 " --> pdb=" O THRHJ 495 " (cutoff:3.500A) Processing helix chain 'HJ' and resid 523 through 528 Processing helix chain 'HJ' and resid 548 through 563 Processing helix chain 'HK' and resid 3 through 8 removed outlier: 4.358A pdb=" N TYRHK 7 " --> pdb=" O ASPHK 3 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARGHK 8 " --> pdb=" O ASPHK 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'HK' and resid 3 through 8' Processing helix chain 'HK' and resid 10 through 18 removed outlier: 3.661A pdb=" N ARGHK 14 " --> pdb=" O PHEHK 10 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VALHK 16 " --> pdb=" O CYSHK 12 " (cutoff:3.500A) Processing helix chain 'HK' and resid 21 through 37 removed outlier: 3.637A pdb=" N SERHK 28 " --> pdb=" O THRHK 24 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VALHK 31 " --> pdb=" O GLUHK 27 " (cutoff:3.500A) Processing helix chain 'HK' and resid 102 through 124 removed outlier: 4.016A pdb=" N PHEHK 106 " --> pdb=" O SERHK 102 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALAHK 108 " --> pdb=" O ALAHK 104 " (cutoff:3.500A) Proline residue: HK 114 - end of helix removed outlier: 3.922A pdb=" N ALAHK 121 " --> pdb=" O LYSHK 117 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLUHK 122 " --> pdb=" O HISHK 118 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYSHK 124 " --> pdb=" O METHK 120 " (cutoff:3.500A) Processing helix chain 'HL' and resid 2 through 18 removed outlier: 4.173A pdb=" N GLNHL 6 " --> pdb=" O GLNHL 2 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALAHL 10 " --> pdb=" O GLNHL 6 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAHL 11 " --> pdb=" O THRHL 7 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYSHL 12 " --> pdb=" O LYSHL 8 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYSHL 16 " --> pdb=" O LYSHL 12 " (cutoff:3.500A) Processing helix chain 'HL' and resid 31 through 37 Processing helix chain 'HL' and resid 43 through 55 removed outlier: 3.768A pdb=" N LEUHL 48 " --> pdb=" O TRPHL 44 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYSHL 51 " --> pdb=" O SERHL 47 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HISHL 53 " --> pdb=" O GLNHL 49 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEUHL 54 " --> pdb=" O VALHL 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLUHL 55 " --> pdb=" O CYSHL 51 " (cutoff:3.500A) Processing helix chain 'HL' and resid 66 through 83 removed outlier: 3.817A pdb=" N GLUHL 71 " --> pdb=" O ALAHL 67 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYSHL 72 " --> pdb=" O GLYHL 68 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALAHL 78 " --> pdb=" O THRHL 74 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VALHL 79 " --> pdb=" O GLNHL 75 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLYHL 83 " --> pdb=" O VALHL 79 " (cutoff:3.500A) Processing helix chain 'HM' and resid 16 through 24 removed outlier: 3.940A pdb=" N PHEHM 22 " --> pdb=" O PROHM 18 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEUHM 23 " --> pdb=" O ALAHM 19 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SERHM 24 " --> pdb=" O GLNHM 20 " (cutoff:3.500A) Processing helix chain 'HM' and resid 25 through 27 No H-bonds generated for 'chain 'HM' and resid 25 through 27' Processing helix chain 'HM' and resid 29 through 43 removed outlier: 3.712A pdb=" N ARGHM 34 " --> pdb=" O PROHM 30 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLUHM 39 " --> pdb=" O SERHM 35 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALAHM 40 " --> pdb=" O LEUHM 36 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THRHM 41 " --> pdb=" O LEUHM 37 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLNHM 42 " --> pdb=" O ARGHM 38 " (cutoff:3.500A) Processing helix chain 'HM' and resid 47 through 61 removed outlier: 3.597A pdb=" N ARGHM 52 " --> pdb=" O PROHM 48 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHEHM 59 " --> pdb=" O SERHM 55 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALAHM 60 " --> pdb=" O GLNHM 56 " (cutoff:3.500A) Processing helix chain 'HM' and resid 62 through 64 No H-bonds generated for 'chain 'HM' and resid 62 through 64' Processing helix chain 'HM' and resid 66 through 77 removed outlier: 3.821A pdb=" N PHEHM 77 " --> pdb=" O ILEHM 73 " (cutoff:3.500A) Processing helix chain 'HM' and resid 86 through 93 removed outlier: 3.858A pdb=" N ALAHM 90 " --> pdb=" O ALAHM 86 " (cutoff:3.500A) Processing helix chain 'HM' and resid 104 through 115 removed outlier: 3.781A pdb=" N LEUHM 110 " --> pdb=" O ARGHM 106 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALAHM 115 " --> pdb=" O LEUHM 111 " (cutoff:3.500A) Processing helix chain 'HM' and resid 124 through 134 removed outlier: 4.003A pdb=" N GLUHM 134 " --> pdb=" O LYSHM 130 " (cutoff:3.500A) Processing helix chain 'HM' and resid 140 through 154 removed outlier: 4.108A pdb=" N ARGHM 149 " --> pdb=" O ASPHM 145 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THRHM 150 " --> pdb=" O SERHM 146 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SERHM 153 " --> pdb=" O ARGHM 149 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEUHM 154 " --> pdb=" O THRHM 150 " (cutoff:3.500A) Processing helix chain 'HM' and resid 158 through 178 removed outlier: 3.800A pdb=" N LEUHM 165 " --> pdb=" O LEUHM 161 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLNHM 168 " --> pdb=" O GLYHM 164 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALAHM 169 " --> pdb=" O LEUHM 165 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLNHM 170 " --> pdb=" O ALAHM 166 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEUHM 171 " --> pdb=" O THRHM 167 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASPHM 175 " --> pdb=" O LEUHM 171 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEUHM 176 " --> pdb=" O LEUHM 172 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALAHM 178 " --> pdb=" O SERHM 174 " (cutoff:3.500A) Processing helix chain 'HM' and resid 188 through 192 removed outlier: 3.806A pdb=" N ARGHM 192 " --> pdb=" O GLUHM 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'HM' and resid 188 through 192' Processing helix chain 'HM' and resid 195 through 207 removed outlier: 3.756A pdb=" N ARGHM 200 " --> pdb=" O ALAHM 196 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYSHM 201 " --> pdb=" O LEUHM 197 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLYHM 204 " --> pdb=" O ARGHM 200 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARGHM 207 " --> pdb=" O GLUHM 203 " (cutoff:3.500A) Processing helix chain 'HM' and resid 212 through 220 removed outlier: 3.860A pdb=" N VALHM 216 " --> pdb=" O GLNHM 212 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASPHM 217 " --> pdb=" O SERHM 213 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALAHM 218 " --> pdb=" O ALAHM 214 " (cutoff:3.500A) Processing helix chain 'HM' and resid 235 through 242 removed outlier: 3.755A pdb=" N VALHM 239 " --> pdb=" O THRHM 235 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALAHM 242 " --> pdb=" O ALAHM 238 " (cutoff:3.500A) Processing helix chain 'HM' and resid 272 through 280 Processing helix chain 'HM' and resid 292 through 302 removed outlier: 4.295A pdb=" N GLUHM 296 " --> pdb=" O GLNHM 292 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALAHM 297 " --> pdb=" O LYSHM 293 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VALHM 298 " --> pdb=" O VALHM 294 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLUHM 299 " --> pdb=" O SERHM 295 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEUHM 300 " --> pdb=" O GLUHM 296 " (cutoff:3.500A) Processing helix chain 'HM' and resid 304 through 309 Processing helix chain 'HM' and resid 311 through 319 Processing helix chain 'HM' and resid 322 through 326 removed outlier: 3.577A pdb=" N ASPHM 326 " --> pdb=" O ALAHM 323 " (cutoff:3.500A) Processing helix chain 'HM' and resid 350 through 367 removed outlier: 3.795A pdb=" N LEUHM 354 " --> pdb=" O GLNHM 350 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEUHM 355 " --> pdb=" O LEUHM 351 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SERHM 356 " --> pdb=" O GLNHM 352 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALAHM 357 " --> pdb=" O GLNHM 353 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEUHM 362 " --> pdb=" O SERHM 358 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHEHM 363 " --> pdb=" O ALAHM 359 " (cutoff:3.500A) Processing helix chain 'HM' and resid 380 through 395 removed outlier: 3.834A pdb=" N GLUHM 384 " --> pdb=" O ALAHM 380 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYSHM 388 " --> pdb=" O GLUHM 384 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THRHM 389 " --> pdb=" O ALAHM 385 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VALHM 390 " --> pdb=" O LEUHM 386 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARGHM 392 " --> pdb=" O LYSHM 388 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASPHM 395 " --> pdb=" O GLUHM 391 " (cutoff:3.500A) Processing helix chain 'HM' and resid 396 through 398 No H-bonds generated for 'chain 'HM' and resid 396 through 398' Processing helix chain 'HM' and resid 400 through 404 removed outlier: 3.769A pdb=" N LEUHM 404 " --> pdb=" O PHEHM 401 " (cutoff:3.500A) Processing helix chain 'HM' and resid 405 through 423 removed outlier: 3.544A pdb=" N ALAHM 411 " --> pdb=" O ARGHM 407 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYSHM 413 " --> pdb=" O ARGHM 409 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLUHM 414 " --> pdb=" O ARGHM 410 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALAHM 415 " --> pdb=" O ALAHM 411 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEUHM 418 " --> pdb=" O GLUHM 414 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHEHM 419 " --> pdb=" O ALAHM 415 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEUHM 420 " --> pdb=" O ALAHM 416 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VALHM 421 " --> pdb=" O SERHM 417 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLUHM 422 " --> pdb=" O LEUHM 418 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALAHM 423 " --> pdb=" O PHEHM 419 " (cutoff:3.500A) Processing helix chain 'HM' and resid 438 through 442 removed outlier: 4.024A pdb=" N LYSHM 441 " --> pdb=" O LEUHM 438 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THRHM 442 " --> pdb=" O ALAHM 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'HM' and resid 438 through 442' Processing helix chain 'HM' and resid 578 through 596 removed outlier: 4.116A pdb=" N ALAHM 582 " --> pdb=" O ILEHM 578 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SERHM 584 " --> pdb=" O PROHM 580 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILEHM 594 " --> pdb=" O GLNHM 590 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARGHM 596 " --> pdb=" O ALAHM 592 " (cutoff:3.500A) Processing helix chain 'HN' and resid 3 through 16 removed outlier: 3.520A pdb=" N LEUHN 8 " --> pdb=" O LYSHN 4 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEUHN 10 " --> pdb=" O ASNHN 6 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARGHN 11 " --> pdb=" O ARGHN 7 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARGHN 16 " --> pdb=" O LYSHN 12 " (cutoff:3.500A) Processing helix chain 'HO' and resid 6 through 10 Processing helix chain 'HO' and resid 56 through 68 removed outlier: 3.630A pdb=" N LYSHO 61 " --> pdb=" O GLUHO 57 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARGHO 62 " --> pdb=" O ARGHO 58 " (cutoff:3.500A) Processing helix chain 'HO' and resid 73 through 77 Processing helix chain 'HO' and resid 84 through 88 Processing helix chain 'HO' and resid 112 through 121 removed outlier: 3.642A pdb=" N GLUHO 119 " --> pdb=" O VALHO 115 " (cutoff:3.500A) Processing helix chain 'HO' and resid 121 through 144 removed outlier: 3.704A pdb=" N GLUHO 127 " --> pdb=" O PROHO 123 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALAHO 128 " --> pdb=" O GLUHO 124 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHEHO 129 " --> pdb=" O ILEHO 125 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYSHO 130 " --> pdb=" O ARGHO 126 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALAHO 131 " --> pdb=" O GLUHO 127 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SERHO 132 " --> pdb=" O ALAHO 128 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYSHO 135 " --> pdb=" O ALAHO 131 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALAHO 137 " --> pdb=" O LYSHO 133 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLUHO 138 " --> pdb=" O ALAHO 134 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALAHO 141 " --> pdb=" O ALAHO 137 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLNHO 142 " --> pdb=" O GLUHO 138 " (cutoff:3.500A) Processing helix chain 'HP' and resid 27 through 33 removed outlier: 3.848A pdb=" N ILEHP 32 " --> pdb=" O GLUHP 29 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THRHP 33 " --> pdb=" O ASPHP 30 " (cutoff:3.500A) Processing helix chain 'HP' and resid 36 through 54 removed outlier: 3.515A pdb=" N VALHP 40 " --> pdb=" O PROHP 36 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALAHP 41 " --> pdb=" O PROHP 37 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARGHP 42 " --> pdb=" O ALAHP 38 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILEHP 44 " --> pdb=" O VALHP 40 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARGHP 45 " --> pdb=" O ALAHP 41 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SERHP 49 " --> pdb=" O ARGHP 45 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARGHP 50 " --> pdb=" O SERHP 46 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VALHP 52 " --> pdb=" O ILEHP 48 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLYHP 54 " --> pdb=" O ARGHP 50 " (cutoff:3.500A) Processing helix chain 'HP' and resid 60 through 74 removed outlier: 3.648A pdb=" N ARGHP 64 " --> pdb=" O METHP 60 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARGHP 70 " --> pdb=" O LYSHP 66 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARGHP 71 " --> pdb=" O TYRHP 67 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEUHP 72 " --> pdb=" O ARGHP 68 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VALHP 73 " --> pdb=" O LEUHP 69 " (cutoff:3.500A) Processing helix chain 'HP' and resid 135 through 143 Processing helix chain 'HP' and resid 193 through 205 removed outlier: 3.747A pdb=" N LEUHP 201 " --> pdb=" O GLUHP 197 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEUHP 204 " --> pdb=" O LEUHP 200 " (cutoff:3.500A) Processing helix chain 'HP' and resid 225 through 245 removed outlier: 3.663A pdb=" N GLYHP 234 " --> pdb=" O ALAHP 230 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLNHP 238 " --> pdb=" O GLYHP 234 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N METHP 241 " --> pdb=" O LEUHP 237 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLUHP 243 " --> pdb=" O GLNHP 239 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 8 through 12 Processing helix chain 'HQ' and resid 26 through 36 removed outlier: 4.008A pdb=" N LEUHQ 30 " --> pdb=" O LEUHQ 26 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SERHQ 31 " --> pdb=" O SERHQ 27 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 78 through 94 removed outlier: 4.101A pdb=" N GLUHQ 82 " --> pdb=" O ALAHQ 78 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILEHQ 84 " --> pdb=" O GLUHQ 80 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARGHQ 86 " --> pdb=" O GLUHQ 82 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYSHQ 87 " --> pdb=" O ARGHQ 83 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYSHQ 89 " --> pdb=" O GLNHQ 85 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILEHQ 90 " --> pdb=" O ARGHQ 86 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEUHQ 91 " --> pdb=" O LYSHQ 87 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLUHQ 92 " --> pdb=" O ILEHQ 88 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 121 through 135 removed outlier: 3.897A pdb=" N LEUHQ 127 " --> pdb=" O ALAHQ 123 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEUHQ 128 " --> pdb=" O VALHQ 124 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEUHQ 129 " --> pdb=" O ASNHQ 125 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEUHQ 130 " --> pdb=" O LEUHQ 126 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLUHQ 135 " --> pdb=" O ALAHQ 131 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 163 through 188 removed outlier: 3.622A pdb=" N TRPHQ 167 " --> pdb=" O GLUHQ 163 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARGHQ 168 " --> pdb=" O ARGHQ 164 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILEHQ 182 " --> pdb=" O TRPHQ 178 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SERHQ 183 " --> pdb=" O ASNHQ 179 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARGHQ 184 " --> pdb=" O LEUHQ 180 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLUHQ 187 " --> pdb=" O SERHQ 183 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEUHQ 188 " --> pdb=" O ARGHQ 184 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 191 through 206 removed outlier: 4.372A pdb=" N PHEHQ 196 " --> pdb=" O HISHQ 192 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEUHQ 197 " --> pdb=" O GLUHQ 193 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 211 through 223 removed outlier: 4.273A pdb=" N ALAHQ 215 " --> pdb=" O VALHQ 211 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUHQ 218 " --> pdb=" O PROHQ 214 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARGHQ 219 " --> pdb=" O ALAHQ 215 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEUHQ 220 " --> pdb=" O LEUHQ 216 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLUHQ 221 " --> pdb=" O LEUHQ 217 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 237 through 241 removed outlier: 3.881A pdb=" N GLUHQ 240 " --> pdb=" O PROHQ 237 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 248 through 253 removed outlier: 3.740A pdb=" N ILEHQ 253 " --> pdb=" O PHEHQ 249 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 257 through 266 removed outlier: 3.644A pdb=" N ALAHQ 262 " --> pdb=" O LEUHQ 258 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VALHQ 263 " --> pdb=" O SERHQ 259 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VALHQ 264 " --> pdb=" O ALAHQ 260 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VALHQ 265 " --> pdb=" O LYSHQ 261 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 303 through 308 removed outlier: 3.741A pdb=" N GLUHQ 307 " --> pdb=" O METHQ 303 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYSHQ 308 " --> pdb=" O GLUHQ 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'HQ' and resid 303 through 308' Processing helix chain 'HQ' and resid 329 through 343 removed outlier: 3.763A pdb=" N THRHQ 335 " --> pdb=" O LYSHQ 331 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEUHQ 338 " --> pdb=" O ALAHQ 334 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HISHQ 339 " --> pdb=" O THRHQ 335 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLYHQ 340 " --> pdb=" O METHQ 336 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARGHQ 341 " --> pdb=" O ALAHQ 337 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLNHQ 342 " --> pdb=" O LEUHQ 338 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALAHQ 343 " --> pdb=" O HISHQ 339 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 349 through 361 removed outlier: 4.542A pdb=" N SERHQ 355 " --> pdb=" O SERHQ 351 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VALHQ 356 " --> pdb=" O SERHQ 352 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALAHQ 357 " --> pdb=" O LEUHQ 353 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 372 through 386 removed outlier: 3.608A pdb=" N GLYHQ 386 " --> pdb=" O ALAHQ 382 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 388 through 393 Processing helix chain 'HQ' and resid 396 through 404 Processing helix chain 'HQ' and resid 411 through 429 removed outlier: 3.763A pdb=" N HISHQ 417 " --> pdb=" O ARGHQ 413 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VALHQ 421 " --> pdb=" O HISHQ 417 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEUHQ 422 " --> pdb=" O LEUHQ 418 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARGHQ 423 " --> pdb=" O GLUHQ 419 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLYHQ 424 " --> pdb=" O ALAHQ 420 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 453 through 465 removed outlier: 3.682A pdb=" N SERHQ 460 " --> pdb=" O ARGHQ 456 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 473 through 477 removed outlier: 3.763A pdb=" N VALHQ 477 " --> pdb=" O PHEHQ 474 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 507 through 521 removed outlier: 3.630A pdb=" N VALHQ 511 " --> pdb=" O TRPHQ 507 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEUHQ 516 " --> pdb=" O LEUHQ 512 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SERHQ 517 " --> pdb=" O ALAHQ 513 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHEHQ 519 " --> pdb=" O LEUHQ 515 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 529 through 546 removed outlier: 3.894A pdb=" N SERHQ 542 " --> pdb=" O ALAHQ 538 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEUHQ 543 " --> pdb=" O LEUHQ 539 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARGHQ 545 " --> pdb=" O ASNHQ 541 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THRHQ 546 " --> pdb=" O SERHQ 542 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 568 through 580 removed outlier: 3.906A pdb=" N ALAHQ 574 " --> pdb=" O LYSHQ 570 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEUHQ 575 " --> pdb=" O GLUHQ 571 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEUHQ 576 " --> pdb=" O THRHQ 572 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SERHQ 578 " --> pdb=" O ALAHQ 574 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHEHQ 579 " --> pdb=" O LEUHQ 575 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALAHQ 580 " --> pdb=" O LEUHQ 576 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 590 through 596 removed outlier: 3.756A pdb=" N VALHQ 595 " --> pdb=" O ALAHQ 592 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLUHQ 596 " --> pdb=" O CYSHQ 593 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 602 through 608 Processing helix chain 'HQ' and resid 622 through 631 removed outlier: 4.326A pdb=" N GLUHQ 626 " --> pdb=" O SERHQ 622 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLUHQ 627 " --> pdb=" O SERHQ 623 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLUHQ 629 " --> pdb=" O ALAHQ 625 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 632 through 634 No H-bonds generated for 'chain 'HQ' and resid 632 through 634' Processing helix chain 'HQ' and resid 643 through 655 removed outlier: 4.053A pdb=" N ASPHQ 647 " --> pdb=" O ALAHQ 643 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYSHQ 648 " --> pdb=" O THRHQ 644 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALAHQ 649 " --> pdb=" O PROHQ 645 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THRHQ 650 " --> pdb=" O GLYHQ 646 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 680 through 694 removed outlier: 3.915A pdb=" N LEUHQ 694 " --> pdb=" O GLNHQ 690 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 703 through 713 removed outlier: 3.762A pdb=" N LEUHQ 709 " --> pdb=" O PROHQ 705 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 729 through 740 removed outlier: 4.126A pdb=" N GLUHQ 734 " --> pdb=" O GLNHQ 730 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THRHQ 735 " --> pdb=" O ARGHQ 731 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHEHQ 736 " --> pdb=" O SERHQ 732 " (cutoff:3.500A) Processing helix chain 'HQ' and resid 747 through 751 removed outlier: 3.649A pdb=" N SERHQ 750 " --> pdb=" O LEUHQ 747 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEUHQ 751 " --> pdb=" O LEUHQ 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'HQ' and resid 747 through 751' Processing helix chain 'HR' and resid 76 through 94 removed outlier: 4.418A pdb=" N ARGHR 80 " --> pdb=" O TRPHR 76 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VALHR 85 " --> pdb=" O ALAHR 81 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEUHR 86 " --> pdb=" O LYSHR 82 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYSHR 88 " --> pdb=" O VALHR 84 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLNHR 89 " --> pdb=" O VALHR 85 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEUHR 90 " --> pdb=" O LEUHR 86 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLNHR 91 " --> pdb=" O LEUHR 87 " (cutoff:3.500A) Processing helix chain 'HR' and resid 141 through 162 removed outlier: 3.758A pdb=" N ALAHR 145 " --> pdb=" O METHR 141 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALAHR 146 " --> pdb=" O GLYHR 142 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYRHR 147 " --> pdb=" O PHEHR 143 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VALHR 151 " --> pdb=" O TYRHR 147 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARGHR 154 " --> pdb=" O ALAHR 150 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARGHR 159 " --> pdb=" O ARGHR 155 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLUHR 160 " --> pdb=" O GLNHR 156 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASNHR 161 " --> pdb=" O LYSHR 157 " (cutoff:3.500A) Processing helix chain 'HS' and resid 89 through 93 removed outlier: 4.231A pdb=" N HISHS 92 " --> pdb=" O THRHS 89 " (cutoff:3.500A) Processing helix chain 'HS' and resid 110 through 124 removed outlier: 3.769A pdb=" N ASPHS 123 " --> pdb=" O GLNHS 119 " (cutoff:3.500A) Processing helix chain 'HS' and resid 146 through 155 removed outlier: 4.009A pdb=" N TYRHS 150 " --> pdb=" O HISHS 146 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N METHS 151 " --> pdb=" O ALAHS 147 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARGHS 153 " --> pdb=" O SERHS 149 " (cutoff:3.500A) Processing helix chain 'HS' and resid 191 through 198 removed outlier: 3.759A pdb=" N LYSHS 195 " --> pdb=" O ALAHS 191 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLNHS 196 " --> pdb=" O PROHS 192 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLNHS 197 " --> pdb=" O GLYHS 193 " (cutoff:3.500A) Processing helix chain 'HT' and resid 5 through 15 removed outlier: 3.749A pdb=" N ARGHT 10 " --> pdb=" O SERHT 6 " (cutoff:3.500A) Processing helix chain 'HT' and resid 19 through 34 removed outlier: 3.954A pdb=" N LYSHT 23 " --> pdb=" O HISHT 19 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VALHT 26 " --> pdb=" O ARGHT 22 " (cutoff:3.500A) Processing helix chain 'HT' and resid 43 through 48 removed outlier: 3.874A pdb=" N VALHT 47 " --> pdb=" O GLUHT 43 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARGHT 48 " --> pdb=" O GLUHT 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'HT' and resid 43 through 48' Processing helix chain 'HT' and resid 51 through 56 removed outlier: 3.559A pdb=" N METHT 55 " --> pdb=" O GLNHT 51 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N METHT 56 " --> pdb=" O GLYHT 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'HT' and resid 51 through 56' Processing helix chain 'HT' and resid 71 through 82 removed outlier: 3.552A pdb=" N PHEHT 75 " --> pdb=" O METHT 71 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLNHT 76 " --> pdb=" O ALAHT 72 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHEHT 82 " --> pdb=" O GLNHT 78 " (cutoff:3.500A) Processing helix chain 'HT' and resid 88 through 95 removed outlier: 4.000A pdb=" N THRHT 93 " --> pdb=" O VALHT 89 " (cutoff:3.500A) Processing helix chain 'HT' and resid 97 through 104 Processing helix chain 'HT' and resid 104 through 110 removed outlier: 4.197A pdb=" N ALAHT 110 " --> pdb=" O ASPHT 106 " (cutoff:3.500A) Processing helix chain 'HT' and resid 116 through 120 Processing helix chain 'HT' and resid 122 through 137 removed outlier: 4.343A pdb=" N ASPHT 128 " --> pdb=" O PROHT 124 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEUHT 129 " --> pdb=" O THRHT 125 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THRHT 135 " --> pdb=" O GLYHT 131 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEUHT 136 " --> pdb=" O LEUHT 132 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYSHT 137 " --> pdb=" O TYRHT 133 " (cutoff:3.500A) Processing helix chain 'HT' and resid 290 through 301 removed outlier: 3.514A pdb=" N LEUHT 297 " --> pdb=" O ALAHT 293 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLYHT 298 " --> pdb=" O GLUHT 294 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLNHT 299 " --> pdb=" O THRHT 295 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALAHT 301 " --> pdb=" O LEUHT 297 " (cutoff:3.500A) Processing helix chain 'HT' and resid 326 through 346 removed outlier: 3.999A pdb=" N GLUHT 334 " --> pdb=" O ARGHT 330 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLNHT 335 " --> pdb=" O LYSHT 331 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THRHT 339 " --> pdb=" O GLNHT 335 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEUHT 340 " --> pdb=" O SERHT 336 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HISHT 346 " --> pdb=" O ALAHT 342 " (cutoff:3.500A) Processing helix chain 'HT' and resid 350 through 355 Processing helix chain 'HT' and resid 362 through 375 removed outlier: 3.750A pdb=" N ARGHT 367 " --> pdb=" O PROHT 363 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARGHT 368 " --> pdb=" O LEUHT 364 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARGHT 375 " --> pdb=" O SERHT 371 " (cutoff:3.500A) Processing helix chain 'HT' and resid 383 through 391 removed outlier: 3.765A pdb=" N ARGHT 387 " --> pdb=" O GLYHT 383 " (cutoff:3.500A) Processing helix chain 'HT' and resid 397 through 401 removed outlier: 3.519A pdb=" N LYSHT 401 " --> pdb=" O PROHT 398 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'HA' and resid 9 through 12 removed outlier: 3.634A pdb=" N VALHA 45 " --> pdb=" O ARGHA 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'HA' and resid 173 through 177 removed outlier: 3.626A pdb=" N GLUHA 177 " --> pdb=" O ALAHA 359 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEUHA 410 " --> pdb=" O VALHA 356 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALAHA 414 " --> pdb=" O VALHA 360 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHEHA 146 " --> pdb=" O LYSHA 411 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N CYSHA 413 " --> pdb=" O PHEHA 146 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEUHA 147 " --> pdb=" O ARGHA 438 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'HA' and resid 369 through 373 removed outlier: 5.099A pdb=" N ILEHA 386 " --> pdb=" O SERHA 370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'HB' and resid 33 through 39 removed outlier: 3.534A pdb=" N GLYHB 38 " --> pdb=" O ALAHB 45 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'HB' and resid 56 through 57 removed outlier: 3.696A pdb=" N ARGHB 57 " --> pdb=" O LEUHB 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'HC' and resid 45 through 48 removed outlier: 6.977A pdb=" N SERHC 132 " --> pdb=" O ARGHC 8 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEUHC 10 " --> pdb=" O ARGHC 130 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARGHC 130 " --> pdb=" O LEUHC 10 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VALHC 12 " --> pdb=" O SERHC 128 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SERHC 128 " --> pdb=" O VALHC 12 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYRHC 14 " --> pdb=" O CYSHC 126 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N CYSHC 126 " --> pdb=" O TYRHC 14 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHEHC 131 " --> pdb=" O TYRHP 163 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYRHP 163 " --> pdb=" O PHEHC 131 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VALHP 161 " --> pdb=" O TRPHC 133 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRPHP 182 " --> pdb=" O HISHP 162 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'HC' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'HC' and resid 59 through 60 removed outlier: 3.817A pdb=" N ALAHC 89 " --> pdb=" O TRPHC 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'HE' and resid 24 through 25 removed outlier: 4.114A pdb=" N PHEHE 24 " --> pdb=" O LEUHE 15 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEUHE 15 " --> pdb=" O PHEHE 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'HI' and resid 88 through 90 Processing sheet with id=AB2, first strand: chain 'HJ' and resid 222 through 223 Processing sheet with id=AB3, first strand: chain 'HK' and resid 75 through 78 removed outlier: 4.275A pdb=" N GLUHK 86 " --> pdb=" O ARGHK 77 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'HM' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'HO' and resid 39 through 49 removed outlier: 3.744A pdb=" N PHEHO 41 " --> pdb=" O ALAHO 97 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALAHO 97 " --> pdb=" O PHEHO 41 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYSHO 95 " --> pdb=" O CYSHO 43 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THRHO 93 " --> pdb=" O GLYHO 45 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILEHO 91 " --> pdb=" O ILEHO 47 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARGHO 49 " --> pdb=" O LYSHO 89 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYSHO 89 " --> pdb=" O ARGHO 49 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SERHO 111 " --> pdb=" O PROHO 94 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEUHO 96 " --> pdb=" O ALAHO 109 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALAHO 109 " --> pdb=" O LEUHO 96 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHEHO 98 " --> pdb=" O LEUHO 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'HR' and resid 17 through 19 Processing sheet with id=AB7, first strand: chain 'HR' and resid 112 through 114 removed outlier: 3.603A pdb=" N TYRHR 113 " --> pdb=" O VALHR 122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VALHR 122 " --> pdb=" O TYRHR 113 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRPHR 121 " --> pdb=" O PHEHR 136 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHEHR 136 " --> pdb=" O TRPHR 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'HR' and resid 126 through 127 Processing sheet with id=AB9, first strand: chain 'HS' and resid 142 through 144 removed outlier: 4.341A pdb=" N ASNHS 172 " --> pdb=" O LYSHS 97 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'HS' and resid 165 through 167 removed outlier: 4.246A pdb=" N SERHS 165 " --> pdb=" O GLNHS 103 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLNHS 103 " --> pdb=" O SERHS 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALAHS 137 " --> pdb=" O LEUHS 102 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VALHS 130 " --> pdb=" O VALHS 186 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'HT' and resid 69 through 70 removed outlier: 3.895A pdb=" N VALHT 69 " --> pdb=" O HISHT 358 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HISHT 358 " --> pdb=" O VALHT 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 1024 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6409 1.30 - 1.43: 12659 1.43 - 1.56: 22563 1.56 - 1.69: 563 1.69 - 1.82: 225 Bond restraints: 42419 Sorted by residual: bond pdb=" O3' AhG 40 " pdb=" P AhG 41 " ideal model delta sigma weight residual 1.607 1.799 -0.192 1.50e-02 4.44e+03 1.65e+02 bond pdb=" C3' AhG 40 " pdb=" O3' AhG 40 " ideal model delta sigma weight residual 1.417 1.286 0.131 1.50e-02 4.44e+03 7.68e+01 bond pdb=" C3' UhL 17 " pdb=" O3' UhL 17 " ideal model delta sigma weight residual 1.417 1.521 -0.104 1.50e-02 4.44e+03 4.76e+01 bond pdb=" N9 AhG 64 " pdb=" C4 AhG 64 " ideal model delta sigma weight residual 1.374 1.337 0.037 6.00e-03 2.78e+04 3.77e+01 bond pdb=" CZ ARGHA 423 " pdb=" NH2 ARGHA 423 " ideal model delta sigma weight residual 1.330 1.251 0.079 1.30e-02 5.92e+03 3.66e+01 ... (remaining 42414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.67: 58329 4.67 - 9.35: 271 9.35 - 14.02: 20 14.02 - 18.70: 6 18.70 - 23.37: 2 Bond angle restraints: 58628 Sorted by residual: angle pdb=" C4' AhG 40 " pdb=" C3' AhG 40 " pdb=" O3' AhG 40 " ideal model delta sigma weight residual 113.00 136.37 -23.37 1.50e+00 4.44e-01 2.43e+02 angle pdb=" O3' UhL 17 " pdb=" P AhL 18 " pdb=" O5' AhL 18 " ideal model delta sigma weight residual 104.00 123.75 -19.75 1.50e+00 4.44e-01 1.73e+02 angle pdb=" O3' GhG 56 " pdb=" C3' GhG 56 " pdb=" C2' GhG 56 " ideal model delta sigma weight residual 109.50 127.81 -18.31 1.50e+00 4.44e-01 1.49e+02 angle pdb=" O3' AhG 40 " pdb=" C3' AhG 40 " pdb=" C2' AhG 40 " ideal model delta sigma weight residual 113.70 96.39 17.31 1.50e+00 4.44e-01 1.33e+02 angle pdb=" C3' AhG 40 " pdb=" O3' AhG 40 " pdb=" P AhG 41 " ideal model delta sigma weight residual 120.20 103.01 17.19 1.50e+00 4.44e-01 1.31e+02 ... (remaining 58623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 24996 35.84 - 71.69: 1140 71.69 - 107.53: 107 107.53 - 143.37: 4 143.37 - 179.22: 11 Dihedral angle restraints: 26258 sinusoidal: 13559 harmonic: 12699 Sorted by residual: dihedral pdb=" C5' UhD 6 " pdb=" C4' UhD 6 " pdb=" C3' UhD 6 " pdb=" O3' UhD 6 " ideal model delta sinusoidal sigma weight residual 147.00 79.19 67.81 1 8.00e+00 1.56e-02 9.33e+01 dihedral pdb=" C4' UhD 1 " pdb=" C3' UhD 1 " pdb=" C2' UhD 1 " pdb=" C1' UhD 1 " ideal model delta sinusoidal sigma weight residual -35.00 32.44 -67.44 1 8.00e+00 1.56e-02 9.25e+01 dihedral pdb=" C4' UhD 6 " pdb=" C3' UhD 6 " pdb=" C2' UhD 6 " pdb=" C1' UhD 6 " ideal model delta sinusoidal sigma weight residual -35.00 32.24 -67.24 1 8.00e+00 1.56e-02 9.20e+01 ... (remaining 26255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 6530 0.199 - 0.397: 119 0.397 - 0.596: 6 0.596 - 0.794: 2 0.794 - 0.993: 3 Chirality restraints: 6660 Sorted by residual: chirality pdb=" P GhG 57 " pdb=" OP1 GhG 57 " pdb=" OP2 GhG 57 " pdb=" O5' GhG 57 " both_signs ideal model delta sigma weight residual True 2.41 -1.42 0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" P AhG 41 " pdb=" OP1 AhG 41 " pdb=" OP2 AhG 41 " pdb=" O5' AhG 41 " both_signs ideal model delta sigma weight residual True 2.41 -3.32 -0.91 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" C3' AhG 40 " pdb=" C4' AhG 40 " pdb=" O3' AhG 40 " pdb=" C2' AhG 40 " both_signs ideal model delta sigma weight residual False -2.48 -1.67 -0.81 2.00e-01 2.50e+01 1.63e+01 ... (remaining 6657 not shown) Planarity restraints: 6558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' UhL 25 " 0.628 2.00e-02 2.50e+03 2.84e-01 1.81e+03 pdb=" N1 UhL 25 " -0.180 2.00e-02 2.50e+03 pdb=" C2 UhL 25 " -0.162 2.00e-02 2.50e+03 pdb=" O2 UhL 25 " -0.235 2.00e-02 2.50e+03 pdb=" N3 UhL 25 " 0.075 2.00e-02 2.50e+03 pdb=" C4 UhL 25 " 0.082 2.00e-02 2.50e+03 pdb=" O4 UhL 25 " 0.279 2.00e-02 2.50e+03 pdb=" C5 UhL 25 " -0.187 2.00e-02 2.50e+03 pdb=" C6 UhL 25 " -0.301 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GhR 10 " -0.521 2.00e-02 2.50e+03 2.11e-01 1.33e+03 pdb=" N9 GhR 10 " 0.075 2.00e-02 2.50e+03 pdb=" C8 GhR 10 " 0.235 2.00e-02 2.50e+03 pdb=" N7 GhR 10 " 0.201 2.00e-02 2.50e+03 pdb=" C5 GhR 10 " 0.073 2.00e-02 2.50e+03 pdb=" C6 GhR 10 " -0.108 2.00e-02 2.50e+03 pdb=" O6 GhR 10 " -0.300 2.00e-02 2.50e+03 pdb=" N1 GhR 10 " -0.077 2.00e-02 2.50e+03 pdb=" C2 GhR 10 " 0.061 2.00e-02 2.50e+03 pdb=" N2 GhR 10 " 0.106 2.00e-02 2.50e+03 pdb=" N3 GhR 10 " 0.128 2.00e-02 2.50e+03 pdb=" C4 GhR 10 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AhL 18 " 0.462 2.00e-02 2.50e+03 1.95e-01 1.04e+03 pdb=" N9 AhL 18 " -0.063 2.00e-02 2.50e+03 pdb=" C8 AhL 18 " -0.190 2.00e-02 2.50e+03 pdb=" N7 AhL 18 " -0.133 2.00e-02 2.50e+03 pdb=" C5 AhL 18 " -0.060 2.00e-02 2.50e+03 pdb=" C6 AhL 18 " 0.082 2.00e-02 2.50e+03 pdb=" N6 AhL 18 " 0.263 2.00e-02 2.50e+03 pdb=" N1 AhL 18 " 0.056 2.00e-02 2.50e+03 pdb=" C2 AhL 18 " -0.089 2.00e-02 2.50e+03 pdb=" N3 AhL 18 " -0.189 2.00e-02 2.50e+03 pdb=" C4 AhL 18 " -0.139 2.00e-02 2.50e+03 ... (remaining 6555 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 97 2.55 - 3.14: 28856 3.14 - 3.73: 59011 3.73 - 4.31: 76779 4.31 - 4.90: 125900 Nonbonded interactions: 290643 Sorted by model distance: nonbonded pdb=" O LEUHK 126 " pdb=" OXT LEUHK 127 " model vdw 1.964 3.040 nonbonded pdb=" O2' UhD 1 " pdb=" OP2 UhD 2 " model vdw 2.309 3.040 nonbonded pdb=" OD1 ASNHQ 294 " pdb=" OG1 THRHQ 297 " model vdw 2.331 3.040 nonbonded pdb=" OG1 THRHH 76 " pdb=" OD2 ASPHH 79 " model vdw 2.343 3.040 nonbonded pdb=" O2' GhB 17 " pdb=" OP2 AhB 18 " model vdw 2.349 3.040 ... (remaining 290638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'hD' selection = (chain 'hS' and resid 3 through 17) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 37.110 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3965 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.192 42419 Z= 0.773 Angle : 1.259 23.370 58628 Z= 1.039 Chirality : 0.086 0.993 6660 Planarity : 0.013 0.284 6558 Dihedral : 18.467 179.219 17974 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.72 % Favored : 93.21 % Rotamer: Outliers : 0.08 % Allowed : 9.56 % Favored : 90.35 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.13), residues: 4268 helix: 0.63 (0.14), residues: 1616 sheet: -1.26 (0.41), residues: 168 loop : -1.97 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARGHA 423 TYR 0.093 0.006 TYRHF 339 PHE 0.104 0.005 PHEHQ 598 TRP 0.126 0.006 TRPHK 50 HIS 0.023 0.003 HISHQ 236 Details of bonding type rmsd/Z covalent geometry : bond 0.01097 / 0.77 (42419) covalent geometry : angle 1.25863 / 1.04 (58628) hydrogen bonds : bond 0.33194 / 21.92 ( 1057) hydrogen bonds : angle 7.02640 / 4.87 ( 2968) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1245 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: HA 35 MET cc_start: 0.6083 (mtm) cc_final: 0.5666 (mtp) REVERT: HA 38 SER cc_start: 0.6408 (m) cc_final: 0.5892 (p) REVERT: HA 46 MET cc_start: 0.5094 (ttm) cc_final: 0.3362 (pmm) REVERT: HA 169 GLU cc_start: 0.6248 (mt-10) cc_final: 0.5933 (mt-10) REVERT: HA 172 TRP cc_start: 0.6063 (m-10) cc_final: 0.5724 (m100) REVERT: HA 177 GLU cc_start: 0.5796 (tp30) cc_final: 0.5039 (tp30) REVERT: HA 179 LEU cc_start: 0.6524 (tp) cc_final: 0.6219 (mm) REVERT: HA 182 ARG cc_start: 0.6189 (ttp-170) cc_final: 0.5970 (mtm110) REVERT: HA 190 ILE cc_start: 0.5830 (mt) cc_final: 0.5505 (mt) REVERT: HA 191 LYS cc_start: 0.7187 (mmtt) cc_final: 0.6737 (tppt) REVERT: HA 200 GLN cc_start: 0.6885 (mt0) cc_final: 0.6343 (mt0) REVERT: HA 205 GLN cc_start: 0.6636 (tt0) cc_final: 0.6263 (mt0) REVERT: HA 209 GLU cc_start: 0.6290 (mt-10) cc_final: 0.6021 (mt-10) REVERT: HA 237 VAL cc_start: 0.2549 (t) cc_final: 0.1652 (m) REVERT: HA 313 MET cc_start: 0.4738 (ttm) cc_final: 0.4350 (ttm) REVERT: HA 339 GLN cc_start: 0.6534 (tt0) cc_final: 0.6256 (tt0) REVERT: HA 343 GLU cc_start: 0.6911 (tt0) cc_final: 0.6415 (tt0) REVERT: HA 386 ILE cc_start: 0.5534 (mt) cc_final: 0.5333 (mp) REVERT: HA 402 ASP cc_start: 0.6085 (t70) cc_final: 0.5352 (t70) REVERT: HA 407 GLN cc_start: 0.7354 (tp40) cc_final: 0.7055 (tp40) REVERT: HA 434 GLN cc_start: 0.6728 (mt0) cc_final: 0.6242 (tm-30) REVERT: HA 436 GLU cc_start: 0.6110 (mt-10) cc_final: 0.5396 (tt0) REVERT: HB 11 ILE cc_start: 0.5038 (pt) cc_final: 0.4821 (pt) REVERT: HB 47 VAL cc_start: 0.6624 (t) cc_final: 0.6276 (m) REVERT: HB 51 ARG cc_start: 0.6616 (tmt90) cc_final: 0.6205 (ttt180) REVERT: HB 114 ARG cc_start: 0.6388 (mtt180) cc_final: 0.6085 (mtt180) REVERT: HB 131 MET cc_start: 0.6418 (mtt) cc_final: 0.6140 (mtt) REVERT: HC 96 GLU cc_start: 0.5807 (pt0) cc_final: 0.5541 (pt0) REVERT: HC 236 TRP cc_start: 0.2982 (p90) cc_final: 0.2516 (p90) REVERT: HD 2 ASN cc_start: 0.6003 (t0) cc_final: 0.5284 (t0) REVERT: HD 12 ASN cc_start: 0.4217 (t0) cc_final: 0.3845 (t0) REVERT: HD 48 ILE cc_start: 0.4907 (mt) cc_final: 0.4500 (mt) REVERT: HD 61 MET cc_start: 0.5103 (mmm) cc_final: 0.4722 (tpp) REVERT: HD 83 MET cc_start: 0.6274 (tpt) cc_final: 0.6011 (mmm) REVERT: HD 88 ARG cc_start: 0.7019 (mtt180) cc_final: 0.5736 (tpt170) REVERT: HD 94 LYS cc_start: 0.6647 (ttpt) cc_final: 0.6180 (ttpp) REVERT: HD 101 LEU cc_start: 0.5105 (mp) cc_final: 0.4853 (mp) REVERT: HE 144 GLU cc_start: 0.6446 (tt0) cc_final: 0.5961 (tt0) REVERT: HE 154 MET cc_start: 0.5481 (tpp) cc_final: 0.4994 (tpp) REVERT: HE 156 LYS cc_start: 0.6345 (tptt) cc_final: 0.5894 (tptt) REVERT: HE 157 MET cc_start: 0.5828 (mtm) cc_final: 0.5450 (mtp) REVERT: HE 158 LEU cc_start: 0.6432 (tp) cc_final: 0.6033 (tp) REVERT: HE 160 LYS cc_start: 0.7602 (tttt) cc_final: 0.6904 (ttmm) REVERT: HE 173 ARG cc_start: 0.5569 (mmt-90) cc_final: 0.5149 (tpp-160) REVERT: HE 175 GLU cc_start: 0.6104 (tt0) cc_final: 0.5897 (tt0) REVERT: HF 9 GLU cc_start: 0.6439 (mp0) cc_final: 0.6041 (mp0) REVERT: HF 24 GLU cc_start: 0.4211 (tp30) cc_final: 0.3986 (tp30) REVERT: HF 51 GLN cc_start: 0.6901 (tt0) cc_final: 0.6657 (tt0) REVERT: HF 52 PHE cc_start: 0.6720 (t80) cc_final: 0.6274 (t80) REVERT: HF 74 ASN cc_start: 0.4876 (t0) cc_final: 0.4583 (m110) REVERT: HF 117 ASP cc_start: 0.7652 (t0) cc_final: 0.7429 (t0) REVERT: HF 119 GLN cc_start: 0.6278 (mt0) cc_final: 0.5984 (mt0) REVERT: HF 156 VAL cc_start: 0.7768 (t) cc_final: 0.7561 (m) REVERT: HF 212 PHE cc_start: 0.5313 (m-80) cc_final: 0.4950 (m-10) REVERT: HF 213 ARG cc_start: 0.7295 (ttt-90) cc_final: 0.6635 (ttm-80) REVERT: HF 238 LYS cc_start: 0.7541 (mttm) cc_final: 0.7268 (mttm) REVERT: HF 240 GLU cc_start: 0.5679 (tt0) cc_final: 0.5347 (tt0) REVERT: HF 266 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6288 (mm-30) REVERT: HF 284 GLU cc_start: 0.8068 (tt0) cc_final: 0.7233 (tt0) REVERT: HF 288 LYS cc_start: 0.8196 (mttt) cc_final: 0.7617 (mtmm) REVERT: HF 295 GLU cc_start: 0.6979 (tt0) cc_final: 0.6510 (mt-10) REVERT: HF 306 TYR cc_start: 0.6494 (m-80) cc_final: 0.6239 (m-10) REVERT: HF 314 PHE cc_start: 0.6587 (m-80) cc_final: 0.6157 (m-80) REVERT: HF 317 PHE cc_start: 0.6991 (m-80) cc_final: 0.6610 (m-80) REVERT: HF 345 THR cc_start: 0.6722 (m) cc_final: 0.6459 (p) REVERT: HG 29 TYR cc_start: 0.6107 (t80) cc_final: 0.5817 (t80) REVERT: HG 37 LEU cc_start: 0.4720 (mt) cc_final: 0.4415 (mt) REVERT: HG 67 MET cc_start: 0.7324 (mtt) cc_final: 0.6968 (mtt) REVERT: HG 74 THR cc_start: 0.5813 (m) cc_final: 0.5436 (p) REVERT: HG 88 LYS cc_start: 0.7925 (mttt) cc_final: 0.7436 (mmtt) REVERT: HG 95 TYR cc_start: 0.6647 (m-80) cc_final: 0.6369 (m-80) REVERT: HH 18 TYR cc_start: 0.7686 (t80) cc_final: 0.6913 (t80) REVERT: HH 22 VAL cc_start: 0.6320 (m) cc_final: 0.6101 (p) REVERT: HH 52 GLU cc_start: 0.6285 (mm-30) cc_final: 0.5850 (mm-30) REVERT: HH 59 GLU cc_start: 0.6982 (tp30) cc_final: 0.6552 (mm-30) REVERT: HH 60 MET cc_start: 0.6461 (ttp) cc_final: 0.5356 (mmt) REVERT: HH 74 ASP cc_start: 0.7741 (t0) cc_final: 0.7342 (t70) REVERT: HI 4 TYR cc_start: 0.4025 (m-80) cc_final: 0.3474 (m-80) REVERT: HI 109 LYS cc_start: 0.5732 (mttp) cc_final: 0.5419 (mmtm) REVERT: HI 115 TRP cc_start: 0.4294 (t60) cc_final: 0.4024 (t60) REVERT: HI 131 LYS cc_start: 0.7378 (mmtt) cc_final: 0.7033 (mmtt) REVERT: HI 138 GLN cc_start: 0.6350 (pt0) cc_final: 0.6086 (pm20) REVERT: HJ 149 LEU cc_start: 0.6338 (tp) cc_final: 0.5650 (tp) REVERT: HJ 153 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6727 (mt-10) REVERT: HJ 164 ARG cc_start: 0.6583 (mtp180) cc_final: 0.6346 (mtp180) REVERT: HJ 173 PHE cc_start: 0.7635 (p90) cc_final: 0.7098 (p90) REVERT: HJ 296 ARG cc_start: 0.6537 (mtt-85) cc_final: 0.6190 (mtt-85) REVERT: HJ 386 ASP cc_start: 0.6931 (t0) cc_final: 0.6525 (m-30) REVERT: HJ 426 GLU cc_start: 0.6518 (mt-10) cc_final: 0.6056 (mp0) REVERT: HJ 431 ASN cc_start: 0.7965 (m-40) cc_final: 0.7627 (m-40) REVERT: HJ 433 MET cc_start: 0.8260 (mmt) cc_final: 0.7819 (mmt) REVERT: HJ 444 LEU cc_start: 0.6403 (tp) cc_final: 0.6035 (tt) REVERT: HJ 460 ASP cc_start: 0.5931 (t0) cc_final: 0.5541 (p0) REVERT: HJ 483 ASP cc_start: 0.5848 (t70) cc_final: 0.5395 (t0) REVERT: HJ 551 GLU cc_start: 0.6076 (tt0) cc_final: 0.5779 (tt0) REVERT: HJ 555 ASP cc_start: 0.5888 (t70) cc_final: 0.5474 (t0) REVERT: HJ 557 GLU cc_start: 0.7118 (tp30) cc_final: 0.6102 (tp30) REVERT: HJ 559 LYS cc_start: 0.7196 (mtmt) cc_final: 0.6712 (mtmt) REVERT: HJ 560 PHE cc_start: 0.7195 (t80) cc_final: 0.6867 (t80) REVERT: HK 23 ARG cc_start: 0.7049 (ttt180) cc_final: 0.6788 (ttt180) REVERT: HK 100 LEU cc_start: 0.4969 (mt) cc_final: 0.4544 (tp) REVERT: HL 17 MET cc_start: 0.6888 (ttt) cc_final: 0.6626 (ttt) REVERT: HL 48 LEU cc_start: 0.5618 (tp) cc_final: 0.5349 (mp) REVERT: HL 56 MET cc_start: 0.5635 (tpp) cc_final: 0.5151 (tpp) REVERT: HM 17 LEU cc_start: 0.5996 (tp) cc_final: 0.5528 (tt) REVERT: HM 31 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6299 (mm-30) REVERT: HM 38 ARG cc_start: 0.6488 (mtt-85) cc_final: 0.6082 (ttm-80) REVERT: HM 45 ILE cc_start: 0.6191 (pt) cc_final: 0.5878 (mp) REVERT: HM 53 VAL cc_start: 0.6844 (t) cc_final: 0.6602 (t) REVERT: HM 56 GLN cc_start: 0.7184 (mt0) cc_final: 0.6785 (mt0) REVERT: HM 65 PHE cc_start: 0.6797 (m-80) cc_final: 0.5410 (m-80) REVERT: HM 85 GLU cc_start: 0.6643 (pt0) cc_final: 0.6235 (pt0) REVERT: HM 95 LEU cc_start: 0.7681 (tp) cc_final: 0.7341 (tp) REVERT: HM 98 GLN cc_start: 0.6594 (mt0) cc_final: 0.5996 (mm-40) REVERT: HM 203 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6611 (pp20) REVERT: HM 345 ARG cc_start: 0.6319 (ptp-110) cc_final: 0.5900 (ptp-110) REVERT: HM 352 GLN cc_start: 0.6773 (tm-30) cc_final: 0.6371 (tm-30) REVERT: HM 363 PHE cc_start: 0.5980 (t80) cc_final: 0.5757 (t80) REVERT: HM 392 ARG cc_start: 0.5905 (ptp90) cc_final: 0.5608 (ptp90) REVERT: HM 400 GLN cc_start: 0.6063 (mm110) cc_final: 0.5665 (mt0) REVERT: HM 409 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.6529 (mtt-85) REVERT: HM 587 LEU cc_start: 0.7419 (mp) cc_final: 0.7147 (mp) REVERT: HM 593 LEU cc_start: 0.6967 (mt) cc_final: 0.6736 (mt) REVERT: HN 6 ASN cc_start: 0.5940 (m-40) cc_final: 0.5716 (m110) REVERT: HN 7 ARG cc_start: 0.4279 (ttm170) cc_final: 0.3990 (ttm-80) REVERT: HN 21 VAL cc_start: 0.5790 (t) cc_final: 0.4993 (m) REVERT: HO 5 ARG cc_start: 0.5372 (ptm160) cc_final: 0.5077 (ptp90) REVERT: HO 108 GLU cc_start: 0.5921 (tt0) cc_final: 0.5515 (tt0) REVERT: HP 13 ASN cc_start: 0.6160 (t0) cc_final: 0.5895 (t0) REVERT: HP 164 ASP cc_start: 0.4548 (m-30) cc_final: 0.4323 (m-30) REVERT: HP 195 SER cc_start: 0.7558 (t) cc_final: 0.7323 (p) REVERT: HP 197 GLU cc_start: 0.7023 (tt0) cc_final: 0.6731 (tm-30) REVERT: HP 245 LYS cc_start: 0.6431 (mttt) cc_final: 0.6216 (mttt) REVERT: HQ 12 PHE cc_start: 0.5141 (m-80) cc_final: 0.4739 (m-80) REVERT: HQ 17 LYS cc_start: 0.4777 (mttt) cc_final: 0.4355 (mttm) REVERT: HQ 178 TRP cc_start: 0.8136 (t60) cc_final: 0.7790 (t-100) REVERT: HQ 190 LEU cc_start: 0.6994 (mt) cc_final: 0.6588 (tp) REVERT: HQ 194 ASP cc_start: 0.5355 (m-30) cc_final: 0.4921 (m-30) REVERT: HQ 208 PHE cc_start: 0.5902 (m-80) cc_final: 0.5442 (m-10) REVERT: HQ 216 LEU cc_start: 0.6262 (mp) cc_final: 0.6031 (mp) REVERT: HQ 252 LEU cc_start: 0.6599 (tp) cc_final: 0.6396 (tp) REVERT: HQ 279 GLU cc_start: 0.0917 (tm-30) cc_final: -0.0266 (mp0) REVERT: HQ 281 TRP cc_start: 0.5203 (t-100) cc_final: 0.4911 (t-100) REVERT: HQ 282 LEU cc_start: 0.5757 (tp) cc_final: 0.5449 (tp) REVERT: HQ 297 THR cc_start: 0.3859 (p) cc_final: 0.3291 (p) REVERT: HQ 302 ASP cc_start: 0.5943 (t0) cc_final: 0.5362 (t0) REVERT: HQ 303 MET cc_start: 0.3242 (mtm) cc_final: 0.3022 (mmm) REVERT: HQ 309 LYS cc_start: 0.5344 (mttt) cc_final: 0.4905 (mtmm) REVERT: HQ 315 ARG cc_start: 0.5891 (mtp85) cc_final: 0.5604 (tpp80) REVERT: HQ 419 GLU cc_start: 0.6557 (tp30) cc_final: 0.6333 (tp30) REVERT: HQ 427 GLU cc_start: 0.6725 (tp30) cc_final: 0.6439 (tp30) REVERT: HQ 541 ASN cc_start: 0.7228 (t0) cc_final: 0.7014 (t0) REVERT: HQ 630 GLN cc_start: 0.7107 (tm130) cc_final: 0.6845 (tm130) REVERT: HQ 702 LEU cc_start: 0.5556 (mt) cc_final: 0.5257 (mt) REVERT: HQ 707 LYS cc_start: 0.6204 (tttt) cc_final: 0.5969 (ttpp) REVERT: HQ 715 GLN cc_start: 0.5922 (mm-40) cc_final: 0.5709 (mt0) REVERT: HR 161 ASN cc_start: 0.7653 (m-40) cc_final: 0.6940 (p0) REVERT: HS 101 ASP cc_start: 0.7014 (m-30) cc_final: 0.6680 (t0) REVERT: HS 112 MET cc_start: 0.6446 (mpm) cc_final: 0.6134 (mpm) REVERT: HS 135 ARG cc_start: 0.6334 (mtm180) cc_final: 0.6102 (mtm180) REVERT: HS 145 VAL cc_start: 0.6013 (p) cc_final: 0.5625 (m) REVERT: HS 146 HIS cc_start: 0.5705 (t70) cc_final: 0.5321 (t70) REVERT: HS 153 ARG cc_start: 0.7606 (tpt-90) cc_final: 0.7260 (mmm160) REVERT: HS 186 VAL cc_start: 0.6084 (t) cc_final: 0.5826 (m) REVERT: HT 23 LYS cc_start: 0.6802 (mmtt) cc_final: 0.6361 (mptt) REVERT: HT 28 ASP cc_start: 0.6298 (t70) cc_final: 0.5930 (t70) REVERT: HT 31 LYS cc_start: 0.7385 (tttt) cc_final: 0.6933 (mtpp) REVERT: HT 44 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7585 (mt-10) REVERT: HT 51 GLN cc_start: 0.5313 (mm-40) cc_final: 0.5067 (mm-40) REVERT: HT 57 LYS cc_start: 0.6142 (mttt) cc_final: 0.5941 (ttmm) REVERT: HT 65 MET cc_start: 0.6435 (ttm) cc_final: 0.5347 (mtp) REVERT: HT 105 ARG cc_start: 0.7905 (ttp-110) cc_final: 0.7325 (ttp80) REVERT: HT 362 ASP cc_start: 0.5498 (t0) cc_final: 0.5287 (t0) outliers start: 3 outliers final: 1 residues processed: 1248 average time/residue: 0.2917 time to fit residues: 558.8625 Evaluate side-chains 1066 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1065 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HK residue 47 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.0870 chunk 401 optimal weight: 0.7980 chunk 424 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** HA 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HE 131 HIS HF 21 HIS HF 67 GLN HF 154 GLN HF 210 HIS HF 291 ASN HI 16 HIS HJ 489 HIS HL 35 ASN ** HM 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HP 225 GLN HP 238 GLN HP 239 GLN HQ 206 ASN ** HQ 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HQ 429 ASN HQ 712 ASN HQ 718 HIS HR 20 ASN HS 140 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.196597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.169344 restraints weight = 65763.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.173437 restraints weight = 37938.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.173942 restraints weight = 22149.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.174296 restraints weight = 20698.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174552 restraints weight = 17665.700| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 42419 Z= 0.224 Angle : 0.747 14.246 58628 Z= 0.392 Chirality : 0.046 0.325 6660 Planarity : 0.006 0.084 6558 Dihedral : 17.963 172.807 9205 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.89 % Favored : 93.06 % Rotamer: Outliers : 2.71 % Allowed : 15.66 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.12), residues: 4268 helix: -0.11 (0.12), residues: 1790 sheet: -0.99 (0.41), residues: 177 loop : -2.21 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGHQ 693 TYR 0.026 0.003 TYRHB 134 PHE 0.035 0.003 PHEHQ 685 TRP 0.021 0.003 TRPHK 44 HIS 0.012 0.001 HISHJ 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (42419) covalent geometry : angle 0.74709 / 0.39 (58628) hydrogen bonds : bond 0.07841 / 5.23 ( 1057) hydrogen bonds : angle 5.19728 / 3.66 ( 2968) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 1140 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: HA 10 ARG cc_start: 0.7162 (ptm160) cc_final: 0.6329 (mmt180) REVERT: HA 28 GLU cc_start: 0.7312 (pp20) cc_final: 0.7061 (pp20) REVERT: HA 32 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7041 (t0) REVERT: HA 46 MET cc_start: 0.3373 (ttm) cc_final: 0.2634 (pmm) REVERT: HA 56 MET cc_start: 0.7291 (mtt) cc_final: 0.7055 (mtm) REVERT: HA 162 TYR cc_start: 0.6991 (t80) cc_final: 0.6491 (t80) REVERT: HA 313 MET cc_start: 0.4821 (ttm) cc_final: 0.4589 (ttm) REVERT: HA 358 ILE cc_start: 0.7538 (mp) cc_final: 0.7336 (mm) REVERT: HA 398 SER cc_start: 0.7085 (t) cc_final: 0.6617 (p) REVERT: HA 399 ARG cc_start: 0.7746 (mtm180) cc_final: 0.7458 (mtm-85) REVERT: HA 402 ASP cc_start: 0.6876 (t70) cc_final: 0.6222 (t70) REVERT: HA 437 ILE cc_start: 0.7917 (mm) cc_final: 0.7641 (mm) REVERT: HB 20 MET cc_start: 0.5343 (mmm) cc_final: 0.5093 (mmm) REVERT: HB 47 VAL cc_start: 0.7199 (t) cc_final: 0.6980 (m) REVERT: HB 50 ARG cc_start: 0.7228 (mmm-85) cc_final: 0.6546 (mmm-85) REVERT: HB 51 ARG cc_start: 0.7523 (tmt90) cc_final: 0.7140 (ttt180) REVERT: HB 63 ASP cc_start: 0.5592 (t70) cc_final: 0.5260 (t70) REVERT: HB 94 ILE cc_start: 0.4689 (mt) cc_final: 0.4428 (mt) REVERT: HB 109 ARG cc_start: 0.7916 (ttt180) cc_final: 0.7688 (ttt180) REVERT: HB 153 MET cc_start: 0.6991 (tpp) cc_final: 0.6708 (tpt) REVERT: HC 17 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7523 (mtt-85) REVERT: HC 203 GLU cc_start: 0.7743 (tp30) cc_final: 0.7310 (tp30) REVERT: HD 12 ASN cc_start: 0.7075 (t0) cc_final: 0.6735 (t0) REVERT: HD 20 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7340 (tp) REVERT: HD 40 GLN cc_start: 0.7142 (mt0) cc_final: 0.6794 (mt0) REVERT: HD 69 SER cc_start: 0.7331 (t) cc_final: 0.7051 (p) REVERT: HD 89 GLU cc_start: 0.5714 (mt-10) cc_final: 0.5450 (tt0) REVERT: HD 91 TRP cc_start: 0.7300 (m100) cc_final: 0.6583 (m100) REVERT: HD 95 TYR cc_start: 0.8249 (m-80) cc_final: 0.8012 (m-80) REVERT: HE 9 ARG cc_start: 0.7581 (ttp-110) cc_final: 0.7378 (mtp85) REVERT: HE 154 MET cc_start: 0.7452 (tpp) cc_final: 0.6952 (tpp) REVERT: HE 160 LYS cc_start: 0.8595 (tttt) cc_final: 0.7988 (ttmm) REVERT: HE 162 CYS cc_start: 0.7745 (m) cc_final: 0.7223 (t) REVERT: HF 24 GLU cc_start: 0.6727 (tp30) cc_final: 0.6384 (tp30) REVERT: HF 67 GLN cc_start: 0.6958 (mm-40) cc_final: 0.6687 (tp40) REVERT: HF 86 LYS cc_start: 0.7725 (ttmm) cc_final: 0.7494 (ttmt) REVERT: HF 88 GLU cc_start: 0.6467 (mt-10) cc_final: 0.6011 (pt0) REVERT: HF 108 THR cc_start: 0.8246 (m) cc_final: 0.7765 (t) REVERT: HF 130 GLU cc_start: 0.5605 (mp0) cc_final: 0.5382 (mp0) REVERT: HF 204 ASP cc_start: 0.6676 (t0) cc_final: 0.6423 (m-30) REVERT: HF 237 LYS cc_start: 0.7462 (mtmm) cc_final: 0.6781 (mtmm) REVERT: HF 240 GLU cc_start: 0.5953 (tt0) cc_final: 0.5663 (tt0) REVERT: HF 266 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6462 (mm-30) REVERT: HF 273 ARG cc_start: 0.7613 (mtt90) cc_final: 0.7400 (mtt90) REVERT: HF 295 GLU cc_start: 0.6538 (tt0) cc_final: 0.6313 (mt-10) REVERT: HG 37 LEU cc_start: 0.6680 (mt) cc_final: 0.6458 (mt) REVERT: HG 88 LYS cc_start: 0.8096 (mttt) cc_final: 0.7822 (mttt) REVERT: HH 11 HIS cc_start: 0.1823 (OUTLIER) cc_final: 0.1217 (m-70) REVERT: HH 59 GLU cc_start: 0.7130 (tp30) cc_final: 0.6675 (mm-30) REVERT: HH 60 MET cc_start: 0.6223 (ttp) cc_final: 0.6004 (mmp) REVERT: HI 2 PHE cc_start: 0.7745 (m-80) cc_final: 0.6750 (m-80) REVERT: HI 4 TYR cc_start: 0.8761 (m-80) cc_final: 0.8489 (m-80) REVERT: HI 5 ARG cc_start: 0.7646 (ttp-170) cc_final: 0.7314 (ttp-170) REVERT: HI 46 MET cc_start: 0.7159 (tpp) cc_final: 0.6944 (tpp) REVERT: HI 59 LYS cc_start: 0.7259 (tptt) cc_final: 0.6442 (tptt) REVERT: HI 63 MET cc_start: 0.6219 (mtm) cc_final: 0.5001 (mtm) REVERT: HI 118 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7380 (mttt) REVERT: HI 129 LYS cc_start: 0.7273 (mttt) cc_final: 0.6857 (mttt) REVERT: HJ 153 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7152 (mt-10) REVERT: HJ 331 ASN cc_start: 0.7659 (m-40) cc_final: 0.7079 (m-40) REVERT: HJ 397 ASP cc_start: 0.6752 (p0) cc_final: 0.5317 (t70) REVERT: HJ 398 PHE cc_start: 0.7095 (t80) cc_final: 0.5997 (t80) REVERT: HJ 431 ASN cc_start: 0.8097 (m-40) cc_final: 0.7873 (m110) REVERT: HJ 433 MET cc_start: 0.7920 (mmt) cc_final: 0.7674 (mmt) REVERT: HJ 441 GLU cc_start: 0.5690 (mt-10) cc_final: 0.5385 (mt-10) REVERT: HJ 479 PHE cc_start: 0.5853 (m-80) cc_final: 0.5253 (m-10) REVERT: HJ 557 GLU cc_start: 0.6986 (tp30) cc_final: 0.6548 (tp30) REVERT: HK 40 ARG cc_start: 0.5732 (mmt90) cc_final: 0.5365 (mmt90) REVERT: HK 77 ARG cc_start: 0.3903 (tpt170) cc_final: 0.3591 (tpt170) REVERT: HK 103 GLU cc_start: 0.6282 (mm-30) cc_final: 0.5940 (mm-30) REVERT: HL 56 MET cc_start: 0.5670 (tpp) cc_final: 0.5409 (tpp) REVERT: HM 33 TYR cc_start: 0.7068 (t80) cc_final: 0.6628 (t80) REVERT: HM 45 ILE cc_start: 0.7195 (pt) cc_final: 0.6981 (mp) REVERT: HM 53 VAL cc_start: 0.7685 (t) cc_final: 0.7332 (p) REVERT: HM 65 PHE cc_start: 0.6922 (m-80) cc_final: 0.6636 (m-80) REVERT: HM 163 ASP cc_start: 0.6739 (t0) cc_final: 0.6494 (t0) REVERT: HM 198 LEU cc_start: 0.7091 (mp) cc_final: 0.6790 (mm) REVERT: HM 203 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6703 (tm-30) REVERT: HM 267 THR cc_start: 0.6683 (OUTLIER) cc_final: 0.6404 (p) REVERT: HM 321 ARG cc_start: 0.4177 (mtt180) cc_final: 0.3629 (mtt180) REVERT: HM 342 MET cc_start: 0.6974 (tpp) cc_final: 0.6760 (tpp) REVERT: HM 352 GLN cc_start: 0.6848 (tm-30) cc_final: 0.6546 (tm-30) REVERT: HM 353 GLN cc_start: 0.6886 (tt0) cc_final: 0.6321 (tt0) REVERT: HM 361 VAL cc_start: 0.7460 (m) cc_final: 0.7158 (p) REVERT: HM 587 LEU cc_start: 0.7434 (mp) cc_final: 0.7233 (mp) REVERT: HN 6 ASN cc_start: 0.6961 (m-40) cc_final: 0.6522 (m110) REVERT: HO 14 ARG cc_start: 0.6044 (ttp80) cc_final: 0.5447 (ttt180) REVERT: HO 129 PHE cc_start: 0.6479 (m-80) cc_final: 0.5749 (m-80) REVERT: HP 198 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6313 (tm-30) REVERT: HP 239 GLN cc_start: 0.7845 (tp-100) cc_final: 0.7383 (tm-30) REVERT: HQ 17 LYS cc_start: 0.6590 (mttt) cc_final: 0.6353 (mttt) REVERT: HQ 122 ASP cc_start: 0.6812 (t70) cc_final: 0.6548 (m-30) REVERT: HQ 178 TRP cc_start: 0.8080 (t60) cc_final: 0.7820 (t-100) REVERT: HQ 194 ASP cc_start: 0.5831 (m-30) cc_final: 0.5271 (m-30) REVERT: HQ 209 ASP cc_start: 0.7737 (m-30) cc_final: 0.7462 (m-30) REVERT: HQ 217 LEU cc_start: 0.7564 (tp) cc_final: 0.7177 (mt) REVERT: HQ 221 GLU cc_start: 0.7036 (tt0) cc_final: 0.6659 (tt0) REVERT: HQ 252 LEU cc_start: 0.7895 (tp) cc_final: 0.7675 (tp) REVERT: HQ 282 LEU cc_start: 0.7719 (tp) cc_final: 0.7340 (tp) REVERT: HQ 331 LYS cc_start: 0.7603 (mtpp) cc_final: 0.7208 (mtpp) REVERT: HQ 346 ARG cc_start: 0.5587 (ttm110) cc_final: 0.5180 (ttm110) REVERT: HQ 383 GLU cc_start: 0.6379 (mm-30) cc_final: 0.6027 (tm-30) REVERT: HQ 411 THR cc_start: 0.6588 (m) cc_final: 0.6375 (m) REVERT: HQ 427 GLU cc_start: 0.6801 (tp30) cc_final: 0.6547 (tp30) REVERT: HQ 463 GLN cc_start: 0.6893 (tp40) cc_final: 0.6652 (tp40) REVERT: HQ 627 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7219 (mp0) REVERT: HQ 630 GLN cc_start: 0.7643 (tm130) cc_final: 0.7092 (tm130) REVERT: HQ 707 LYS cc_start: 0.7822 (tttt) cc_final: 0.7561 (ttpt) REVERT: HR 28 ASP cc_start: 0.8040 (t0) cc_final: 0.7729 (t0) REVERT: HR 156 GLN cc_start: 0.7011 (tm-30) cc_final: 0.6799 (tm-30) REVERT: HT 26 VAL cc_start: 0.7507 (t) cc_final: 0.7215 (m) REVERT: HT 32 LYS cc_start: 0.8299 (mtpt) cc_final: 0.8064 (mtpt) REVERT: HT 44 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6812 (mt-10) REVERT: HT 45 GLN cc_start: 0.7762 (mp10) cc_final: 0.7374 (mp10) REVERT: HT 54 GLN cc_start: 0.6803 (tp40) cc_final: 0.6523 (tp40) REVERT: HT 57 LYS cc_start: 0.7708 (mttt) cc_final: 0.7417 (ttmm) REVERT: HT 105 ARG cc_start: 0.7572 (ttp-110) cc_final: 0.7196 (ttp-110) outliers start: 101 outliers final: 57 residues processed: 1172 average time/residue: 0.2734 time to fit residues: 496.8977 Evaluate side-chains 1119 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 1056 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 19 GLU Chi-restraints excluded: chain HA residue 32 ASP Chi-restraints excluded: chain HA residue 146 PHE Chi-restraints excluded: chain HA residue 197 VAL Chi-restraints excluded: chain HA residue 300 LEU Chi-restraints excluded: chain HB residue 53 THR Chi-restraints excluded: chain HB residue 78 LEU Chi-restraints excluded: chain HC residue 10 LEU Chi-restraints excluded: chain HC residue 41 SER Chi-restraints excluded: chain HC residue 194 LEU Chi-restraints excluded: chain HD residue 1 LEU Chi-restraints excluded: chain HD residue 20 LEU Chi-restraints excluded: chain HD residue 59 ILE Chi-restraints excluded: chain HD residue 84 LEU Chi-restraints excluded: chain HE residue 110 LEU Chi-restraints excluded: chain HF residue 196 VAL Chi-restraints excluded: chain HF residue 256 HIS Chi-restraints excluded: chain HF residue 262 LEU Chi-restraints excluded: chain HF residue 263 LYS Chi-restraints excluded: chain HF residue 322 MET Chi-restraints excluded: chain HF residue 323 VAL Chi-restraints excluded: chain HG residue 70 LEU Chi-restraints excluded: chain HH residue 11 HIS Chi-restraints excluded: chain HI residue 34 MET Chi-restraints excluded: chain HI residue 92 THR Chi-restraints excluded: chain HI residue 118 LYS Chi-restraints excluded: chain HJ residue 162 THR Chi-restraints excluded: chain HJ residue 228 VAL Chi-restraints excluded: chain HJ residue 238 LEU Chi-restraints excluded: chain HJ residue 329 ILE Chi-restraints excluded: chain HK residue 33 SER Chi-restraints excluded: chain HK residue 47 TYR Chi-restraints excluded: chain HM residue 70 ILE Chi-restraints excluded: chain HM residue 73 ILE Chi-restraints excluded: chain HM residue 151 VAL Chi-restraints excluded: chain HM residue 267 THR Chi-restraints excluded: chain HM residue 412 LEU Chi-restraints excluded: chain HM residue 418 LEU Chi-restraints excluded: chain HM residue 607 ILE Chi-restraints excluded: chain HN residue 2 MET Chi-restraints excluded: chain HO residue 115 VAL Chi-restraints excluded: chain HO residue 150 SER Chi-restraints excluded: chain HP residue 40 VAL Chi-restraints excluded: chain HP residue 60 MET Chi-restraints excluded: chain HP residue 187 VAL Chi-restraints excluded: chain HP residue 198 GLN Chi-restraints excluded: chain HP residue 213 THR Chi-restraints excluded: chain HQ residue 179 ASN Chi-restraints excluded: chain HQ residue 223 SER Chi-restraints excluded: chain HQ residue 238 ILE Chi-restraints excluded: chain HQ residue 253 ILE Chi-restraints excluded: chain HQ residue 314 VAL Chi-restraints excluded: chain HQ residue 409 SER Chi-restraints excluded: chain HQ residue 477 VAL Chi-restraints excluded: chain HQ residue 626 GLU Chi-restraints excluded: chain HQ residue 692 TRP Chi-restraints excluded: chain HQ residue 710 ILE Chi-restraints excluded: chain HR residue 6 TRP Chi-restraints excluded: chain HR residue 126 ASN Chi-restraints excluded: chain HR residue 158 LEU Chi-restraints excluded: chain HT residue 92 THR Chi-restraints excluded: chain HT residue 161 THR Chi-restraints excluded: chain HT residue 340 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 176 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 340 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 418 optimal weight: 6.9990 chunk 233 optimal weight: 0.9980 chunk 81 optimal weight: 0.0770 chunk 102 optimal weight: 0.5980 chunk 310 optimal weight: 0.5980 chunk 444 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... HA 200 GLN ** HA 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HE 131 HIS HF 36 GLN HF 154 GLN ** HF 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HF 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HI 138 GLN HJ 416 GLN HJ 419 ASN HJ 475 ASN ** HL 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HM 212 GLN ** HM 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HM 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HM 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HM 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HO 142 GLN ** HP 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HQ 206 ASN HQ 236 HIS HQ 299 HIS HQ 463 GLN HR 24 ASN HS 197 GLN HS 198 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.191082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.162960 restraints weight = 64908.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.167340 restraints weight = 39065.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.167791 restraints weight = 21522.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.167928 restraints weight = 20352.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.168239 restraints weight = 18162.840| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 42419 Z= 0.184 Angle : 0.680 16.022 58628 Z= 0.348 Chirality : 0.042 0.343 6660 Planarity : 0.006 0.103 6558 Dihedral : 17.894 172.750 9205 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.91 % Favored : 93.04 % Rotamer: Outliers : 3.79 % Allowed : 17.84 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.12), residues: 4268 helix: 0.03 (0.12), residues: 1815 sheet: -1.18 (0.41), residues: 172 loop : -2.26 (0.12), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGHK 77 TYR 0.023 0.002 TYRHT 36 PHE 0.028 0.002 PHEHM 393 TRP 0.054 0.002 TRPHB 30 HIS 0.014 0.001 HISHR 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (42419) covalent geometry : angle 0.68030 / 0.35 (58628) hydrogen bonds : bond 0.06679 / 4.40 ( 1057) hydrogen bonds : angle 4.64125 / 3.24 ( 2968) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1107 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: HA 10 ARG cc_start: 0.6991 (ptm160) cc_final: 0.6303 (mmp-170) REVERT: HA 32 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.7027 (t0) REVERT: HA 46 MET cc_start: 0.3370 (ttm) cc_final: 0.2684 (pmm) REVERT: HA 172 TRP cc_start: 0.7102 (m100) cc_final: 0.6534 (m100) REVERT: HA 301 TRP cc_start: 0.8003 (m100) cc_final: 0.7436 (m100) REVERT: HA 313 MET cc_start: 0.4877 (ttm) cc_final: 0.4542 (ttm) REVERT: HA 339 GLN cc_start: 0.7322 (tt0) cc_final: 0.6657 (tt0) REVERT: HA 363 TRP cc_start: 0.7669 (t60) cc_final: 0.6685 (t60) REVERT: HA 398 SER cc_start: 0.7153 (t) cc_final: 0.6736 (p) REVERT: HA 399 ARG cc_start: 0.7587 (mtm180) cc_final: 0.7376 (mtm-85) REVERT: HA 402 ASP cc_start: 0.6802 (t70) cc_final: 0.5192 (t70) REVERT: HA 405 GLN cc_start: 0.6708 (mp10) cc_final: 0.6359 (mp10) REVERT: HA 426 ARG cc_start: 0.5326 (ptt-90) cc_final: 0.3711 (ptt-90) REVERT: HA 437 ILE cc_start: 0.8110 (mm) cc_final: 0.7579 (mm) REVERT: HA 450 ASN cc_start: 0.7810 (m-40) cc_final: 0.7571 (m110) REVERT: HA 457 LYS cc_start: 0.7957 (mttp) cc_final: 0.7716 (ttmm) REVERT: HA 466 ARG cc_start: 0.6596 (mpt180) cc_final: 0.6225 (mmt-90) REVERT: HB 20 MET cc_start: 0.5330 (mmm) cc_final: 0.5036 (mmm) REVERT: HB 50 ARG cc_start: 0.7413 (mmm-85) cc_final: 0.6762 (mmm-85) REVERT: HB 51 ARG cc_start: 0.7848 (tmt90) cc_final: 0.7339 (ttt180) REVERT: HB 78 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8188 (mp) REVERT: HB 109 ARG cc_start: 0.7970 (ttt180) cc_final: 0.7567 (ttt180) REVERT: HB 148 MET cc_start: 0.6702 (mtm) cc_final: 0.6447 (mtm) REVERT: HB 153 MET cc_start: 0.7155 (tpp) cc_final: 0.6832 (tpt) REVERT: HC 2 LEU cc_start: 0.7550 (tt) cc_final: 0.7198 (tp) REVERT: HC 96 GLU cc_start: 0.6947 (pt0) cc_final: 0.6574 (pt0) REVERT: HC 195 ARG cc_start: 0.6523 (ttt90) cc_final: 0.6309 (ttt180) REVERT: HC 218 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8034 (tp) REVERT: HD 20 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7424 (tp) REVERT: HD 27 GLU cc_start: 0.6418 (tp30) cc_final: 0.6115 (tp30) REVERT: HD 40 GLN cc_start: 0.7269 (mt0) cc_final: 0.7035 (mt0) REVERT: HD 91 TRP cc_start: 0.8153 (m100) cc_final: 0.6707 (m100) REVERT: HE 39 HIS cc_start: 0.7298 (t-170) cc_final: 0.7081 (t-170) REVERT: HE 136 VAL cc_start: 0.6975 (t) cc_final: 0.6753 (p) REVERT: HE 154 MET cc_start: 0.7470 (tpp) cc_final: 0.7262 (tpp) REVERT: HE 160 LYS cc_start: 0.8630 (tttt) cc_final: 0.7975 (ttmm) REVERT: HE 162 CYS cc_start: 0.7903 (m) cc_final: 0.7264 (t) REVERT: HF 24 GLU cc_start: 0.6130 (tp30) cc_final: 0.5768 (tp30) REVERT: HF 61 ARG cc_start: 0.7426 (ttm110) cc_final: 0.7127 (ttp80) REVERT: HF 88 GLU cc_start: 0.6618 (mt-10) cc_final: 0.6136 (pt0) REVERT: HF 101 ASN cc_start: 0.7418 (t0) cc_final: 0.7137 (m-40) REVERT: HF 108 THR cc_start: 0.7943 (m) cc_final: 0.7605 (t) REVERT: HF 123 SER cc_start: 0.8054 (OUTLIER) cc_final: 0.7776 (p) REVERT: HF 130 GLU cc_start: 0.5814 (mp0) cc_final: 0.5605 (mp0) REVERT: HF 204 ASP cc_start: 0.6816 (t0) cc_final: 0.6517 (m-30) REVERT: HF 232 MET cc_start: 0.7035 (ttt) cc_final: 0.6776 (ttp) REVERT: HF 266 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6488 (mm-30) REVERT: HG 37 LEU cc_start: 0.6901 (mt) cc_final: 0.6635 (mt) REVERT: HG 88 LYS cc_start: 0.7985 (mttt) cc_final: 0.7668 (mttt) REVERT: HH 54 VAL cc_start: 0.7207 (OUTLIER) cc_final: 0.6958 (t) REVERT: HH 59 GLU cc_start: 0.7381 (tp30) cc_final: 0.6991 (mm-30) REVERT: HH 60 MET cc_start: 0.6406 (ttp) cc_final: 0.6090 (mmp) REVERT: HH 74 ASP cc_start: 0.7768 (t0) cc_final: 0.7420 (t0) REVERT: HI 2 PHE cc_start: 0.7459 (m-80) cc_final: 0.6857 (m-80) REVERT: HI 5 ARG cc_start: 0.7633 (ttp-170) cc_final: 0.7367 (ttp-170) REVERT: HI 59 LYS cc_start: 0.7227 (tptt) cc_final: 0.6357 (tptt) REVERT: HI 63 MET cc_start: 0.6292 (mtm) cc_final: 0.5061 (mtm) REVERT: HI 109 LYS cc_start: 0.7010 (mmtm) cc_final: 0.6699 (mmtm) REVERT: HI 118 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7395 (mttt) REVERT: HI 125 GLN cc_start: 0.6030 (tm-30) cc_final: 0.5711 (pp30) REVERT: HI 126 PRO cc_start: 0.5857 (Cg_endo) cc_final: 0.5188 (Cg_exo) REVERT: HI 129 LYS cc_start: 0.7287 (mttt) cc_final: 0.6832 (mttt) REVERT: HJ 167 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.7797 (mtp85) REVERT: HJ 331 ASN cc_start: 0.7807 (m-40) cc_final: 0.7214 (m-40) REVERT: HJ 394 ARG cc_start: 0.6962 (ttp-170) cc_final: 0.6670 (ptm-80) REVERT: HJ 434 LYS cc_start: 0.8339 (mtpt) cc_final: 0.8125 (mtmm) REVERT: HJ 441 GLU cc_start: 0.5599 (mt-10) cc_final: 0.5334 (mt-10) REVERT: HJ 442 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6381 (mt-10) REVERT: HJ 482 LEU cc_start: 0.6622 (tp) cc_final: 0.6373 (tp) REVERT: HJ 527 MET cc_start: 0.6722 (mtm) cc_final: 0.6459 (ptp) REVERT: HJ 557 GLU cc_start: 0.6970 (tp30) cc_final: 0.6568 (tp30) REVERT: HK 77 ARG cc_start: 0.3704 (tpt170) cc_final: 0.2997 (tpt170) REVERT: HK 103 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6247 (mm-30) REVERT: HL 38 GLN cc_start: 0.6855 (pp30) cc_final: 0.6517 (pt0) REVERT: HM 45 ILE cc_start: 0.7112 (pt) cc_final: 0.6858 (mp) REVERT: HM 53 VAL cc_start: 0.7500 (t) cc_final: 0.7242 (p) REVERT: HM 95 LEU cc_start: 0.8062 (tp) cc_final: 0.7758 (tt) REVERT: HM 203 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6506 (tm-30) REVERT: HM 212 GLN cc_start: 0.4256 (OUTLIER) cc_final: 0.3971 (pt0) REVERT: HM 310 THR cc_start: 0.7302 (t) cc_final: 0.6920 (p) REVERT: HM 317 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5871 (tp) REVERT: HM 321 ARG cc_start: 0.4175 (mtt180) cc_final: 0.3950 (mtt180) REVERT: HM 353 GLN cc_start: 0.6842 (tt0) cc_final: 0.6244 (tt0) REVERT: HM 361 VAL cc_start: 0.7451 (m) cc_final: 0.7151 (p) REVERT: HM 581 GLN cc_start: 0.7081 (mm-40) cc_final: 0.6676 (mm-40) REVERT: HM 587 LEU cc_start: 0.7464 (mp) cc_final: 0.7249 (mp) REVERT: HN 2 MET cc_start: 0.5259 (mmm) cc_final: 0.5011 (mmm) REVERT: HO 14 ARG cc_start: 0.6417 (ttp80) cc_final: 0.5674 (ttt180) REVERT: HO 15 ARG cc_start: 0.4421 (ptt180) cc_final: 0.3939 (ptt180) REVERT: HO 129 PHE cc_start: 0.6282 (m-80) cc_final: 0.5584 (m-80) REVERT: HO 142 GLN cc_start: 0.6736 (OUTLIER) cc_final: 0.6530 (pt0) REVERT: HP 149 SER cc_start: 0.7322 (t) cc_final: 0.7052 (t) REVERT: HP 198 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6394 (tm-30) REVERT: HP 235 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: HP 239 GLN cc_start: 0.7750 (tp-100) cc_final: 0.7013 (tm-30) REVERT: HP 241 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7937 (mtp) REVERT: HP 242 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7635 (mtt-85) REVERT: HP 243 GLU cc_start: 0.6521 (mp0) cc_final: 0.6264 (mp0) REVERT: HQ 178 TRP cc_start: 0.8261 (t60) cc_final: 0.7763 (t-100) REVERT: HQ 179 ASN cc_start: 0.7021 (OUTLIER) cc_final: 0.6778 (t0) REVERT: HQ 217 LEU cc_start: 0.7624 (tp) cc_final: 0.7276 (mp) REVERT: HQ 232 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.7069 (ttmm) REVERT: HQ 252 LEU cc_start: 0.7988 (tp) cc_final: 0.7510 (tp) REVERT: HQ 282 LEU cc_start: 0.7653 (tp) cc_final: 0.7424 (tp) REVERT: HQ 309 LYS cc_start: 0.7195 (mtmm) cc_final: 0.6990 (mtmm) REVERT: HQ 310 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7188 (mm-40) REVERT: HQ 328 ASP cc_start: 0.5774 (t0) cc_final: 0.5254 (t0) REVERT: HQ 383 GLU cc_start: 0.6217 (mm-30) cc_final: 0.5851 (tm-30) REVERT: HQ 427 GLU cc_start: 0.6882 (tp30) cc_final: 0.6597 (tp30) REVERT: HQ 543 LEU cc_start: 0.7114 (mt) cc_final: 0.6795 (mt) REVERT: HQ 627 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7208 (mp0) REVERT: HQ 630 GLN cc_start: 0.7506 (tm130) cc_final: 0.7071 (tm130) REVERT: HQ 707 LYS cc_start: 0.7964 (tttt) cc_final: 0.7642 (ttpt) REVERT: HR 28 ASP cc_start: 0.8044 (t0) cc_final: 0.7735 (t0) REVERT: HR 156 GLN cc_start: 0.7104 (tm-30) cc_final: 0.6838 (tm-30) REVERT: HS 119 GLN cc_start: 0.7405 (mm-40) cc_final: 0.7090 (mm-40) REVERT: HS 131 LYS cc_start: 0.7233 (tttm) cc_final: 0.7017 (tptt) REVERT: HS 190 ARG cc_start: 0.6758 (ptm160) cc_final: 0.6226 (mtp180) REVERT: HT 26 VAL cc_start: 0.7770 (t) cc_final: 0.7411 (m) REVERT: HT 28 ASP cc_start: 0.6494 (t0) cc_final: 0.6260 (t0) REVERT: HT 32 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7764 (mtpp) REVERT: HT 36 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.6075 (t80) REVERT: HT 57 LYS cc_start: 0.7659 (mttt) cc_final: 0.7353 (ttmm) REVERT: HT 105 ARG cc_start: 0.7557 (ttp-110) cc_final: 0.7045 (ttp80) REVERT: HT 118 LYS cc_start: 0.7483 (mmtt) cc_final: 0.7139 (mmmt) outliers start: 141 outliers final: 77 residues processed: 1161 average time/residue: 0.2759 time to fit residues: 496.8176 Evaluate side-chains 1145 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 1052 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 17 LEU Chi-restraints excluded: chain HA residue 32 ASP Chi-restraints excluded: chain HA residue 36 ILE Chi-restraints excluded: chain HA residue 146 PHE Chi-restraints excluded: chain HA residue 200 GLN Chi-restraints excluded: chain HA residue 208 LEU Chi-restraints excluded: chain HA residue 410 LEU Chi-restraints excluded: chain HA residue 440 VAL Chi-restraints excluded: chain HB residue 53 THR Chi-restraints excluded: chain HB residue 78 LEU Chi-restraints excluded: chain HC residue 10 LEU Chi-restraints excluded: chain HC residue 42 SER Chi-restraints excluded: chain HC residue 100 TYR Chi-restraints excluded: chain HC residue 194 LEU Chi-restraints excluded: chain HC residue 218 ILE Chi-restraints excluded: chain HC residue 222 LEU Chi-restraints excluded: chain HD residue 20 LEU Chi-restraints excluded: chain HD residue 42 LEU Chi-restraints excluded: chain HD residue 59 ILE Chi-restraints excluded: chain HD residue 84 LEU Chi-restraints excluded: chain HE residue 27 SER Chi-restraints excluded: chain HE residue 110 LEU Chi-restraints excluded: chain HF residue 123 SER Chi-restraints excluded: chain HF residue 132 LEU Chi-restraints excluded: chain HF residue 154 GLN Chi-restraints excluded: chain HF residue 256 HIS Chi-restraints excluded: chain HF residue 322 MET Chi-restraints excluded: chain HF residue 323 VAL Chi-restraints excluded: chain HG residue 15 LEU Chi-restraints excluded: chain HG residue 70 LEU Chi-restraints excluded: chain HG residue 74 THR Chi-restraints excluded: chain HH residue 48 ILE Chi-restraints excluded: chain HH residue 54 VAL Chi-restraints excluded: chain HI residue 92 THR Chi-restraints excluded: chain HI residue 118 LYS Chi-restraints excluded: chain HI residue 132 VAL Chi-restraints excluded: chain HI residue 138 GLN Chi-restraints excluded: chain HJ residue 165 LEU Chi-restraints excluded: chain HJ residue 171 LEU Chi-restraints excluded: chain HJ residue 238 LEU Chi-restraints excluded: chain HJ residue 244 SER Chi-restraints excluded: chain HJ residue 421 VAL Chi-restraints excluded: chain HJ residue 435 MET Chi-restraints excluded: chain HJ residue 459 LEU Chi-restraints excluded: chain HK residue 33 SER Chi-restraints excluded: chain HK residue 47 TYR Chi-restraints excluded: chain HK residue 98 VAL Chi-restraints excluded: chain HL residue 51 CYS Chi-restraints excluded: chain HM residue 70 ILE Chi-restraints excluded: chain HM residue 73 ILE Chi-restraints excluded: chain HM residue 151 VAL Chi-restraints excluded: chain HM residue 212 GLN Chi-restraints excluded: chain HM residue 267 THR Chi-restraints excluded: chain HM residue 298 VAL Chi-restraints excluded: chain HM residue 317 LEU Chi-restraints excluded: chain HM residue 412 LEU Chi-restraints excluded: chain HM residue 607 ILE Chi-restraints excluded: chain HO residue 17 VAL Chi-restraints excluded: chain HO residue 112 MET Chi-restraints excluded: chain HO residue 142 GLN Chi-restraints excluded: chain HP residue 40 VAL Chi-restraints excluded: chain HP residue 57 THR Chi-restraints excluded: chain HP residue 60 MET Chi-restraints excluded: chain HP residue 197 GLU Chi-restraints excluded: chain HP residue 198 GLN Chi-restraints excluded: chain HP residue 235 ASP Chi-restraints excluded: chain HP residue 241 MET Chi-restraints excluded: chain HQ residue 124 VAL Chi-restraints excluded: chain HQ residue 179 ASN Chi-restraints excluded: chain HQ residue 192 HIS Chi-restraints excluded: chain HQ residue 223 SER Chi-restraints excluded: chain HQ residue 232 LYS Chi-restraints excluded: chain HQ residue 253 ILE Chi-restraints excluded: chain HQ residue 259 SER Chi-restraints excluded: chain HQ residue 314 VAL Chi-restraints excluded: chain HQ residue 322 LYS Chi-restraints excluded: chain HQ residue 353 LEU Chi-restraints excluded: chain HQ residue 421 VAL Chi-restraints excluded: chain HQ residue 534 LEU Chi-restraints excluded: chain HQ residue 575 LEU Chi-restraints excluded: chain HQ residue 626 GLU Chi-restraints excluded: chain HQ residue 695 VAL Chi-restraints excluded: chain HR residue 6 TRP Chi-restraints excluded: chain HR residue 36 CYS Chi-restraints excluded: chain HR residue 45 VAL Chi-restraints excluded: chain HR residue 96 LEU Chi-restraints excluded: chain HR residue 126 ASN Chi-restraints excluded: chain HS residue 102 LEU Chi-restraints excluded: chain HS residue 156 GLU Chi-restraints excluded: chain HS residue 175 MET Chi-restraints excluded: chain HT residue 36 TYR Chi-restraints excluded: chain HT residue 92 THR Chi-restraints excluded: chain HT residue 361 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 348 optimal weight: 0.7980 chunk 237 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 272 optimal weight: 0.3980 chunk 361 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... HA 161 ASN ** HA 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HB 46 HIS ** HB 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HC 31 ASN HE 131 HIS HF 291 ASN HJ 297 ASN HJ 324 HIS HJ 416 GLN HJ 419 ASN HJ 431 ASN ** HL 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HL 49 GLN HM 20 GLN HM 56 GLN ** HM 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HM 318 HIS ** HM 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HM 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HP 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HP 239 GLN HQ 342 GLN ** HQ 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HQ 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HQ 715 GLN HT 307 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.186692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.158232 restraints weight = 64116.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.161842 restraints weight = 37730.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.163473 restraints weight = 22602.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.163654 restraints weight = 19808.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.163874 restraints weight = 17141.668| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 42419 Z= 0.212 Angle : 0.700 14.497 58628 Z= 0.359 Chirality : 0.044 0.273 6660 Planarity : 0.006 0.090 6558 Dihedral : 18.019 172.340 9205 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.61 % Favored : 92.34 % Rotamer: Outliers : 4.38 % Allowed : 20.42 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.12), residues: 4268 helix: -0.08 (0.12), residues: 1816 sheet: -1.46 (0.40), residues: 173 loop : -2.27 (0.12), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGHQ 544 TYR 0.026 0.002 TYRHH 18 PHE 0.022 0.002 PHEHI 123 TRP 0.059 0.002 TRPHB 30 HIS 0.009 0.001 HISHQ 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (42419) covalent geometry : angle 0.69972 / 0.36 (58628) hydrogen bonds : bond 0.06079 / 3.99 ( 1057) hydrogen bonds : angle 4.66523 / 3.27 ( 2968) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1109 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: HA 10 ARG cc_start: 0.7066 (ptm160) cc_final: 0.6095 (mmm160) REVERT: HA 46 MET cc_start: 0.3282 (ttm) cc_final: 0.2729 (pmm) REVERT: HA 172 TRP cc_start: 0.7103 (m100) cc_final: 0.6430 (m100) REVERT: HA 301 TRP cc_start: 0.8018 (m100) cc_final: 0.7317 (m100) REVERT: HA 313 MET cc_start: 0.5092 (ttm) cc_final: 0.4659 (ttm) REVERT: HA 339 GLN cc_start: 0.7295 (tt0) cc_final: 0.6512 (tt0) REVERT: HA 347 GLN cc_start: 0.7717 (tp40) cc_final: 0.7403 (tp40) REVERT: HA 383 ASN cc_start: 0.7324 (m110) cc_final: 0.6984 (m110) REVERT: HA 399 ARG cc_start: 0.7530 (mtm180) cc_final: 0.7317 (mtm-85) REVERT: HA 426 ARG cc_start: 0.6135 (ptt-90) cc_final: 0.3029 (ptt-90) REVERT: HA 435 GLU cc_start: 0.6271 (pm20) cc_final: 0.6045 (mp0) REVERT: HA 437 ILE cc_start: 0.8051 (mm) cc_final: 0.7575 (mm) REVERT: HA 457 LYS cc_start: 0.7989 (mttp) cc_final: 0.7712 (ttmm) REVERT: HB 50 ARG cc_start: 0.7330 (mmm-85) cc_final: 0.6589 (mmm-85) REVERT: HB 51 ARG cc_start: 0.7990 (tmt90) cc_final: 0.7602 (ttt180) REVERT: HB 78 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8329 (mp) REVERT: HB 109 ARG cc_start: 0.7967 (ttt180) cc_final: 0.7439 (ttt180) REVERT: HB 148 MET cc_start: 0.6933 (mtm) cc_final: 0.6226 (mtt) REVERT: HC 2 LEU cc_start: 0.7363 (tt) cc_final: 0.7078 (tp) REVERT: HC 96 GLU cc_start: 0.7095 (pt0) cc_final: 0.6772 (pt0) REVERT: HD 18 ASP cc_start: 0.7932 (t70) cc_final: 0.7669 (t0) REVERT: HD 27 GLU cc_start: 0.6474 (tp30) cc_final: 0.6194 (tp30) REVERT: HD 40 GLN cc_start: 0.7201 (mt0) cc_final: 0.6786 (mt0) REVERT: HE 10 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6410 (tpp80) REVERT: HE 154 MET cc_start: 0.7565 (tpp) cc_final: 0.7264 (tpp) REVERT: HE 158 LEU cc_start: 0.8263 (tp) cc_final: 0.8012 (tp) REVERT: HE 162 CYS cc_start: 0.7900 (m) cc_final: 0.7318 (t) REVERT: HF 24 GLU cc_start: 0.6545 (tp30) cc_final: 0.6179 (tp30) REVERT: HF 61 ARG cc_start: 0.7611 (ttm110) cc_final: 0.7278 (ttp80) REVERT: HF 101 ASN cc_start: 0.7412 (t0) cc_final: 0.7145 (m-40) REVERT: HF 108 THR cc_start: 0.7927 (m) cc_final: 0.7583 (t) REVERT: HF 123 SER cc_start: 0.8145 (OUTLIER) cc_final: 0.7865 (p) REVERT: HF 130 GLU cc_start: 0.6031 (mp0) cc_final: 0.5821 (mp0) REVERT: HF 204 ASP cc_start: 0.7009 (t0) cc_final: 0.6695 (m-30) REVERT: HF 232 MET cc_start: 0.7118 (ttt) cc_final: 0.6688 (ttp) REVERT: HF 237 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7612 (mtmm) REVERT: HF 266 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6541 (mm-30) REVERT: HG 88 LYS cc_start: 0.7897 (mttt) cc_final: 0.7571 (mttt) REVERT: HH 54 VAL cc_start: 0.7437 (OUTLIER) cc_final: 0.6937 (t) REVERT: HH 59 GLU cc_start: 0.7410 (tp30) cc_final: 0.7148 (mm-30) REVERT: HH 60 MET cc_start: 0.6582 (ttp) cc_final: 0.6069 (mmp) REVERT: HH 74 ASP cc_start: 0.7704 (t0) cc_final: 0.7317 (t0) REVERT: HI 59 LYS cc_start: 0.7211 (tptt) cc_final: 0.6394 (tptt) REVERT: HI 63 MET cc_start: 0.6341 (mtm) cc_final: 0.4971 (mtm) REVERT: HI 109 LYS cc_start: 0.7076 (mmtm) cc_final: 0.6747 (mmtm) REVERT: HI 125 GLN cc_start: 0.6313 (tm-30) cc_final: 0.6029 (pp30) REVERT: HI 126 PRO cc_start: 0.6573 (Cg_endo) cc_final: 0.5777 (Cg_exo) REVERT: HI 129 LYS cc_start: 0.7237 (mttt) cc_final: 0.6864 (mttt) REVERT: HI 138 GLN cc_start: 0.6238 (OUTLIER) cc_final: 0.6022 (mm-40) REVERT: HJ 167 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.7949 (mtp85) REVERT: HJ 177 ASP cc_start: 0.6528 (t0) cc_final: 0.6251 (t0) REVERT: HJ 204 LYS cc_start: 0.7641 (tttt) cc_final: 0.7369 (tttt) REVERT: HJ 244 SER cc_start: 0.7938 (OUTLIER) cc_final: 0.7441 (t) REVERT: HJ 331 ASN cc_start: 0.7725 (m-40) cc_final: 0.7153 (m-40) REVERT: HJ 374 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7437 (tm-30) REVERT: HJ 394 ARG cc_start: 0.7004 (ttp-170) cc_final: 0.6650 (ptm-80) REVERT: HJ 467 LYS cc_start: 0.7194 (tptt) cc_final: 0.6917 (tptt) REVERT: HJ 550 LEU cc_start: 0.8113 (mt) cc_final: 0.7809 (mm) REVERT: HJ 557 GLU cc_start: 0.6965 (tp30) cc_final: 0.6583 (tp30) REVERT: HJ 560 PHE cc_start: 0.6937 (t80) cc_final: 0.6562 (t80) REVERT: HK 77 ARG cc_start: 0.3911 (tpt170) cc_final: 0.3308 (tpt170) REVERT: HK 103 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6645 (mm-30) REVERT: HL 38 GLN cc_start: 0.7081 (pp30) cc_final: 0.6735 (pt0) REVERT: HM 21 ARG cc_start: 0.6784 (ptp-110) cc_final: 0.6172 (mtp-110) REVERT: HM 95 LEU cc_start: 0.8157 (tp) cc_final: 0.7829 (tt) REVERT: HM 203 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6540 (tm-30) REVERT: HM 274 LEU cc_start: 0.6913 (tp) cc_final: 0.6607 (mp) REVERT: HM 281 ASP cc_start: 0.5704 (m-30) cc_final: 0.5502 (t0) REVERT: HM 317 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.5997 (tp) REVERT: HM 353 GLN cc_start: 0.6908 (tt0) cc_final: 0.6235 (tt0) REVERT: HM 360 LEU cc_start: 0.6960 (mp) cc_final: 0.6746 (mm) REVERT: HM 361 VAL cc_start: 0.7690 (m) cc_final: 0.7401 (p) REVERT: HM 581 GLN cc_start: 0.7265 (mm-40) cc_final: 0.6966 (mm-40) REVERT: HM 587 LEU cc_start: 0.7461 (mp) cc_final: 0.7255 (mp) REVERT: HM 608 PRO cc_start: 0.6830 (Cg_endo) cc_final: 0.6597 (Cg_exo) REVERT: HN 6 ASN cc_start: 0.7864 (m-40) cc_final: 0.7526 (m110) REVERT: HO 8 LEU cc_start: 0.8592 (mm) cc_final: 0.8374 (mm) REVERT: HO 14 ARG cc_start: 0.6538 (ttp80) cc_final: 0.5880 (ttt180) REVERT: HO 129 PHE cc_start: 0.6205 (m-80) cc_final: 0.5715 (m-80) REVERT: HP 69 LEU cc_start: 0.7322 (tp) cc_final: 0.7072 (tp) REVERT: HP 71 ARG cc_start: 0.7054 (mmm-85) cc_final: 0.6810 (mmm-85) REVERT: HP 235 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: HP 242 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7580 (mtt-85) REVERT: HQ 178 TRP cc_start: 0.8291 (t60) cc_final: 0.7810 (t-100) REVERT: HQ 209 ASP cc_start: 0.7420 (m-30) cc_final: 0.5142 (t70) REVERT: HQ 216 LEU cc_start: 0.8147 (mt) cc_final: 0.7812 (tt) REVERT: HQ 217 LEU cc_start: 0.7832 (tp) cc_final: 0.7599 (mp) REVERT: HQ 232 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.7048 (ttmm) REVERT: HQ 252 LEU cc_start: 0.7957 (tp) cc_final: 0.7479 (tp) REVERT: HQ 310 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7146 (mm-40) REVERT: HQ 326 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7255 (mm-40) REVERT: HQ 328 ASP cc_start: 0.5996 (t0) cc_final: 0.5499 (t0) REVERT: HQ 431 PHE cc_start: 0.5177 (m-80) cc_final: 0.4701 (m-80) REVERT: HQ 521 ARG cc_start: 0.6123 (ttp-110) cc_final: 0.5900 (ptp-110) REVERT: HQ 543 LEU cc_start: 0.7257 (mt) cc_final: 0.6805 (tp) REVERT: HQ 597 HIS cc_start: 0.6438 (t-90) cc_final: 0.6232 (t-90) REVERT: HQ 599 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6664 (tt) REVERT: HQ 630 GLN cc_start: 0.7545 (tm130) cc_final: 0.7055 (tm130) REVERT: HQ 707 LYS cc_start: 0.8022 (tttt) cc_final: 0.7611 (ttpt) REVERT: HR 28 ASP cc_start: 0.8031 (t0) cc_final: 0.7773 (t0) REVERT: HR 156 GLN cc_start: 0.7260 (tm-30) cc_final: 0.6808 (tm-30) REVERT: HS 97 LYS cc_start: 0.6985 (ptpt) cc_final: 0.6756 (ptpt) REVERT: HS 142 GLN cc_start: 0.7569 (mt0) cc_final: 0.7143 (mt0) REVERT: HS 153 ARG cc_start: 0.7436 (tpt90) cc_final: 0.7159 (mmm160) REVERT: HS 190 ARG cc_start: 0.6934 (ptm160) cc_final: 0.6659 (ptp-170) REVERT: HT 22 ARG cc_start: 0.4690 (ttp-110) cc_final: 0.4373 (ttp80) REVERT: HT 23 LYS cc_start: 0.7488 (mmtt) cc_final: 0.6938 (mmtm) REVERT: HT 26 VAL cc_start: 0.7774 (t) cc_final: 0.7443 (m) REVERT: HT 32 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7864 (ttpt) REVERT: HT 36 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.6354 (t80) REVERT: HT 45 GLN cc_start: 0.7920 (mp10) cc_final: 0.7571 (mp10) REVERT: HT 57 LYS cc_start: 0.7602 (mttt) cc_final: 0.7240 (ttmm) REVERT: HT 105 ARG cc_start: 0.7474 (ttp-110) cc_final: 0.7244 (ttp80) REVERT: HT 118 LYS cc_start: 0.7627 (mmtt) cc_final: 0.7344 (mmmt) REVERT: HT 312 ARG cc_start: 0.5688 (ptt90) cc_final: 0.3993 (ptp-170) outliers start: 163 outliers final: 110 residues processed: 1168 average time/residue: 0.2956 time to fit residues: 530.2872 Evaluate side-chains 1200 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 1079 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 17 LEU Chi-restraints excluded: chain HA residue 146 PHE Chi-restraints excluded: chain HA residue 182 ARG Chi-restraints excluded: chain HA residue 200 GLN Chi-restraints excluded: chain HA residue 208 LEU Chi-restraints excluded: chain HA residue 410 LEU Chi-restraints excluded: chain HA residue 470 ASP Chi-restraints excluded: chain HB residue 47 VAL Chi-restraints excluded: chain HB residue 53 THR Chi-restraints excluded: chain HB residue 78 LEU Chi-restraints excluded: chain HB residue 131 MET Chi-restraints excluded: chain HC residue 10 LEU Chi-restraints excluded: chain HC residue 42 SER Chi-restraints excluded: chain HC residue 100 TYR Chi-restraints excluded: chain HC residue 194 LEU Chi-restraints excluded: chain HD residue 1 LEU Chi-restraints excluded: chain HD residue 16 GLN Chi-restraints excluded: chain HD residue 20 LEU Chi-restraints excluded: chain HD residue 42 LEU Chi-restraints excluded: chain HD residue 59 ILE Chi-restraints excluded: chain HD residue 84 LEU Chi-restraints excluded: chain HE residue 10 ARG Chi-restraints excluded: chain HE residue 27 SER Chi-restraints excluded: chain HE residue 110 LEU Chi-restraints excluded: chain HE residue 127 LEU Chi-restraints excluded: chain HE residue 163 VAL Chi-restraints excluded: chain HF residue 51 GLN Chi-restraints excluded: chain HF residue 102 CYS Chi-restraints excluded: chain HF residue 123 SER Chi-restraints excluded: chain HF residue 135 LEU Chi-restraints excluded: chain HF residue 226 VAL Chi-restraints excluded: chain HF residue 256 HIS Chi-restraints excluded: chain HF residue 262 LEU Chi-restraints excluded: chain HF residue 306 TYR Chi-restraints excluded: chain HF residue 322 MET Chi-restraints excluded: chain HG residue 70 LEU Chi-restraints excluded: chain HG residue 74 THR Chi-restraints excluded: chain HH residue 22 VAL Chi-restraints excluded: chain HH residue 48 ILE Chi-restraints excluded: chain HH residue 54 VAL Chi-restraints excluded: chain HI residue 34 MET Chi-restraints excluded: chain HI residue 66 LEU Chi-restraints excluded: chain HI residue 92 THR Chi-restraints excluded: chain HI residue 132 VAL Chi-restraints excluded: chain HI residue 138 GLN Chi-restraints excluded: chain HJ residue 165 LEU Chi-restraints excluded: chain HJ residue 171 LEU Chi-restraints excluded: chain HJ residue 228 VAL Chi-restraints excluded: chain HJ residue 238 LEU Chi-restraints excluded: chain HJ residue 244 SER Chi-restraints excluded: chain HJ residue 329 ILE Chi-restraints excluded: chain HJ residue 376 CYS Chi-restraints excluded: chain HJ residue 411 ASP Chi-restraints excluded: chain HJ residue 413 VAL Chi-restraints excluded: chain HJ residue 421 VAL Chi-restraints excluded: chain HJ residue 435 MET Chi-restraints excluded: chain HJ residue 459 LEU Chi-restraints excluded: chain HK residue 47 TYR Chi-restraints excluded: chain HK residue 98 VAL Chi-restraints excluded: chain HL residue 42 ILE Chi-restraints excluded: chain HL residue 51 CYS Chi-restraints excluded: chain HM residue 20 GLN Chi-restraints excluded: chain HM residue 70 ILE Chi-restraints excluded: chain HM residue 73 ILE Chi-restraints excluded: chain HM residue 151 VAL Chi-restraints excluded: chain HM residue 198 LEU Chi-restraints excluded: chain HM residue 267 THR Chi-restraints excluded: chain HM residue 317 LEU Chi-restraints excluded: chain HM residue 362 LEU Chi-restraints excluded: chain HM residue 394 LEU Chi-restraints excluded: chain HM residue 412 LEU Chi-restraints excluded: chain HM residue 418 LEU Chi-restraints excluded: chain HM residue 607 ILE Chi-restraints excluded: chain HO residue 17 VAL Chi-restraints excluded: chain HO residue 112 MET Chi-restraints excluded: chain HO residue 115 VAL Chi-restraints excluded: chain HO residue 161 VAL Chi-restraints excluded: chain HP residue 13 ASN Chi-restraints excluded: chain HP residue 40 VAL Chi-restraints excluded: chain HP residue 57 THR Chi-restraints excluded: chain HP residue 60 MET Chi-restraints excluded: chain HP residue 172 VAL Chi-restraints excluded: chain HP residue 197 GLU Chi-restraints excluded: chain HP residue 213 THR Chi-restraints excluded: chain HP residue 235 ASP Chi-restraints excluded: chain HQ residue 124 VAL Chi-restraints excluded: chain HQ residue 126 LEU Chi-restraints excluded: chain HQ residue 179 ASN Chi-restraints excluded: chain HQ residue 192 HIS Chi-restraints excluded: chain HQ residue 223 SER Chi-restraints excluded: chain HQ residue 232 LYS Chi-restraints excluded: chain HQ residue 238 ILE Chi-restraints excluded: chain HQ residue 253 ILE Chi-restraints excluded: chain HQ residue 314 VAL Chi-restraints excluded: chain HQ residue 316 THR Chi-restraints excluded: chain HQ residue 399 LEU Chi-restraints excluded: chain HQ residue 411 THR Chi-restraints excluded: chain HQ residue 534 LEU Chi-restraints excluded: chain HQ residue 535 LEU Chi-restraints excluded: chain HQ residue 546 THR Chi-restraints excluded: chain HQ residue 575 LEU Chi-restraints excluded: chain HQ residue 576 LEU Chi-restraints excluded: chain HQ residue 586 VAL Chi-restraints excluded: chain HQ residue 599 LEU Chi-restraints excluded: chain HQ residue 626 GLU Chi-restraints excluded: chain HR residue 6 TRP Chi-restraints excluded: chain HR residue 36 CYS Chi-restraints excluded: chain HR residue 45 VAL Chi-restraints excluded: chain HR residue 96 LEU Chi-restraints excluded: chain HR residue 125 TRP Chi-restraints excluded: chain HR residue 126 ASN Chi-restraints excluded: chain HS residue 102 LEU Chi-restraints excluded: chain HS residue 130 VAL Chi-restraints excluded: chain HS residue 156 GLU Chi-restraints excluded: chain HS residue 175 MET Chi-restraints excluded: chain HT residue 17 THR Chi-restraints excluded: chain HT residue 30 ARG Chi-restraints excluded: chain HT residue 36 TYR Chi-restraints excluded: chain HT residue 92 THR Chi-restraints excluded: chain HT residue 161 THR Chi-restraints excluded: chain HT residue 361 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 90 optimal weight: 0.0870 chunk 276 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 430 optimal weight: 20.0000 chunk 344 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 194 optimal weight: 0.1980 chunk 180 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... HA 200 GLN ** HA 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HC 31 ASN ** HI 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HL 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HL 49 GLN HM 352 GLN ** HP 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HQ 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HQ 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HQ 715 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.186930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.158324 restraints weight = 63960.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.161448 restraints weight = 38742.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.163261 restraints weight = 23217.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.163129 restraints weight = 20559.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.163480 restraints weight = 18125.467| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 42419 Z= 0.146 Angle : 0.636 12.465 58628 Z= 0.322 Chirality : 0.041 0.246 6660 Planarity : 0.005 0.087 6558 Dihedral : 17.994 176.663 9205 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.89 % Favored : 93.06 % Rotamer: Outliers : 3.95 % Allowed : 22.43 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.13), residues: 4268 helix: 0.08 (0.12), residues: 1824 sheet: -1.67 (0.37), residues: 188 loop : -2.19 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGHI 6 TYR 0.026 0.002 TYRHH 18 PHE 0.022 0.001 PHEHI 123 TRP 0.037 0.002 TRPHO 6 HIS 0.009 0.001 HISHQ 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (42419) covalent geometry : angle 0.63624 / 0.32 (58628) hydrogen bonds : bond 0.05334 / 3.50 ( 1057) hydrogen bonds : angle 4.43300 / 3.11 ( 2968) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1094 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: HA 10 ARG cc_start: 0.7063 (ptm160) cc_final: 0.6081 (mmm160) REVERT: HA 46 MET cc_start: 0.3279 (ttm) cc_final: 0.2932 (pmm) REVERT: HA 59 GLU cc_start: 0.7754 (tt0) cc_final: 0.7518 (tt0) REVERT: HA 172 TRP cc_start: 0.7143 (m100) cc_final: 0.6042 (m100) REVERT: HA 301 TRP cc_start: 0.8071 (m100) cc_final: 0.7465 (m100) REVERT: HA 313 MET cc_start: 0.5088 (ttm) cc_final: 0.4656 (ttm) REVERT: HA 339 GLN cc_start: 0.7326 (tt0) cc_final: 0.6576 (tt0) REVERT: HA 347 GLN cc_start: 0.7704 (tp40) cc_final: 0.7388 (tp40) REVERT: HA 383 ASN cc_start: 0.7367 (m110) cc_final: 0.7008 (m110) REVERT: HA 399 ARG cc_start: 0.7507 (mtm180) cc_final: 0.7255 (mtm-85) REVERT: HA 426 ARG cc_start: 0.6181 (OUTLIER) cc_final: 0.3295 (ptt-90) REVERT: HA 437 ILE cc_start: 0.8019 (mm) cc_final: 0.7543 (mm) REVERT: HA 457 LYS cc_start: 0.7975 (mttp) cc_final: 0.7733 (ttmm) REVERT: HA 466 ARG cc_start: 0.6491 (mpt180) cc_final: 0.5833 (mmt-90) REVERT: HB 51 ARG cc_start: 0.7963 (tmt90) cc_final: 0.7552 (ttt180) REVERT: HB 109 ARG cc_start: 0.7730 (ttt180) cc_final: 0.7149 (ttt180) REVERT: HB 148 MET cc_start: 0.6997 (mtm) cc_final: 0.6354 (mtt) REVERT: HB 153 MET cc_start: 0.7251 (tpp) cc_final: 0.6791 (tpp) REVERT: HC 2 LEU cc_start: 0.7353 (tt) cc_final: 0.7106 (tp) REVERT: HC 203 GLU cc_start: 0.7249 (tp30) cc_final: 0.7033 (tp30) REVERT: HC 205 ILE cc_start: 0.8425 (mm) cc_final: 0.8107 (mm) REVERT: HD 18 ASP cc_start: 0.7895 (t70) cc_final: 0.7666 (t0) REVERT: HD 20 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7554 (tp) REVERT: HD 27 GLU cc_start: 0.6476 (tp30) cc_final: 0.6249 (tp30) REVERT: HD 40 GLN cc_start: 0.7179 (mt0) cc_final: 0.6836 (mt0) REVERT: HE 154 MET cc_start: 0.7484 (tpp) cc_final: 0.7253 (tpp) REVERT: HE 158 LEU cc_start: 0.8318 (tp) cc_final: 0.8033 (tp) REVERT: HE 162 CYS cc_start: 0.7769 (m) cc_final: 0.7270 (t) REVERT: HF 24 GLU cc_start: 0.6178 (tp30) cc_final: 0.5888 (tp30) REVERT: HF 61 ARG cc_start: 0.7534 (ttm110) cc_final: 0.7237 (ttp80) REVERT: HF 101 ASN cc_start: 0.7359 (t0) cc_final: 0.7147 (m-40) REVERT: HF 108 THR cc_start: 0.7956 (m) cc_final: 0.7608 (t) REVERT: HF 123 SER cc_start: 0.8141 (m) cc_final: 0.7881 (p) REVERT: HF 204 ASP cc_start: 0.6896 (t0) cc_final: 0.6586 (m-30) REVERT: HF 232 MET cc_start: 0.7250 (ttt) cc_final: 0.6943 (ttp) REVERT: HF 237 LYS cc_start: 0.7850 (mtmm) cc_final: 0.6670 (mtmm) REVERT: HF 240 GLU cc_start: 0.6414 (tt0) cc_final: 0.5808 (tt0) REVERT: HF 266 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6487 (mm-30) REVERT: HG 88 LYS cc_start: 0.7884 (mttt) cc_final: 0.7539 (mttt) REVERT: HG 95 TYR cc_start: 0.7674 (m-80) cc_final: 0.7355 (m-80) REVERT: HH 54 VAL cc_start: 0.7331 (OUTLIER) cc_final: 0.6856 (t) REVERT: HH 59 GLU cc_start: 0.7403 (tp30) cc_final: 0.7155 (mm-30) REVERT: HH 60 MET cc_start: 0.6624 (ttp) cc_final: 0.6062 (mmp) REVERT: HH 74 ASP cc_start: 0.7671 (t0) cc_final: 0.7270 (t0) REVERT: HI 6 ARG cc_start: 0.7089 (mtm-85) cc_final: 0.6001 (mtm-85) REVERT: HI 32 GLU cc_start: 0.6850 (tp30) cc_final: 0.6504 (tp30) REVERT: HI 59 LYS cc_start: 0.7195 (tptt) cc_final: 0.6347 (tptt) REVERT: HI 63 MET cc_start: 0.6312 (mtm) cc_final: 0.4940 (mtm) REVERT: HI 109 LYS cc_start: 0.7069 (mmtm) cc_final: 0.6659 (mmtm) REVERT: HI 125 GLN cc_start: 0.6224 (tm-30) cc_final: 0.5831 (pp30) REVERT: HI 129 LYS cc_start: 0.7189 (mttt) cc_final: 0.6840 (mttt) REVERT: HJ 167 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.7924 (mtp85) REVERT: HJ 177 ASP cc_start: 0.6456 (t0) cc_final: 0.6185 (t0) REVERT: HJ 204 LYS cc_start: 0.7644 (tttt) cc_final: 0.7365 (tttt) REVERT: HJ 244 SER cc_start: 0.7997 (m) cc_final: 0.7528 (t) REVERT: HJ 331 ASN cc_start: 0.7726 (m-40) cc_final: 0.7120 (m-40) REVERT: HJ 374 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7145 (tm-30) REVERT: HJ 392 PHE cc_start: 0.6088 (t80) cc_final: 0.5763 (t80) REVERT: HJ 393 ARG cc_start: 0.7570 (ttp80) cc_final: 0.6617 (ttp80) REVERT: HJ 416 GLN cc_start: 0.6096 (mm110) cc_final: 0.5758 (mm-40) REVERT: HJ 425 ASP cc_start: 0.6082 (t70) cc_final: 0.5763 (t0) REVERT: HJ 467 LYS cc_start: 0.7184 (tptt) cc_final: 0.6908 (tptt) REVERT: HJ 527 MET cc_start: 0.6915 (mtm) cc_final: 0.6605 (ptp) REVERT: HJ 557 GLU cc_start: 0.6927 (tp30) cc_final: 0.6571 (tp30) REVERT: HJ 560 PHE cc_start: 0.7103 (t80) cc_final: 0.6756 (t80) REVERT: HK 77 ARG cc_start: 0.4013 (tpt170) cc_final: 0.3480 (tpt170) REVERT: HK 103 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6597 (mm-30) REVERT: HL 38 GLN cc_start: 0.6997 (pp30) cc_final: 0.6660 (pt0) REVERT: HM 21 ARG cc_start: 0.6703 (ptp-110) cc_final: 0.6002 (mtp-110) REVERT: HM 95 LEU cc_start: 0.8207 (tp) cc_final: 0.7876 (tt) REVERT: HM 165 LEU cc_start: 0.7686 (mp) cc_final: 0.7335 (mm) REVERT: HM 203 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6666 (tm-30) REVERT: HM 274 LEU cc_start: 0.6853 (tp) cc_final: 0.6520 (mp) REVERT: HM 310 THR cc_start: 0.7452 (t) cc_final: 0.7136 (p) REVERT: HM 352 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: HM 361 VAL cc_start: 0.7764 (m) cc_final: 0.7463 (p) REVERT: HM 581 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6960 (mm-40) REVERT: HM 587 LEU cc_start: 0.7557 (mp) cc_final: 0.7324 (mp) REVERT: HM 608 PRO cc_start: 0.6850 (Cg_endo) cc_final: 0.6646 (Cg_exo) REVERT: HN 6 ASN cc_start: 0.7790 (m-40) cc_final: 0.7510 (m110) REVERT: HO 14 ARG cc_start: 0.6579 (ttp80) cc_final: 0.5843 (ttt180) REVERT: HO 129 PHE cc_start: 0.6145 (m-80) cc_final: 0.5658 (m-80) REVERT: HP 69 LEU cc_start: 0.7295 (tp) cc_final: 0.7074 (tp) REVERT: HP 235 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: HP 243 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6283 (mp0) REVERT: HQ 113 LYS cc_start: 0.7991 (tmtm) cc_final: 0.7778 (tmtm) REVERT: HQ 178 TRP cc_start: 0.8279 (t60) cc_final: 0.7744 (t-100) REVERT: HQ 209 ASP cc_start: 0.7381 (m-30) cc_final: 0.5295 (t0) REVERT: HQ 232 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.7099 (ttmm) REVERT: HQ 252 LEU cc_start: 0.7918 (tp) cc_final: 0.7450 (tp) REVERT: HQ 310 GLN cc_start: 0.7523 (mm-40) cc_final: 0.7090 (mm-40) REVERT: HQ 325 ARG cc_start: 0.7215 (ptm-80) cc_final: 0.6982 (ttt180) REVERT: HQ 326 GLN cc_start: 0.7543 (mm-40) cc_final: 0.7331 (mm-40) REVERT: HQ 328 ASP cc_start: 0.6001 (t0) cc_final: 0.5505 (t0) REVERT: HQ 347 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.5019 (m-30) REVERT: HQ 431 PHE cc_start: 0.5240 (m-80) cc_final: 0.4851 (m-80) REVERT: HQ 543 LEU cc_start: 0.7332 (mt) cc_final: 0.7077 (mt) REVERT: HQ 597 HIS cc_start: 0.6459 (t-90) cc_final: 0.6258 (t-90) REVERT: HQ 630 GLN cc_start: 0.7489 (tm130) cc_final: 0.7003 (tm130) REVERT: HQ 707 LYS cc_start: 0.7942 (tttt) cc_final: 0.7602 (ttpt) REVERT: HR 28 ASP cc_start: 0.8000 (t0) cc_final: 0.7754 (t0) REVERT: HR 156 GLN cc_start: 0.7192 (tm-30) cc_final: 0.6763 (tm-30) REVERT: HS 97 LYS cc_start: 0.7079 (ptpt) cc_final: 0.6700 (ptpt) REVERT: HS 142 GLN cc_start: 0.7451 (mt0) cc_final: 0.6806 (mt0) REVERT: HS 153 ARG cc_start: 0.7398 (tpt90) cc_final: 0.7101 (mmm160) REVERT: HT 17 THR cc_start: 0.7704 (m) cc_final: 0.7403 (m) REVERT: HT 19 HIS cc_start: 0.7146 (t70) cc_final: 0.6876 (t-90) REVERT: HT 23 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7106 (mmtm) REVERT: HT 26 VAL cc_start: 0.7773 (t) cc_final: 0.7299 (m) REVERT: HT 36 TYR cc_start: 0.6990 (OUTLIER) cc_final: 0.6334 (t80) REVERT: HT 45 GLN cc_start: 0.7833 (mp10) cc_final: 0.7494 (mp10) REVERT: HT 50 LEU cc_start: 0.6817 (mp) cc_final: 0.6142 (mt) REVERT: HT 57 LYS cc_start: 0.7540 (mttt) cc_final: 0.7175 (ttmm) REVERT: HT 68 ASP cc_start: 0.6439 (t0) cc_final: 0.6096 (t0) REVERT: HT 105 ARG cc_start: 0.7466 (ttp-110) cc_final: 0.7237 (ttp80) REVERT: HT 118 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7540 (mmmt) REVERT: HT 153 ASP cc_start: 0.5880 (t0) cc_final: 0.5442 (m-30) REVERT: HT 312 ARG cc_start: 0.5486 (ptt90) cc_final: 0.3868 (ptp-170) outliers start: 147 outliers final: 104 residues processed: 1150 average time/residue: 0.2982 time to fit residues: 528.2210 Evaluate side-chains 1194 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1081 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 17 LEU Chi-restraints excluded: chain HA residue 36 ILE Chi-restraints excluded: chain HA residue 146 PHE Chi-restraints excluded: chain HA residue 200 GLN Chi-restraints excluded: chain HA residue 208 LEU Chi-restraints excluded: chain HA residue 410 LEU Chi-restraints excluded: chain HA residue 426 ARG Chi-restraints excluded: chain HB residue 47 VAL Chi-restraints excluded: chain HB residue 53 THR Chi-restraints excluded: chain HC residue 10 LEU Chi-restraints excluded: chain HC residue 42 SER Chi-restraints excluded: chain HC residue 46 SER Chi-restraints excluded: chain HC residue 57 SER Chi-restraints excluded: chain HC residue 100 TYR Chi-restraints excluded: chain HC residue 194 LEU Chi-restraints excluded: chain HC residue 222 LEU Chi-restraints excluded: chain HD residue 20 LEU Chi-restraints excluded: chain HD residue 42 LEU Chi-restraints excluded: chain HD residue 84 LEU Chi-restraints excluded: chain HE residue 108 SER Chi-restraints excluded: chain HE residue 110 LEU Chi-restraints excluded: chain HE residue 176 GLU Chi-restraints excluded: chain HF residue 51 GLN Chi-restraints excluded: chain HF residue 102 CYS Chi-restraints excluded: chain HF residue 135 LEU Chi-restraints excluded: chain HF residue 190 VAL Chi-restraints excluded: chain HF residue 197 LEU Chi-restraints excluded: chain HF residue 226 VAL Chi-restraints excluded: chain HF residue 256 HIS Chi-restraints excluded: chain HF residue 306 TYR Chi-restraints excluded: chain HF residue 322 MET Chi-restraints excluded: chain HG residue 15 LEU Chi-restraints excluded: chain HG residue 70 LEU Chi-restraints excluded: chain HG residue 74 THR Chi-restraints excluded: chain HH residue 22 VAL Chi-restraints excluded: chain HH residue 54 VAL Chi-restraints excluded: chain HI residue 34 MET Chi-restraints excluded: chain HI residue 66 LEU Chi-restraints excluded: chain HI residue 83 PHE Chi-restraints excluded: chain HI residue 92 THR Chi-restraints excluded: chain HI residue 138 GLN Chi-restraints excluded: chain HJ residue 165 LEU Chi-restraints excluded: chain HJ residue 171 LEU Chi-restraints excluded: chain HJ residue 238 LEU Chi-restraints excluded: chain HJ residue 381 SER Chi-restraints excluded: chain HJ residue 411 ASP Chi-restraints excluded: chain HJ residue 413 VAL Chi-restraints excluded: chain HJ residue 421 VAL Chi-restraints excluded: chain HJ residue 427 ILE Chi-restraints excluded: chain HJ residue 435 MET Chi-restraints excluded: chain HJ residue 459 LEU Chi-restraints excluded: chain HK residue 47 TYR Chi-restraints excluded: chain HK residue 98 VAL Chi-restraints excluded: chain HL residue 42 ILE Chi-restraints excluded: chain HL residue 51 CYS Chi-restraints excluded: chain HL residue 75 GLN Chi-restraints excluded: chain HM residue 20 GLN Chi-restraints excluded: chain HM residue 70 ILE Chi-restraints excluded: chain HM residue 73 ILE Chi-restraints excluded: chain HM residue 352 GLN Chi-restraints excluded: chain HM residue 362 LEU Chi-restraints excluded: chain HM residue 394 LEU Chi-restraints excluded: chain HM residue 412 LEU Chi-restraints excluded: chain HM residue 418 LEU Chi-restraints excluded: chain HM residue 607 ILE Chi-restraints excluded: chain HO residue 17 VAL Chi-restraints excluded: chain HO residue 96 LEU Chi-restraints excluded: chain HO residue 112 MET Chi-restraints excluded: chain HO residue 155 ASP Chi-restraints excluded: chain HO residue 166 THR Chi-restraints excluded: chain HP residue 13 ASN Chi-restraints excluded: chain HP residue 40 VAL Chi-restraints excluded: chain HP residue 57 THR Chi-restraints excluded: chain HP residue 172 VAL Chi-restraints excluded: chain HP residue 197 GLU Chi-restraints excluded: chain HP residue 235 ASP Chi-restraints excluded: chain HP residue 243 GLU Chi-restraints excluded: chain HQ residue 124 VAL Chi-restraints excluded: chain HQ residue 126 LEU Chi-restraints excluded: chain HQ residue 192 HIS Chi-restraints excluded: chain HQ residue 202 MET Chi-restraints excluded: chain HQ residue 232 LYS Chi-restraints excluded: chain HQ residue 238 ILE Chi-restraints excluded: chain HQ residue 249 PHE Chi-restraints excluded: chain HQ residue 253 ILE Chi-restraints excluded: chain HQ residue 314 VAL Chi-restraints excluded: chain HQ residue 316 THR Chi-restraints excluded: chain HQ residue 347 ASP Chi-restraints excluded: chain HQ residue 353 LEU Chi-restraints excluded: chain HQ residue 399 LEU Chi-restraints excluded: chain HQ residue 411 THR Chi-restraints excluded: chain HQ residue 534 LEU Chi-restraints excluded: chain HQ residue 535 LEU Chi-restraints excluded: chain HQ residue 586 VAL Chi-restraints excluded: chain HQ residue 626 GLU Chi-restraints excluded: chain HQ residue 710 ILE Chi-restraints excluded: chain HQ residue 723 VAL Chi-restraints excluded: chain HR residue 21 SER Chi-restraints excluded: chain HR residue 96 LEU Chi-restraints excluded: chain HR residue 122 VAL Chi-restraints excluded: chain HR residue 125 TRP Chi-restraints excluded: chain HR residue 126 ASN Chi-restraints excluded: chain HS residue 102 LEU Chi-restraints excluded: chain HS residue 117 LEU Chi-restraints excluded: chain HS residue 130 VAL Chi-restraints excluded: chain HS residue 156 GLU Chi-restraints excluded: chain HS residue 175 MET Chi-restraints excluded: chain HT residue 30 ARG Chi-restraints excluded: chain HT residue 36 TYR Chi-restraints excluded: chain HT residue 89 VAL Chi-restraints excluded: chain HT residue 92 THR Chi-restraints excluded: chain HT residue 361 PHE Chi-restraints excluded: chain HT residue 378 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 422 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 193 optimal weight: 0.0000 chunk 19 optimal weight: 1.9990 chunk 402 optimal weight: 0.0670 chunk 436 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 76 optimal weight: 0.3980 chunk 291 optimal weight: 2.9990 chunk 154 optimal weight: 0.2980 overall best weight: 0.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... HA 200 GLN ** HA 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HB 139 GLN HC 31 ASN HF 65 GLN ** HI 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HJ 416 GLN ** HL 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HL 49 GLN HM 272 GLN HP 142 HIS HP 239 GLN HQ 345 HIS ** HQ 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HS 198 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.187457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.159416 restraints weight = 63909.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.163048 restraints weight = 36343.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.165273 restraints weight = 21939.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.165374 restraints weight = 18058.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.165499 restraints weight = 15484.598| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 42419 Z= 0.124 Angle : 0.618 12.949 58628 Z= 0.310 Chirality : 0.039 0.266 6660 Planarity : 0.005 0.070 6558 Dihedral : 17.939 178.280 9205 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.91 % Favored : 93.04 % Rotamer: Outliers : 3.84 % Allowed : 23.48 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.13), residues: 4268 helix: 0.20 (0.12), residues: 1825 sheet: -1.65 (0.36), residues: 196 loop : -2.16 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGHP 242 TYR 0.034 0.001 TYRHH 18 PHE 0.024 0.001 PHEHI 123 TRP 0.028 0.001 TRPHO 6 HIS 0.012 0.001 HISHQ 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (42419) covalent geometry : angle 0.61831 / 0.31 (58628) hydrogen bonds : bond 0.04782 / 3.13 ( 1057) hydrogen bonds : angle 4.30735 / 3.03 ( 2968) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1083 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: HA 10 ARG cc_start: 0.7094 (ptm160) cc_final: 0.6061 (mmm160) REVERT: HA 46 MET cc_start: 0.3273 (ttm) cc_final: 0.2906 (pmm) REVERT: HA 172 TRP cc_start: 0.7133 (m100) cc_final: 0.6509 (m100) REVERT: HA 244 ARG cc_start: 0.6498 (mtp180) cc_final: 0.6296 (mtp180) REVERT: HA 301 TRP cc_start: 0.8045 (m100) cc_final: 0.7507 (m100) REVERT: HA 313 MET cc_start: 0.5078 (ttm) cc_final: 0.4628 (ttm) REVERT: HA 339 GLN cc_start: 0.7267 (tt0) cc_final: 0.6537 (tt0) REVERT: HA 347 GLN cc_start: 0.7719 (tp40) cc_final: 0.7411 (tp40) REVERT: HA 383 ASN cc_start: 0.7338 (m110) cc_final: 0.6959 (m110) REVERT: HA 399 ARG cc_start: 0.7478 (mtm180) cc_final: 0.7276 (mtm-85) REVERT: HA 402 ASP cc_start: 0.6876 (t70) cc_final: 0.6215 (t70) REVERT: HA 405 GLN cc_start: 0.6425 (mp10) cc_final: 0.6046 (mp10) REVERT: HA 426 ARG cc_start: 0.6140 (OUTLIER) cc_final: 0.2792 (ptt-90) REVERT: HA 437 ILE cc_start: 0.7998 (mm) cc_final: 0.7540 (mm) REVERT: HA 457 LYS cc_start: 0.7999 (mttp) cc_final: 0.7749 (ttmm) REVERT: HB 51 ARG cc_start: 0.7934 (tmt90) cc_final: 0.7477 (ttt180) REVERT: HB 109 ARG cc_start: 0.7722 (ttt180) cc_final: 0.7128 (ttt180) REVERT: HB 148 MET cc_start: 0.6990 (mtm) cc_final: 0.6349 (mtt) REVERT: HB 153 MET cc_start: 0.7236 (tpp) cc_final: 0.6501 (tpp) REVERT: HC 2 LEU cc_start: 0.7386 (tt) cc_final: 0.6974 (tp) REVERT: HC 96 GLU cc_start: 0.7210 (pt0) cc_final: 0.6837 (pt0) REVERT: HD 18 ASP cc_start: 0.7852 (t70) cc_final: 0.7585 (t0) REVERT: HD 20 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7558 (tp) REVERT: HD 27 GLU cc_start: 0.6522 (tp30) cc_final: 0.6285 (tp30) REVERT: HD 40 GLN cc_start: 0.7155 (mt0) cc_final: 0.6776 (mt0) REVERT: HE 154 MET cc_start: 0.7490 (tpp) cc_final: 0.7254 (tpp) REVERT: HE 158 LEU cc_start: 0.8313 (tp) cc_final: 0.7980 (tp) REVERT: HE 162 CYS cc_start: 0.7707 (m) cc_final: 0.7247 (t) REVERT: HF 61 ARG cc_start: 0.7457 (ttm110) cc_final: 0.7205 (ttp80) REVERT: HF 63 ASP cc_start: 0.6980 (m-30) cc_final: 0.6477 (t0) REVERT: HF 108 THR cc_start: 0.7950 (m) cc_final: 0.7586 (t) REVERT: HF 121 LEU cc_start: 0.7884 (mt) cc_final: 0.7669 (mp) REVERT: HF 123 SER cc_start: 0.8093 (m) cc_final: 0.7554 (t) REVERT: HF 204 ASP cc_start: 0.6862 (t0) cc_final: 0.6549 (m-30) REVERT: HF 232 MET cc_start: 0.7289 (ttt) cc_final: 0.6985 (ttp) REVERT: HF 237 LYS cc_start: 0.7815 (mtmm) cc_final: 0.6914 (mtmm) REVERT: HF 240 GLU cc_start: 0.6462 (tt0) cc_final: 0.6205 (tt0) REVERT: HF 246 LEU cc_start: 0.8623 (mt) cc_final: 0.8359 (mp) REVERT: HF 266 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6475 (mm-30) REVERT: HG 88 LYS cc_start: 0.7852 (mttt) cc_final: 0.7495 (mttt) REVERT: HH 18 TYR cc_start: 0.7664 (t80) cc_final: 0.7407 (t80) REVERT: HH 59 GLU cc_start: 0.7440 (tp30) cc_final: 0.7173 (mm-30) REVERT: HH 60 MET cc_start: 0.6649 (ttp) cc_final: 0.6050 (mmp) REVERT: HH 74 ASP cc_start: 0.7660 (t0) cc_final: 0.7437 (t0) REVERT: HI 32 GLU cc_start: 0.6810 (tp30) cc_final: 0.6585 (tp30) REVERT: HI 42 MET cc_start: 0.8547 (mmm) cc_final: 0.8220 (mmm) REVERT: HI 59 LYS cc_start: 0.7174 (tptt) cc_final: 0.6295 (tptt) REVERT: HI 63 MET cc_start: 0.6285 (mtm) cc_final: 0.4940 (mtm) REVERT: HI 109 LYS cc_start: 0.7076 (mmtm) cc_final: 0.6701 (mmtm) REVERT: HI 125 GLN cc_start: 0.6242 (tm-30) cc_final: 0.5803 (pp30) REVERT: HI 129 LYS cc_start: 0.7333 (mttt) cc_final: 0.6913 (mttt) REVERT: HJ 167 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.7878 (mtp85) REVERT: HJ 177 ASP cc_start: 0.6453 (t0) cc_final: 0.6158 (t0) REVERT: HJ 204 LYS cc_start: 0.7689 (tttt) cc_final: 0.7418 (tttt) REVERT: HJ 244 SER cc_start: 0.8071 (m) cc_final: 0.7535 (t) REVERT: HJ 272 LEU cc_start: 0.6863 (mp) cc_final: 0.6444 (mp) REVERT: HJ 296 ARG cc_start: 0.6619 (mtt-85) cc_final: 0.6263 (mtt-85) REVERT: HJ 331 ASN cc_start: 0.7692 (m-40) cc_final: 0.7269 (m-40) REVERT: HJ 374 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7456 (tm-30) REVERT: HJ 392 PHE cc_start: 0.6029 (t80) cc_final: 0.5648 (t80) REVERT: HJ 393 ARG cc_start: 0.7544 (ttp80) cc_final: 0.6602 (ttp80) REVERT: HJ 416 GLN cc_start: 0.6269 (mm-40) cc_final: 0.6023 (mm-40) REVERT: HJ 425 ASP cc_start: 0.6126 (t70) cc_final: 0.5767 (t0) REVERT: HJ 467 LYS cc_start: 0.7153 (tptt) cc_final: 0.6873 (tptt) REVERT: HJ 551 GLU cc_start: 0.5999 (tt0) cc_final: 0.5797 (tt0) REVERT: HJ 557 GLU cc_start: 0.6857 (tp30) cc_final: 0.6548 (tp30) REVERT: HJ 560 PHE cc_start: 0.7157 (t80) cc_final: 0.6794 (t80) REVERT: HK 77 ARG cc_start: 0.3984 (tpt170) cc_final: 0.3411 (tpt170) REVERT: HK 103 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6611 (mm-30) REVERT: HM 21 ARG cc_start: 0.6679 (ptp-110) cc_final: 0.6057 (mtp-110) REVERT: HM 95 LEU cc_start: 0.8227 (tp) cc_final: 0.7889 (tt) REVERT: HM 144 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7112 (tp) REVERT: HM 203 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6614 (tm-30) REVERT: HM 274 LEU cc_start: 0.6836 (tp) cc_final: 0.6455 (mp) REVERT: HM 310 THR cc_start: 0.7467 (t) cc_final: 0.7144 (p) REVERT: HM 353 GLN cc_start: 0.6538 (mt0) cc_final: 0.5978 (tt0) REVERT: HM 361 VAL cc_start: 0.7731 (m) cc_final: 0.7450 (p) REVERT: HM 581 GLN cc_start: 0.7294 (mm-40) cc_final: 0.7005 (mm-40) REVERT: HM 608 PRO cc_start: 0.6885 (Cg_endo) cc_final: 0.6678 (Cg_exo) REVERT: HN 6 ASN cc_start: 0.7772 (m-40) cc_final: 0.7348 (m110) REVERT: HO 5 ARG cc_start: 0.6953 (ptp-170) cc_final: 0.6673 (ptt180) REVERT: HO 14 ARG cc_start: 0.6593 (ttp80) cc_final: 0.5824 (ttt180) REVERT: HO 129 PHE cc_start: 0.6110 (m-80) cc_final: 0.5607 (m-80) REVERT: HP 69 LEU cc_start: 0.7267 (tp) cc_final: 0.7031 (tp) REVERT: HP 243 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.6031 (mp0) REVERT: HQ 32 ARG cc_start: 0.6857 (ptp-110) cc_final: 0.6641 (ptp90) REVERT: HQ 113 LYS cc_start: 0.7993 (tmtm) cc_final: 0.7730 (tmtm) REVERT: HQ 178 TRP cc_start: 0.8244 (t60) cc_final: 0.7669 (t-100) REVERT: HQ 179 ASN cc_start: 0.7331 (m-40) cc_final: 0.7100 (m-40) REVERT: HQ 209 ASP cc_start: 0.7409 (m-30) cc_final: 0.5234 (t0) REVERT: HQ 216 LEU cc_start: 0.8167 (mt) cc_final: 0.7633 (tp) REVERT: HQ 232 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.7072 (ttmm) REVERT: HQ 252 LEU cc_start: 0.7962 (tp) cc_final: 0.7635 (tp) REVERT: HQ 261 LYS cc_start: 0.6953 (ttmm) cc_final: 0.6516 (ttmm) REVERT: HQ 328 ASP cc_start: 0.5904 (t0) cc_final: 0.5531 (t0) REVERT: HQ 347 ASP cc_start: 0.6119 (OUTLIER) cc_final: 0.5334 (m-30) REVERT: HQ 411 THR cc_start: 0.6864 (m) cc_final: 0.6274 (p) REVERT: HQ 427 GLU cc_start: 0.6769 (tp30) cc_final: 0.6504 (tp30) REVERT: HQ 431 PHE cc_start: 0.5175 (m-80) cc_final: 0.4832 (m-80) REVERT: HQ 465 ARG cc_start: 0.6707 (ttp80) cc_final: 0.6262 (tpp80) REVERT: HQ 627 GLU cc_start: 0.7249 (mt-10) cc_final: 0.7001 (mt-10) REVERT: HQ 630 GLN cc_start: 0.7489 (tm130) cc_final: 0.6997 (tm130) REVERT: HQ 707 LYS cc_start: 0.7857 (tttt) cc_final: 0.7334 (ttpp) REVERT: HQ 731 ARG cc_start: 0.6621 (ptt90) cc_final: 0.5768 (ttt-90) REVERT: HQ 734 GLU cc_start: 0.7140 (pt0) cc_final: 0.6873 (pm20) REVERT: HQ 738 ARG cc_start: 0.6748 (ttp80) cc_final: 0.6523 (ttp80) REVERT: HR 28 ASP cc_start: 0.7922 (t0) cc_final: 0.7669 (t0) REVERT: HR 29 GLN cc_start: 0.6622 (tm-30) cc_final: 0.6257 (tp40) REVERT: HR 156 GLN cc_start: 0.7152 (tm-30) cc_final: 0.6698 (tm-30) REVERT: HS 131 LYS cc_start: 0.7758 (tptt) cc_final: 0.7551 (tptt) REVERT: HS 142 GLN cc_start: 0.7410 (mt0) cc_final: 0.7157 (mt0) REVERT: HS 153 ARG cc_start: 0.7539 (tpt90) cc_final: 0.7253 (mmm160) REVERT: HS 166 VAL cc_start: 0.8784 (t) cc_final: 0.8223 (p) REVERT: HS 190 ARG cc_start: 0.6564 (ptp-170) cc_final: 0.6275 (mtm180) REVERT: HT 17 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7492 (m) REVERT: HT 22 ARG cc_start: 0.5238 (ptm-80) cc_final: 0.4904 (ptm-80) REVERT: HT 23 LYS cc_start: 0.7456 (mmtt) cc_final: 0.7172 (mmtm) REVERT: HT 36 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.6310 (t80) REVERT: HT 45 GLN cc_start: 0.7828 (mp10) cc_final: 0.7460 (mp10) REVERT: HT 50 LEU cc_start: 0.6937 (mp) cc_final: 0.6241 (mt) REVERT: HT 57 LYS cc_start: 0.7575 (mttt) cc_final: 0.7191 (ttmm) REVERT: HT 68 ASP cc_start: 0.6456 (t0) cc_final: 0.6167 (t0) REVERT: HT 105 ARG cc_start: 0.7477 (ttp-110) cc_final: 0.7270 (ttp80) REVERT: HT 118 LYS cc_start: 0.7772 (mmtt) cc_final: 0.7425 (mmmt) REVERT: HT 312 ARG cc_start: 0.5481 (ptt90) cc_final: 0.3818 (ptp-170) outliers start: 143 outliers final: 103 residues processed: 1142 average time/residue: 0.2936 time to fit residues: 514.5171 Evaluate side-chains 1175 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1064 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 17 LEU Chi-restraints excluded: chain HA residue 146 PHE Chi-restraints excluded: chain HA residue 200 GLN Chi-restraints excluded: chain HA residue 208 LEU Chi-restraints excluded: chain HA residue 410 LEU Chi-restraints excluded: chain HA residue 426 ARG Chi-restraints excluded: chain HB residue 47 VAL Chi-restraints excluded: chain HB residue 53 THR Chi-restraints excluded: chain HB residue 77 VAL Chi-restraints excluded: chain HC residue 10 LEU Chi-restraints excluded: chain HC residue 11 ILE Chi-restraints excluded: chain HC residue 42 SER Chi-restraints excluded: chain HC residue 46 SER Chi-restraints excluded: chain HC residue 100 TYR Chi-restraints excluded: chain HC residue 194 LEU Chi-restraints excluded: chain HD residue 1 LEU Chi-restraints excluded: chain HD residue 20 LEU Chi-restraints excluded: chain HD residue 42 LEU Chi-restraints excluded: chain HD residue 84 LEU Chi-restraints excluded: chain HE residue 108 SER Chi-restraints excluded: chain HE residue 110 LEU Chi-restraints excluded: chain HE residue 163 VAL Chi-restraints excluded: chain HE residue 176 GLU Chi-restraints excluded: chain HF residue 135 LEU Chi-restraints excluded: chain HF residue 197 LEU Chi-restraints excluded: chain HF residue 219 GLU Chi-restraints excluded: chain HF residue 226 VAL Chi-restraints excluded: chain HF residue 306 TYR Chi-restraints excluded: chain HF residue 322 MET Chi-restraints excluded: chain HG residue 18 LEU Chi-restraints excluded: chain HG residue 70 LEU Chi-restraints excluded: chain HG residue 74 THR Chi-restraints excluded: chain HH residue 22 VAL Chi-restraints excluded: chain HH residue 54 VAL Chi-restraints excluded: chain HI residue 66 LEU Chi-restraints excluded: chain HI residue 83 PHE Chi-restraints excluded: chain HI residue 132 VAL Chi-restraints excluded: chain HJ residue 165 LEU Chi-restraints excluded: chain HJ residue 171 LEU Chi-restraints excluded: chain HJ residue 381 SER Chi-restraints excluded: chain HJ residue 411 ASP Chi-restraints excluded: chain HJ residue 427 ILE Chi-restraints excluded: chain HJ residue 459 LEU Chi-restraints excluded: chain HJ residue 561 LEU Chi-restraints excluded: chain HK residue 98 VAL Chi-restraints excluded: chain HL residue 42 ILE Chi-restraints excluded: chain HL residue 75 GLN Chi-restraints excluded: chain HL residue 80 VAL Chi-restraints excluded: chain HM residue 70 ILE Chi-restraints excluded: chain HM residue 73 ILE Chi-restraints excluded: chain HM residue 140 ASP Chi-restraints excluded: chain HM residue 144 LEU Chi-restraints excluded: chain HM residue 151 VAL Chi-restraints excluded: chain HM residue 267 THR Chi-restraints excluded: chain HM residue 362 LEU Chi-restraints excluded: chain HM residue 394 LEU Chi-restraints excluded: chain HM residue 412 LEU Chi-restraints excluded: chain HM residue 418 LEU Chi-restraints excluded: chain HO residue 17 VAL Chi-restraints excluded: chain HO residue 62 ARG Chi-restraints excluded: chain HO residue 78 LEU Chi-restraints excluded: chain HO residue 112 MET Chi-restraints excluded: chain HO residue 161 VAL Chi-restraints excluded: chain HO residue 166 THR Chi-restraints excluded: chain HP residue 13 ASN Chi-restraints excluded: chain HP residue 40 VAL Chi-restraints excluded: chain HP residue 57 THR Chi-restraints excluded: chain HP residue 172 VAL Chi-restraints excluded: chain HP residue 197 GLU Chi-restraints excluded: chain HP residue 243 GLU Chi-restraints excluded: chain HQ residue 126 LEU Chi-restraints excluded: chain HQ residue 187 GLU Chi-restraints excluded: chain HQ residue 188 LEU Chi-restraints excluded: chain HQ residue 192 HIS Chi-restraints excluded: chain HQ residue 202 MET Chi-restraints excluded: chain HQ residue 232 LYS Chi-restraints excluded: chain HQ residue 238 ILE Chi-restraints excluded: chain HQ residue 249 PHE Chi-restraints excluded: chain HQ residue 253 ILE Chi-restraints excluded: chain HQ residue 314 VAL Chi-restraints excluded: chain HQ residue 316 THR Chi-restraints excluded: chain HQ residue 345 HIS Chi-restraints excluded: chain HQ residue 347 ASP Chi-restraints excluded: chain HQ residue 353 LEU Chi-restraints excluded: chain HQ residue 399 LEU Chi-restraints excluded: chain HQ residue 421 VAL Chi-restraints excluded: chain HQ residue 534 LEU Chi-restraints excluded: chain HQ residue 535 LEU Chi-restraints excluded: chain HQ residue 586 VAL Chi-restraints excluded: chain HQ residue 626 GLU Chi-restraints excluded: chain HQ residue 710 ILE Chi-restraints excluded: chain HR residue 6 TRP Chi-restraints excluded: chain HR residue 21 SER Chi-restraints excluded: chain HR residue 36 CYS Chi-restraints excluded: chain HR residue 51 CYS Chi-restraints excluded: chain HR residue 96 LEU Chi-restraints excluded: chain HR residue 125 TRP Chi-restraints excluded: chain HR residue 126 ASN Chi-restraints excluded: chain HS residue 83 VAL Chi-restraints excluded: chain HS residue 102 LEU Chi-restraints excluded: chain HS residue 117 LEU Chi-restraints excluded: chain HS residue 130 VAL Chi-restraints excluded: chain HS residue 149 SER Chi-restraints excluded: chain HS residue 156 GLU Chi-restraints excluded: chain HS residue 175 MET Chi-restraints excluded: chain HT residue 17 THR Chi-restraints excluded: chain HT residue 21 MET Chi-restraints excluded: chain HT residue 30 ARG Chi-restraints excluded: chain HT residue 36 TYR Chi-restraints excluded: chain HT residue 361 PHE Chi-restraints excluded: chain HT residue 378 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 333 optimal weight: 0.0170 chunk 436 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 351 optimal weight: 2.9990 chunk 322 optimal weight: 0.9980 chunk 274 optimal weight: 0.5980 chunk 212 optimal weight: 0.9990 chunk 438 optimal weight: 3.9990 chunk 314 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 269 optimal weight: 9.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... HA 200 GLN ** HA 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HB 139 GLN HC 31 ASN HH 39 GLN ** HI 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HJ 456 GLN ** HL 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HM 20 GLN HO 36 HIS HQ 342 GLN HQ 345 HIS ** HQ 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HS 103 GLN HT 358 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.183992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.155379 restraints weight = 63284.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.158991 restraints weight = 37299.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.160648 restraints weight = 22583.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.160920 restraints weight = 19426.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.161042 restraints weight = 16600.813| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 42419 Z= 0.192 Angle : 0.680 11.657 58628 Z= 0.345 Chirality : 0.042 0.246 6660 Planarity : 0.005 0.070 6558 Dihedral : 18.050 179.711 9203 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.85 % Favored : 92.10 % Rotamer: Outliers : 4.30 % Allowed : 22.76 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.13), residues: 4268 helix: 0.12 (0.12), residues: 1832 sheet: -1.66 (0.37), residues: 188 loop : -2.26 (0.12), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGHQ 346 TYR 0.022 0.002 TYRHH 18 PHE 0.031 0.002 PHEHH 35 TRP 0.020 0.002 TRPHI 112 HIS 0.017 0.001 HISHQ 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (42419) covalent geometry : angle 0.68038 / 0.34 (58628) hydrogen bonds : bond 0.05422 / 3.55 ( 1057) hydrogen bonds : angle 4.40406 / 3.10 ( 2968) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 1093 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: HA 10 ARG cc_start: 0.7236 (ptm160) cc_final: 0.6212 (mmm160) REVERT: HA 46 MET cc_start: 0.3323 (ttm) cc_final: 0.2967 (pmm) REVERT: HA 56 MET cc_start: 0.7190 (mpp) cc_final: 0.6963 (mpp) REVERT: HA 172 TRP cc_start: 0.7194 (m100) cc_final: 0.6514 (m100) REVERT: HA 205 GLN cc_start: 0.7194 (tt0) cc_final: 0.6940 (mt0) REVERT: HA 244 ARG cc_start: 0.6496 (mtp180) cc_final: 0.6292 (mtp180) REVERT: HA 301 TRP cc_start: 0.8115 (m100) cc_final: 0.7546 (m100) REVERT: HA 313 MET cc_start: 0.5142 (ttm) cc_final: 0.4665 (ttm) REVERT: HA 339 GLN cc_start: 0.7378 (tt0) cc_final: 0.6683 (tt0) REVERT: HA 399 ARG cc_start: 0.7479 (mtm180) cc_final: 0.7207 (mtm-85) REVERT: HA 402 ASP cc_start: 0.6842 (t70) cc_final: 0.6126 (t0) REVERT: HA 426 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.3254 (ptt-90) REVERT: HA 436 GLU cc_start: 0.7081 (pt0) cc_final: 0.5909 (mt-10) REVERT: HA 466 ARG cc_start: 0.6894 (mpt180) cc_final: 0.6231 (mmt-90) REVERT: HB 51 ARG cc_start: 0.8001 (tmt90) cc_final: 0.7569 (ttt180) REVERT: HB 82 PHE cc_start: 0.8054 (t80) cc_final: 0.7694 (t80) REVERT: HB 109 ARG cc_start: 0.7737 (ttt180) cc_final: 0.7355 (ttt-90) REVERT: HB 148 MET cc_start: 0.7038 (mtm) cc_final: 0.6426 (mtt) REVERT: HB 153 MET cc_start: 0.7247 (tpp) cc_final: 0.6670 (tpp) REVERT: HC 2 LEU cc_start: 0.7435 (tt) cc_final: 0.7066 (tp) REVERT: HC 205 ILE cc_start: 0.8442 (mm) cc_final: 0.8139 (mm) REVERT: HD 18 ASP cc_start: 0.7957 (t70) cc_final: 0.7664 (t0) REVERT: HD 20 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7844 (tp) REVERT: HD 40 GLN cc_start: 0.7140 (mt0) cc_final: 0.6811 (mt0) REVERT: HE 154 MET cc_start: 0.7501 (tpp) cc_final: 0.7266 (tpp) REVERT: HE 158 LEU cc_start: 0.8289 (tp) cc_final: 0.7949 (tp) REVERT: HE 162 CYS cc_start: 0.7742 (m) cc_final: 0.7330 (t) REVERT: HF 63 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6461 (t0) REVERT: HF 86 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7934 (ttmm) REVERT: HF 108 THR cc_start: 0.7922 (m) cc_final: 0.7578 (t) REVERT: HF 123 SER cc_start: 0.7852 (m) cc_final: 0.7395 (t) REVERT: HF 204 ASP cc_start: 0.6959 (t0) cc_final: 0.6663 (m-30) REVERT: HF 232 MET cc_start: 0.7289 (ttt) cc_final: 0.7035 (ttp) REVERT: HF 240 GLU cc_start: 0.6449 (tt0) cc_final: 0.6245 (tt0) REVERT: HF 266 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6555 (mm-30) REVERT: HF 297 TRP cc_start: 0.7760 (OUTLIER) cc_final: 0.7550 (m100) REVERT: HG 88 LYS cc_start: 0.7850 (mttt) cc_final: 0.7468 (mttt) REVERT: HH 26 TYR cc_start: 0.7730 (t80) cc_final: 0.6997 (t80) REVERT: HH 54 VAL cc_start: 0.7391 (OUTLIER) cc_final: 0.6991 (t) REVERT: HH 59 GLU cc_start: 0.7416 (tp30) cc_final: 0.7117 (mm-30) REVERT: HH 60 MET cc_start: 0.6556 (ttp) cc_final: 0.5924 (mmp) REVERT: HH 74 ASP cc_start: 0.7617 (t0) cc_final: 0.7402 (t0) REVERT: HI 109 LYS cc_start: 0.7036 (mmtm) cc_final: 0.6607 (mmtm) REVERT: HI 125 GLN cc_start: 0.6334 (tm-30) cc_final: 0.5909 (pp30) REVERT: HI 129 LYS cc_start: 0.7358 (mttt) cc_final: 0.6971 (mttt) REVERT: HJ 167 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.7987 (mtp85) REVERT: HJ 177 ASP cc_start: 0.6516 (t0) cc_final: 0.6234 (t0) REVERT: HJ 244 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7537 (t) REVERT: HJ 272 LEU cc_start: 0.6884 (mp) cc_final: 0.6552 (mp) REVERT: HJ 281 PHE cc_start: 0.5743 (p90) cc_final: 0.4872 (p90) REVERT: HJ 300 ARG cc_start: 0.6918 (mtm180) cc_final: 0.6674 (mtm180) REVERT: HJ 326 GLU cc_start: 0.6218 (tp30) cc_final: 0.5930 (tp30) REVERT: HJ 331 ASN cc_start: 0.7756 (m-40) cc_final: 0.7375 (m-40) REVERT: HJ 374 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7375 (tm-30) REVERT: HJ 392 PHE cc_start: 0.6088 (t80) cc_final: 0.5635 (t80) REVERT: HJ 393 ARG cc_start: 0.7568 (ttp80) cc_final: 0.6684 (ttp80) REVERT: HJ 394 ARG cc_start: 0.6992 (ttp-170) cc_final: 0.6211 (ptm-80) REVERT: HJ 399 PHE cc_start: 0.7405 (m-80) cc_final: 0.7100 (m-80) REVERT: HJ 409 VAL cc_start: 0.4879 (OUTLIER) cc_final: 0.4659 (m) REVERT: HJ 425 ASP cc_start: 0.6099 (t70) cc_final: 0.5764 (t0) REVERT: HJ 467 LYS cc_start: 0.7169 (tptt) cc_final: 0.6864 (tptt) REVERT: HJ 557 GLU cc_start: 0.6845 (tp30) cc_final: 0.6574 (tp30) REVERT: HK 77 ARG cc_start: 0.4011 (tpt170) cc_final: 0.3466 (tpt170) REVERT: HK 103 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6479 (mm-30) REVERT: HL 38 GLN cc_start: 0.6950 (pp30) cc_final: 0.6431 (pt0) REVERT: HM 20 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7618 (tp-100) REVERT: HM 21 ARG cc_start: 0.6781 (ptp-110) cc_final: 0.6189 (mtp-110) REVERT: HM 95 LEU cc_start: 0.8251 (tp) cc_final: 0.7925 (tt) REVERT: HM 139 PHE cc_start: 0.6096 (m-80) cc_final: 0.5880 (m-80) REVERT: HM 144 LEU cc_start: 0.7390 (tt) cc_final: 0.7119 (tp) REVERT: HM 165 LEU cc_start: 0.7657 (mp) cc_final: 0.7318 (mm) REVERT: HM 203 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6707 (tm-30) REVERT: HM 205 LEU cc_start: 0.6902 (tp) cc_final: 0.6648 (tt) REVERT: HM 310 THR cc_start: 0.7588 (t) cc_final: 0.7269 (p) REVERT: HM 353 GLN cc_start: 0.6374 (mt0) cc_final: 0.5849 (tt0) REVERT: HM 361 VAL cc_start: 0.7782 (m) cc_final: 0.7512 (p) REVERT: HM 363 PHE cc_start: 0.6759 (t80) cc_final: 0.6525 (t80) REVERT: HM 397 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7372 (mm) REVERT: HM 409 ARG cc_start: 0.7362 (mtp85) cc_final: 0.7126 (ttm170) REVERT: HM 581 GLN cc_start: 0.7368 (mm-40) cc_final: 0.6918 (mm-40) REVERT: HM 608 PRO cc_start: 0.7035 (Cg_endo) cc_final: 0.6824 (Cg_exo) REVERT: HN 3 ASN cc_start: 0.7635 (p0) cc_final: 0.7074 (p0) REVERT: HN 6 ASN cc_start: 0.7216 (m-40) cc_final: 0.6534 (m110) REVERT: HO 5 ARG cc_start: 0.7104 (ptp-170) cc_final: 0.6828 (ptt180) REVERT: HO 14 ARG cc_start: 0.6686 (ttp80) cc_final: 0.5955 (ttt180) REVERT: HO 129 PHE cc_start: 0.6073 (m-80) cc_final: 0.5561 (m-80) REVERT: HP 69 LEU cc_start: 0.7293 (tp) cc_final: 0.7063 (tp) REVERT: HP 235 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: HP 243 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6059 (mp0) REVERT: HQ 17 LYS cc_start: 0.6649 (mmmt) cc_final: 0.6185 (mmmm) REVERT: HQ 32 ARG cc_start: 0.6932 (ptp-110) cc_final: 0.6622 (ptp90) REVERT: HQ 36 ARG cc_start: 0.6805 (mmt180) cc_final: 0.6605 (mmt90) REVERT: HQ 113 LYS cc_start: 0.8048 (tmtm) cc_final: 0.7734 (tmtm) REVERT: HQ 178 TRP cc_start: 0.8308 (t60) cc_final: 0.7743 (t-100) REVERT: HQ 179 ASN cc_start: 0.7371 (m-40) cc_final: 0.7090 (m-40) REVERT: HQ 186 LYS cc_start: 0.7451 (mtmm) cc_final: 0.7191 (mtmm) REVERT: HQ 232 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.7075 (ttmm) REVERT: HQ 252 LEU cc_start: 0.7970 (tp) cc_final: 0.7658 (tp) REVERT: HQ 261 LYS cc_start: 0.6882 (ttmm) cc_final: 0.6389 (ttmm) REVERT: HQ 303 MET cc_start: 0.8058 (mmm) cc_final: 0.6732 (mtt) REVERT: HQ 371 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6602 (mp0) REVERT: HQ 411 THR cc_start: 0.6902 (m) cc_final: 0.6339 (p) REVERT: HQ 431 PHE cc_start: 0.5290 (m-80) cc_final: 0.4975 (m-80) REVERT: HQ 465 ARG cc_start: 0.6744 (ttp80) cc_final: 0.6313 (tpp80) REVERT: HQ 530 ASP cc_start: 0.6496 (p0) cc_final: 0.6245 (p0) REVERT: HQ 630 GLN cc_start: 0.7511 (tm130) cc_final: 0.6996 (tm130) REVERT: HQ 685 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5508 (t80) REVERT: HQ 693 ARG cc_start: 0.7589 (ttm110) cc_final: 0.6973 (mmm-85) REVERT: HQ 707 LYS cc_start: 0.7942 (tttt) cc_final: 0.7616 (ttpt) REVERT: HQ 731 ARG cc_start: 0.6804 (ptt90) cc_final: 0.6507 (ptt90) REVERT: HQ 734 GLU cc_start: 0.7130 (pt0) cc_final: 0.6761 (pm20) REVERT: HQ 738 ARG cc_start: 0.6784 (ttp80) cc_final: 0.6505 (ttp80) REVERT: HR 28 ASP cc_start: 0.7931 (t0) cc_final: 0.7643 (t0) REVERT: HR 29 GLN cc_start: 0.6602 (tm-30) cc_final: 0.6261 (tp40) REVERT: HR 50 SER cc_start: 0.3123 (OUTLIER) cc_final: 0.2761 (p) REVERT: HR 114 PHE cc_start: 0.8122 (t80) cc_final: 0.7276 (t80) REVERT: HR 124 THR cc_start: 0.7376 (m) cc_final: 0.7139 (p) REVERT: HR 156 GLN cc_start: 0.7484 (tm-30) cc_final: 0.7062 (tm-30) REVERT: HR 168 ARG cc_start: 0.6770 (ttt-90) cc_final: 0.6561 (ttt-90) REVERT: HS 142 GLN cc_start: 0.7448 (mt0) cc_final: 0.7216 (mt0) REVERT: HS 166 VAL cc_start: 0.8825 (t) cc_final: 0.8267 (p) REVERT: HS 187 ASN cc_start: 0.6652 (t0) cc_final: 0.6436 (t0) REVERT: HS 190 ARG cc_start: 0.6720 (ptp-170) cc_final: 0.6418 (mtm180) REVERT: HT 17 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.7458 (m) REVERT: HT 23 LYS cc_start: 0.7601 (mmtt) cc_final: 0.7257 (mmtm) REVERT: HT 36 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6443 (t80) REVERT: HT 45 GLN cc_start: 0.7880 (mp10) cc_final: 0.7545 (mp10) REVERT: HT 50 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6426 (mt) REVERT: HT 57 LYS cc_start: 0.7594 (mttt) cc_final: 0.7161 (ttmm) REVERT: HT 68 ASP cc_start: 0.6553 (t0) cc_final: 0.6288 (t0) REVERT: HT 118 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7482 (mmmt) REVERT: HT 312 ARG cc_start: 0.5644 (ptt90) cc_final: 0.3918 (ptp-170) REVERT: HT 362 ASP cc_start: 0.7434 (t0) cc_final: 0.7063 (t70) outliers start: 160 outliers final: 113 residues processed: 1150 average time/residue: 0.2979 time to fit residues: 526.1271 Evaluate side-chains 1201 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1071 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 17 LEU Chi-restraints excluded: chain HA residue 35 MET Chi-restraints excluded: chain HA residue 146 PHE Chi-restraints excluded: chain HA residue 200 GLN Chi-restraints excluded: chain HA residue 208 LEU Chi-restraints excluded: chain HA residue 239 ARG Chi-restraints excluded: chain HA residue 410 LEU Chi-restraints excluded: chain HA residue 426 ARG Chi-restraints excluded: chain HA residue 470 ASP Chi-restraints excluded: chain HB residue 47 VAL Chi-restraints excluded: chain HB residue 53 THR Chi-restraints excluded: chain HB residue 77 VAL Chi-restraints excluded: chain HB residue 131 MET Chi-restraints excluded: chain HC residue 10 LEU Chi-restraints excluded: chain HC residue 42 SER Chi-restraints excluded: chain HC residue 57 SER Chi-restraints excluded: chain HC residue 100 TYR Chi-restraints excluded: chain HC residue 149 LEU Chi-restraints excluded: chain HC residue 194 LEU Chi-restraints excluded: chain HC residue 222 LEU Chi-restraints excluded: chain HD residue 1 LEU Chi-restraints excluded: chain HD residue 20 LEU Chi-restraints excluded: chain HD residue 42 LEU Chi-restraints excluded: chain HD residue 84 LEU Chi-restraints excluded: chain HE residue 110 LEU Chi-restraints excluded: chain HE residue 127 LEU Chi-restraints excluded: chain HE residue 163 VAL Chi-restraints excluded: chain HE residue 176 GLU Chi-restraints excluded: chain HF residue 63 ASP Chi-restraints excluded: chain HF residue 102 CYS Chi-restraints excluded: chain HF residue 135 LEU Chi-restraints excluded: chain HF residue 197 LEU Chi-restraints excluded: chain HF residue 219 GLU Chi-restraints excluded: chain HF residue 226 VAL Chi-restraints excluded: chain HF residue 230 ILE Chi-restraints excluded: chain HF residue 297 TRP Chi-restraints excluded: chain HF residue 322 MET Chi-restraints excluded: chain HG residue 15 LEU Chi-restraints excluded: chain HG residue 18 LEU Chi-restraints excluded: chain HG residue 70 LEU Chi-restraints excluded: chain HG residue 74 THR Chi-restraints excluded: chain HH residue 22 VAL Chi-restraints excluded: chain HH residue 54 VAL Chi-restraints excluded: chain HI residue 51 MET Chi-restraints excluded: chain HI residue 66 LEU Chi-restraints excluded: chain HI residue 83 PHE Chi-restraints excluded: chain HI residue 132 VAL Chi-restraints excluded: chain HJ residue 171 LEU Chi-restraints excluded: chain HJ residue 238 LEU Chi-restraints excluded: chain HJ residue 244 SER Chi-restraints excluded: chain HJ residue 376 CYS Chi-restraints excluded: chain HJ residue 409 VAL Chi-restraints excluded: chain HJ residue 411 ASP Chi-restraints excluded: chain HJ residue 413 VAL Chi-restraints excluded: chain HJ residue 414 VAL Chi-restraints excluded: chain HJ residue 435 MET Chi-restraints excluded: chain HJ residue 459 LEU Chi-restraints excluded: chain HK residue 34 LYS Chi-restraints excluded: chain HK residue 40 ARG Chi-restraints excluded: chain HK residue 98 VAL Chi-restraints excluded: chain HL residue 42 ILE Chi-restraints excluded: chain HL residue 62 VAL Chi-restraints excluded: chain HL residue 80 VAL Chi-restraints excluded: chain HM residue 20 GLN Chi-restraints excluded: chain HM residue 70 ILE Chi-restraints excluded: chain HM residue 73 ILE Chi-restraints excluded: chain HM residue 140 ASP Chi-restraints excluded: chain HM residue 267 THR Chi-restraints excluded: chain HM residue 362 LEU Chi-restraints excluded: chain HM residue 394 LEU Chi-restraints excluded: chain HM residue 397 LEU Chi-restraints excluded: chain HM residue 412 LEU Chi-restraints excluded: chain HM residue 418 LEU Chi-restraints excluded: chain HO residue 17 VAL Chi-restraints excluded: chain HO residue 62 ARG Chi-restraints excluded: chain HO residue 96 LEU Chi-restraints excluded: chain HO residue 112 MET Chi-restraints excluded: chain HO residue 161 VAL Chi-restraints excluded: chain HO residue 166 THR Chi-restraints excluded: chain HP residue 40 VAL Chi-restraints excluded: chain HP residue 57 THR Chi-restraints excluded: chain HP residue 172 VAL Chi-restraints excluded: chain HP residue 197 GLU Chi-restraints excluded: chain HP residue 235 ASP Chi-restraints excluded: chain HP residue 243 GLU Chi-restraints excluded: chain HP residue 245 LYS Chi-restraints excluded: chain HQ residue 124 VAL Chi-restraints excluded: chain HQ residue 126 LEU Chi-restraints excluded: chain HQ residue 187 GLU Chi-restraints excluded: chain HQ residue 192 HIS Chi-restraints excluded: chain HQ residue 202 MET Chi-restraints excluded: chain HQ residue 223 SER Chi-restraints excluded: chain HQ residue 232 LYS Chi-restraints excluded: chain HQ residue 238 ILE Chi-restraints excluded: chain HQ residue 253 ILE Chi-restraints excluded: chain HQ residue 294 ASN Chi-restraints excluded: chain HQ residue 316 THR Chi-restraints excluded: chain HQ residue 344 ILE Chi-restraints excluded: chain HQ residue 345 HIS Chi-restraints excluded: chain HQ residue 353 LEU Chi-restraints excluded: chain HQ residue 421 VAL Chi-restraints excluded: chain HQ residue 535 LEU Chi-restraints excluded: chain HQ residue 546 THR Chi-restraints excluded: chain HQ residue 576 LEU Chi-restraints excluded: chain HQ residue 586 VAL Chi-restraints excluded: chain HQ residue 626 GLU Chi-restraints excluded: chain HQ residue 685 PHE Chi-restraints excluded: chain HQ residue 710 ILE Chi-restraints excluded: chain HR residue 6 TRP Chi-restraints excluded: chain HR residue 21 SER Chi-restraints excluded: chain HR residue 36 CYS Chi-restraints excluded: chain HR residue 50 SER Chi-restraints excluded: chain HR residue 96 LEU Chi-restraints excluded: chain HR residue 125 TRP Chi-restraints excluded: chain HR residue 126 ASN Chi-restraints excluded: chain HS residue 83 VAL Chi-restraints excluded: chain HS residue 102 LEU Chi-restraints excluded: chain HS residue 117 LEU Chi-restraints excluded: chain HS residue 130 VAL Chi-restraints excluded: chain HS residue 149 SER Chi-restraints excluded: chain HS residue 156 GLU Chi-restraints excluded: chain HT residue 17 THR Chi-restraints excluded: chain HT residue 21 MET Chi-restraints excluded: chain HT residue 30 ARG Chi-restraints excluded: chain HT residue 36 TYR Chi-restraints excluded: chain HT residue 47 VAL Chi-restraints excluded: chain HT residue 50 LEU Chi-restraints excluded: chain HT residue 89 VAL Chi-restraints excluded: chain HT residue 361 PHE Chi-restraints excluded: chain HT residue 378 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 361 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 287 optimal weight: 4.9990 chunk 434 optimal weight: 2.9990 chunk 353 optimal weight: 0.3980 chunk 151 optimal weight: 0.6980 chunk 295 optimal weight: 0.1980 chunk 120 optimal weight: 0.8980 chunk 395 optimal weight: 3.9990 chunk 440 optimal weight: 2.9990 chunk 269 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... HA 161 ASN HA 200 GLN ** HA 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 383 ASN HC 31 ASN ** HH 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HI 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HJ 416 GLN HJ 419 ASN ** HL 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HL 49 GLN HM 212 GLN HM 400 GLN ** HQ 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.184016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.155383 restraints weight = 63272.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.159529 restraints weight = 38021.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.160408 restraints weight = 20765.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.160500 restraints weight = 20363.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.160771 restraints weight = 17384.923| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 42419 Z= 0.158 Angle : 0.663 13.923 58628 Z= 0.334 Chirality : 0.041 0.333 6660 Planarity : 0.005 0.097 6558 Dihedral : 18.045 179.612 9203 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.54 % Favored : 92.41 % Rotamer: Outliers : 3.87 % Allowed : 23.72 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.13), residues: 4268 helix: 0.12 (0.12), residues: 1841 sheet: -1.69 (0.37), residues: 189 loop : -2.22 (0.12), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARGHQ 311 TYR 0.032 0.002 TYRHH 18 PHE 0.029 0.002 PHEHH 35 TRP 0.021 0.002 TRPHO 6 HIS 0.012 0.001 HISHQ 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (42419) covalent geometry : angle 0.66306 / 0.33 (58628) hydrogen bonds : bond 0.05120 / 3.35 ( 1057) hydrogen bonds : angle 4.35759 / 3.07 ( 2968) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1089 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: HA 10 ARG cc_start: 0.7226 (ptm160) cc_final: 0.6297 (mmm160) REVERT: HA 16 ARG cc_start: 0.6369 (OUTLIER) cc_final: 0.5971 (tmm-80) REVERT: HA 28 GLU cc_start: 0.4984 (pm20) cc_final: 0.3950 (pm20) REVERT: HA 46 MET cc_start: 0.3280 (ttm) cc_final: 0.2806 (pmm) REVERT: HA 56 MET cc_start: 0.7223 (mpp) cc_final: 0.6848 (mpp) REVERT: HA 172 TRP cc_start: 0.7182 (m100) cc_final: 0.6093 (m100) REVERT: HA 174 VAL cc_start: 0.7778 (t) cc_final: 0.7510 (m) REVERT: HA 199 ILE cc_start: 0.7466 (pt) cc_final: 0.6836 (mt) REVERT: HA 205 GLN cc_start: 0.7238 (tt0) cc_final: 0.6991 (mt0) REVERT: HA 301 TRP cc_start: 0.8089 (m100) cc_final: 0.7648 (m100) REVERT: HA 313 MET cc_start: 0.5155 (ttm) cc_final: 0.4666 (ttm) REVERT: HA 325 GLU cc_start: 0.6504 (pt0) cc_final: 0.4070 (mt-10) REVERT: HA 339 GLN cc_start: 0.7356 (tt0) cc_final: 0.6675 (tt0) REVERT: HA 351 GLN cc_start: 0.5905 (pp30) cc_final: 0.5595 (pp30) REVERT: HA 399 ARG cc_start: 0.7470 (mtm180) cc_final: 0.7267 (mtm-85) REVERT: HA 402 ASP cc_start: 0.6727 (t70) cc_final: 0.5188 (t70) REVERT: HA 405 GLN cc_start: 0.6566 (mp10) cc_final: 0.5860 (mp10) REVERT: HA 426 ARG cc_start: 0.5956 (ptt-90) cc_final: 0.2857 (ptt-90) REVERT: HA 437 ILE cc_start: 0.7734 (mm) cc_final: 0.7433 (mm) REVERT: HA 466 ARG cc_start: 0.6932 (mpt180) cc_final: 0.6264 (mmt-90) REVERT: HB 51 ARG cc_start: 0.7943 (tmt90) cc_final: 0.7549 (ttt180) REVERT: HB 82 PHE cc_start: 0.7989 (t80) cc_final: 0.7658 (t80) REVERT: HB 109 ARG cc_start: 0.7718 (ttt180) cc_final: 0.7332 (ttt-90) REVERT: HB 148 MET cc_start: 0.7012 (mtm) cc_final: 0.6736 (mtp) REVERT: HB 153 MET cc_start: 0.7279 (tpp) cc_final: 0.6675 (tpp) REVERT: HC 2 LEU cc_start: 0.7442 (tt) cc_final: 0.7058 (tp) REVERT: HC 205 ILE cc_start: 0.8418 (mm) cc_final: 0.8081 (mm) REVERT: HD 18 ASP cc_start: 0.7976 (t70) cc_final: 0.7700 (t0) REVERT: HD 20 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7730 (tp) REVERT: HD 40 GLN cc_start: 0.7178 (mt0) cc_final: 0.6864 (mt0) REVERT: HD 41 ASN cc_start: 0.7606 (m-40) cc_final: 0.7182 (m-40) REVERT: HD 95 TYR cc_start: 0.8435 (m-80) cc_final: 0.7724 (m-80) REVERT: HE 154 MET cc_start: 0.7510 (tpp) cc_final: 0.7278 (tpp) REVERT: HE 162 CYS cc_start: 0.7719 (m) cc_final: 0.7336 (t) REVERT: HF 61 ARG cc_start: 0.7446 (ttm110) cc_final: 0.7188 (ttp80) REVERT: HF 63 ASP cc_start: 0.6806 (m-30) cc_final: 0.6482 (t0) REVERT: HF 86 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7905 (ttmm) REVERT: HF 108 THR cc_start: 0.7891 (m) cc_final: 0.7572 (t) REVERT: HF 141 ILE cc_start: 0.7936 (pt) cc_final: 0.7683 (pt) REVERT: HF 204 ASP cc_start: 0.6931 (t0) cc_final: 0.6672 (m-30) REVERT: HF 232 MET cc_start: 0.7264 (ttt) cc_final: 0.7051 (ttp) REVERT: HF 240 GLU cc_start: 0.6515 (tt0) cc_final: 0.6287 (tt0) REVERT: HF 266 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6545 (mm-30) REVERT: HF 297 TRP cc_start: 0.7804 (OUTLIER) cc_final: 0.7599 (m100) REVERT: HG 88 LYS cc_start: 0.7799 (mttt) cc_final: 0.7438 (mttt) REVERT: HH 59 GLU cc_start: 0.7390 (tp30) cc_final: 0.7138 (mm-30) REVERT: HH 60 MET cc_start: 0.6563 (ttp) cc_final: 0.6104 (mmp) REVERT: HH 74 ASP cc_start: 0.7603 (t0) cc_final: 0.7355 (t0) REVERT: HI 32 GLU cc_start: 0.7167 (tp30) cc_final: 0.6730 (tp30) REVERT: HI 42 MET cc_start: 0.8612 (mmm) cc_final: 0.8267 (mmm) REVERT: HI 125 GLN cc_start: 0.6366 (tm-30) cc_final: 0.5964 (pp30) REVERT: HI 129 LYS cc_start: 0.7313 (mttt) cc_final: 0.7071 (mttt) REVERT: HJ 167 ARG cc_start: 0.8521 (mtm-85) cc_final: 0.7978 (mtp85) REVERT: HJ 177 ASP cc_start: 0.6526 (t0) cc_final: 0.6226 (t0) REVERT: HJ 202 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6540 (mm-30) REVERT: HJ 244 SER cc_start: 0.8069 (OUTLIER) cc_final: 0.7551 (t) REVERT: HJ 272 LEU cc_start: 0.6926 (mp) cc_final: 0.6672 (mp) REVERT: HJ 277 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6178 (tt) REVERT: HJ 281 PHE cc_start: 0.5674 (p90) cc_final: 0.4814 (p90) REVERT: HJ 296 ARG cc_start: 0.6634 (mtt-85) cc_final: 0.6265 (mtt-85) REVERT: HJ 300 ARG cc_start: 0.6968 (mtm180) cc_final: 0.6678 (mtm180) REVERT: HJ 326 GLU cc_start: 0.6199 (tp30) cc_final: 0.5921 (tp30) REVERT: HJ 331 ASN cc_start: 0.7627 (m-40) cc_final: 0.7290 (m-40) REVERT: HJ 374 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7463 (tm-30) REVERT: HJ 393 ARG cc_start: 0.7574 (ttp80) cc_final: 0.6684 (ttp80) REVERT: HJ 394 ARG cc_start: 0.6964 (ttp-170) cc_final: 0.6200 (ptm-80) REVERT: HJ 399 PHE cc_start: 0.7416 (m-80) cc_final: 0.7111 (m-80) REVERT: HJ 425 ASP cc_start: 0.6158 (t70) cc_final: 0.5877 (t0) REVERT: HJ 467 LYS cc_start: 0.7162 (tptt) cc_final: 0.6866 (tptt) REVERT: HK 34 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7247 (ttmt) REVERT: HK 77 ARG cc_start: 0.3695 (tpt170) cc_final: 0.3169 (tpt170) REVERT: HK 103 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6430 (mm-30) REVERT: HL 38 GLN cc_start: 0.6918 (pp30) cc_final: 0.6479 (pt0) REVERT: HM 21 ARG cc_start: 0.6691 (ptp-110) cc_final: 0.6033 (mtp-110) REVERT: HM 77 PHE cc_start: 0.6087 (m-80) cc_final: 0.5830 (m-80) REVERT: HM 95 LEU cc_start: 0.8307 (tp) cc_final: 0.8079 (tp) REVERT: HM 137 TYR cc_start: 0.7274 (p90) cc_final: 0.6852 (p90) REVERT: HM 144 LEU cc_start: 0.7400 (tt) cc_final: 0.7136 (tp) REVERT: HM 203 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6658 (tm-30) REVERT: HM 205 LEU cc_start: 0.6751 (tp) cc_final: 0.6467 (tt) REVERT: HM 272 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6449 (mm-40) REVERT: HM 310 THR cc_start: 0.7617 (t) cc_final: 0.7333 (p) REVERT: HM 353 GLN cc_start: 0.6351 (mt0) cc_final: 0.5906 (tt0) REVERT: HM 361 VAL cc_start: 0.7822 (m) cc_final: 0.7568 (p) REVERT: HM 363 PHE cc_start: 0.6778 (t80) cc_final: 0.6542 (t80) REVERT: HM 581 GLN cc_start: 0.7246 (mm-40) cc_final: 0.6856 (mm-40) REVERT: HN 3 ASN cc_start: 0.7685 (p0) cc_final: 0.7421 (p0) REVERT: HN 6 ASN cc_start: 0.7124 (m-40) cc_final: 0.6892 (m110) REVERT: HO 5 ARG cc_start: 0.7030 (ptp-170) cc_final: 0.6774 (ptt180) REVERT: HO 14 ARG cc_start: 0.6705 (ttp80) cc_final: 0.6031 (ttt180) REVERT: HO 129 PHE cc_start: 0.6025 (m-80) cc_final: 0.5439 (m-80) REVERT: HP 69 LEU cc_start: 0.7297 (tp) cc_final: 0.7075 (tp) REVERT: HQ 32 ARG cc_start: 0.6885 (ptp-110) cc_final: 0.6563 (ptp90) REVERT: HQ 113 LYS cc_start: 0.8039 (tmtm) cc_final: 0.7735 (tmtm) REVERT: HQ 178 TRP cc_start: 0.8304 (t60) cc_final: 0.7711 (t-100) REVERT: HQ 179 ASN cc_start: 0.7384 (m-40) cc_final: 0.7054 (m-40) REVERT: HQ 186 LYS cc_start: 0.7464 (mtmm) cc_final: 0.7188 (mtmm) REVERT: HQ 232 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.7094 (ttmm) REVERT: HQ 252 LEU cc_start: 0.7978 (tp) cc_final: 0.7663 (tp) REVERT: HQ 261 LYS cc_start: 0.6846 (ttmm) cc_final: 0.6376 (ttmm) REVERT: HQ 311 ARG cc_start: 0.5833 (ttp80) cc_final: 0.5400 (ttp80) REVERT: HQ 325 ARG cc_start: 0.7385 (ptm160) cc_final: 0.7092 (ttt180) REVERT: HQ 326 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7549 (mm-40) REVERT: HQ 411 THR cc_start: 0.6918 (m) cc_final: 0.6361 (p) REVERT: HQ 431 PHE cc_start: 0.5281 (m-80) cc_final: 0.4987 (m-80) REVERT: HQ 465 ARG cc_start: 0.6722 (ttp80) cc_final: 0.6312 (tpp80) REVERT: HQ 530 ASP cc_start: 0.6587 (p0) cc_final: 0.6098 (p0) REVERT: HQ 630 GLN cc_start: 0.7484 (tm130) cc_final: 0.6973 (tm130) REVERT: HQ 631 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6982 (tt) REVERT: HQ 685 PHE cc_start: 0.6354 (OUTLIER) cc_final: 0.5512 (t80) REVERT: HQ 693 ARG cc_start: 0.7596 (ttm110) cc_final: 0.6962 (mmm-85) REVERT: HQ 707 LYS cc_start: 0.7928 (tttt) cc_final: 0.7639 (ttpt) REVERT: HQ 731 ARG cc_start: 0.6760 (ptt90) cc_final: 0.6263 (ptt90) REVERT: HQ 734 GLU cc_start: 0.7107 (pt0) cc_final: 0.6701 (pm20) REVERT: HQ 738 ARG cc_start: 0.6657 (ttp80) cc_final: 0.6371 (ttp80) REVERT: HR 28 ASP cc_start: 0.7862 (t0) cc_final: 0.7580 (t0) REVERT: HR 29 GLN cc_start: 0.6555 (tm-30) cc_final: 0.6193 (tp40) REVERT: HR 114 PHE cc_start: 0.8128 (t80) cc_final: 0.7347 (t80) REVERT: HR 124 THR cc_start: 0.7406 (m) cc_final: 0.7145 (p) REVERT: HR 156 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7080 (tm-30) REVERT: HR 168 ARG cc_start: 0.6790 (ttt-90) cc_final: 0.6550 (ttt-90) REVERT: HS 142 GLN cc_start: 0.7401 (mt0) cc_final: 0.7198 (mt0) REVERT: HS 153 ARG cc_start: 0.7431 (tpt90) cc_final: 0.7148 (mmm160) REVERT: HS 166 VAL cc_start: 0.8820 (t) cc_final: 0.8240 (p) REVERT: HS 190 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.6412 (mtm180) REVERT: HT 26 VAL cc_start: 0.7696 (t) cc_final: 0.7306 (m) REVERT: HT 36 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6472 (t80) REVERT: HT 45 GLN cc_start: 0.7879 (mp10) cc_final: 0.7515 (mp10) REVERT: HT 50 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6341 (mt) REVERT: HT 57 LYS cc_start: 0.7554 (mttt) cc_final: 0.7154 (ttmm) REVERT: HT 68 ASP cc_start: 0.6539 (t0) cc_final: 0.6306 (t0) REVERT: HT 92 THR cc_start: 0.7353 (OUTLIER) cc_final: 0.6926 (p) REVERT: HT 113 GLN cc_start: 0.7183 (mt0) cc_final: 0.6856 (mt0) REVERT: HT 118 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7506 (mmmt) REVERT: HT 362 ASP cc_start: 0.7394 (t0) cc_final: 0.6999 (t70) outliers start: 144 outliers final: 110 residues processed: 1147 average time/residue: 0.2935 time to fit residues: 516.6927 Evaluate side-chains 1192 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1069 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 16 ARG Chi-restraints excluded: chain HA residue 17 LEU Chi-restraints excluded: chain HA residue 146 PHE Chi-restraints excluded: chain HA residue 208 LEU Chi-restraints excluded: chain HA residue 239 ARG Chi-restraints excluded: chain HA residue 410 LEU Chi-restraints excluded: chain HB residue 47 VAL Chi-restraints excluded: chain HB residue 53 THR Chi-restraints excluded: chain HB residue 77 VAL Chi-restraints excluded: chain HC residue 10 LEU Chi-restraints excluded: chain HC residue 42 SER Chi-restraints excluded: chain HC residue 46 SER Chi-restraints excluded: chain HC residue 57 SER Chi-restraints excluded: chain HC residue 100 TYR Chi-restraints excluded: chain HC residue 149 LEU Chi-restraints excluded: chain HC residue 194 LEU Chi-restraints excluded: chain HD residue 1 LEU Chi-restraints excluded: chain HD residue 20 LEU Chi-restraints excluded: chain HD residue 42 LEU Chi-restraints excluded: chain HD residue 84 LEU Chi-restraints excluded: chain HE residue 27 SER Chi-restraints excluded: chain HE residue 108 SER Chi-restraints excluded: chain HE residue 110 LEU Chi-restraints excluded: chain HE residue 127 LEU Chi-restraints excluded: chain HE residue 163 VAL Chi-restraints excluded: chain HE residue 176 GLU Chi-restraints excluded: chain HF residue 102 CYS Chi-restraints excluded: chain HF residue 135 LEU Chi-restraints excluded: chain HF residue 197 LEU Chi-restraints excluded: chain HF residue 219 GLU Chi-restraints excluded: chain HF residue 226 VAL Chi-restraints excluded: chain HF residue 230 ILE Chi-restraints excluded: chain HF residue 297 TRP Chi-restraints excluded: chain HF residue 322 MET Chi-restraints excluded: chain HG residue 18 LEU Chi-restraints excluded: chain HG residue 58 THR Chi-restraints excluded: chain HG residue 70 LEU Chi-restraints excluded: chain HG residue 74 THR Chi-restraints excluded: chain HH residue 22 VAL Chi-restraints excluded: chain HH residue 54 VAL Chi-restraints excluded: chain HI residue 11 THR Chi-restraints excluded: chain HI residue 66 LEU Chi-restraints excluded: chain HI residue 83 PHE Chi-restraints excluded: chain HI residue 132 VAL Chi-restraints excluded: chain HJ residue 165 LEU Chi-restraints excluded: chain HJ residue 171 LEU Chi-restraints excluded: chain HJ residue 238 LEU Chi-restraints excluded: chain HJ residue 244 SER Chi-restraints excluded: chain HJ residue 277 LEU Chi-restraints excluded: chain HJ residue 411 ASP Chi-restraints excluded: chain HJ residue 413 VAL Chi-restraints excluded: chain HJ residue 435 MET Chi-restraints excluded: chain HJ residue 459 LEU Chi-restraints excluded: chain HK residue 34 LYS Chi-restraints excluded: chain HK residue 40 ARG Chi-restraints excluded: chain HK residue 47 TYR Chi-restraints excluded: chain HK residue 98 VAL Chi-restraints excluded: chain HL residue 42 ILE Chi-restraints excluded: chain HL residue 62 VAL Chi-restraints excluded: chain HL residue 75 GLN Chi-restraints excluded: chain HL residue 80 VAL Chi-restraints excluded: chain HM residue 140 ASP Chi-restraints excluded: chain HM residue 198 LEU Chi-restraints excluded: chain HM residue 267 THR Chi-restraints excluded: chain HM residue 362 LEU Chi-restraints excluded: chain HM residue 394 LEU Chi-restraints excluded: chain HM residue 412 LEU Chi-restraints excluded: chain HM residue 418 LEU Chi-restraints excluded: chain HO residue 17 VAL Chi-restraints excluded: chain HO residue 62 ARG Chi-restraints excluded: chain HO residue 96 LEU Chi-restraints excluded: chain HO residue 112 MET Chi-restraints excluded: chain HO residue 115 VAL Chi-restraints excluded: chain HO residue 166 THR Chi-restraints excluded: chain HP residue 35 GLU Chi-restraints excluded: chain HP residue 40 VAL Chi-restraints excluded: chain HP residue 57 THR Chi-restraints excluded: chain HP residue 62 THR Chi-restraints excluded: chain HP residue 172 VAL Chi-restraints excluded: chain HP residue 197 GLU Chi-restraints excluded: chain HP residue 213 THR Chi-restraints excluded: chain HP residue 245 LYS Chi-restraints excluded: chain HQ residue 124 VAL Chi-restraints excluded: chain HQ residue 126 LEU Chi-restraints excluded: chain HQ residue 187 GLU Chi-restraints excluded: chain HQ residue 192 HIS Chi-restraints excluded: chain HQ residue 202 MET Chi-restraints excluded: chain HQ residue 223 SER Chi-restraints excluded: chain HQ residue 232 LYS Chi-restraints excluded: chain HQ residue 238 ILE Chi-restraints excluded: chain HQ residue 253 ILE Chi-restraints excluded: chain HQ residue 316 THR Chi-restraints excluded: chain HQ residue 353 LEU Chi-restraints excluded: chain HQ residue 409 SER Chi-restraints excluded: chain HQ residue 421 VAL Chi-restraints excluded: chain HQ residue 535 LEU Chi-restraints excluded: chain HQ residue 586 VAL Chi-restraints excluded: chain HQ residue 626 GLU Chi-restraints excluded: chain HQ residue 631 LEU Chi-restraints excluded: chain HQ residue 685 PHE Chi-restraints excluded: chain HQ residue 710 ILE Chi-restraints excluded: chain HQ residue 723 VAL Chi-restraints excluded: chain HR residue 6 TRP Chi-restraints excluded: chain HR residue 13 THR Chi-restraints excluded: chain HR residue 17 LEU Chi-restraints excluded: chain HR residue 21 SER Chi-restraints excluded: chain HR residue 36 CYS Chi-restraints excluded: chain HR residue 96 LEU Chi-restraints excluded: chain HR residue 125 TRP Chi-restraints excluded: chain HR residue 126 ASN Chi-restraints excluded: chain HS residue 83 VAL Chi-restraints excluded: chain HS residue 102 LEU Chi-restraints excluded: chain HS residue 117 LEU Chi-restraints excluded: chain HS residue 130 VAL Chi-restraints excluded: chain HS residue 156 GLU Chi-restraints excluded: chain HS residue 190 ARG Chi-restraints excluded: chain HT residue 36 TYR Chi-restraints excluded: chain HT residue 47 VAL Chi-restraints excluded: chain HT residue 50 LEU Chi-restraints excluded: chain HT residue 89 VAL Chi-restraints excluded: chain HT residue 92 THR Chi-restraints excluded: chain HT residue 361 PHE Chi-restraints excluded: chain HT residue 378 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 125 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 285 optimal weight: 0.5980 chunk 393 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 350 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 213 optimal weight: 0.6980 chunk 353 optimal weight: 0.7980 chunk 226 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** HA 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 383 ASN HB 139 GLN HC 31 ASN ** HI 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HJ 419 ASN HJ 456 GLN ** HL 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HM 121 HIS ** HM 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HP 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HQ 345 HIS ** HQ 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HQ 715 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.183411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154365 restraints weight = 63254.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.159105 restraints weight = 38996.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.158784 restraints weight = 21855.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.159081 restraints weight = 21356.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.159280 restraints weight = 18893.579| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42419 Z= 0.152 Angle : 0.660 13.843 58628 Z= 0.334 Chirality : 0.041 0.235 6660 Planarity : 0.005 0.075 6558 Dihedral : 18.064 179.179 9203 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.69 % Favored : 92.29 % Rotamer: Outliers : 3.71 % Allowed : 24.26 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.13), residues: 4268 helix: 0.17 (0.12), residues: 1830 sheet: -1.55 (0.38), residues: 185 loop : -2.22 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGHP 242 TYR 0.028 0.002 TYRHH 18 PHE 0.034 0.001 PHEHH 35 TRP 0.028 0.002 TRPHB 30 HIS 0.009 0.001 HISHR 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (42419) covalent geometry : angle 0.66044 / 0.33 (58628) hydrogen bonds : bond 0.04970 / 3.25 ( 1057) hydrogen bonds : angle 4.35877 / 3.08 ( 2968) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 1079 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: HA 10 ARG cc_start: 0.7185 (ptm160) cc_final: 0.6187 (mmm160) REVERT: HA 16 ARG cc_start: 0.6375 (OUTLIER) cc_final: 0.5950 (tmm-80) REVERT: HA 46 MET cc_start: 0.3318 (ttm) cc_final: 0.2836 (pmm) REVERT: HA 56 MET cc_start: 0.7149 (mpp) cc_final: 0.6902 (mpp) REVERT: HA 172 TRP cc_start: 0.7263 (m100) cc_final: 0.6183 (m100) REVERT: HA 174 VAL cc_start: 0.7774 (t) cc_final: 0.7516 (m) REVERT: HA 185 ARG cc_start: 0.7327 (mtp85) cc_final: 0.7052 (mtp85) REVERT: HA 301 TRP cc_start: 0.8077 (m100) cc_final: 0.7651 (m100) REVERT: HA 313 MET cc_start: 0.5195 (ttm) cc_final: 0.4724 (ttm) REVERT: HA 339 GLN cc_start: 0.7344 (tt0) cc_final: 0.6652 (tt0) REVERT: HA 347 GLN cc_start: 0.7901 (tp40) cc_final: 0.7567 (tp40) REVERT: HA 351 GLN cc_start: 0.5988 (pp30) cc_final: 0.5707 (pp30) REVERT: HA 399 ARG cc_start: 0.7451 (mtm180) cc_final: 0.7173 (mtm-85) REVERT: HA 402 ASP cc_start: 0.6545 (t70) cc_final: 0.6222 (t70) REVERT: HA 426 ARG cc_start: 0.6134 (OUTLIER) cc_final: 0.3002 (ptt-90) REVERT: HA 433 ARG cc_start: 0.6419 (mtt180) cc_final: 0.6085 (mtt90) REVERT: HA 435 GLU cc_start: 0.6065 (pm20) cc_final: 0.5780 (pm20) REVERT: HA 466 ARG cc_start: 0.6933 (mpt180) cc_final: 0.6288 (mmt-90) REVERT: HB 51 ARG cc_start: 0.7918 (tmt90) cc_final: 0.7519 (ttt180) REVERT: HB 82 PHE cc_start: 0.7936 (t80) cc_final: 0.7629 (t80) REVERT: HB 109 ARG cc_start: 0.7706 (ttt180) cc_final: 0.7326 (ttt-90) REVERT: HB 148 MET cc_start: 0.7025 (mtm) cc_final: 0.6741 (mtt) REVERT: HB 153 MET cc_start: 0.7273 (tpp) cc_final: 0.6647 (tpp) REVERT: HC 2 LEU cc_start: 0.7466 (tt) cc_final: 0.7136 (tp) REVERT: HC 205 ILE cc_start: 0.8417 (mm) cc_final: 0.8096 (mm) REVERT: HD 18 ASP cc_start: 0.8009 (t70) cc_final: 0.7692 (t0) REVERT: HD 20 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7724 (tp) REVERT: HD 40 GLN cc_start: 0.7222 (mt0) cc_final: 0.6887 (mt0) REVERT: HE 154 MET cc_start: 0.7505 (tpp) cc_final: 0.7277 (tpp) REVERT: HE 162 CYS cc_start: 0.7735 (m) cc_final: 0.7361 (t) REVERT: HF 63 ASP cc_start: 0.6800 (m-30) cc_final: 0.6532 (t0) REVERT: HF 108 THR cc_start: 0.7884 (m) cc_final: 0.7563 (t) REVERT: HF 141 ILE cc_start: 0.7951 (pt) cc_final: 0.7694 (pt) REVERT: HF 204 ASP cc_start: 0.7009 (t0) cc_final: 0.6730 (m-30) REVERT: HF 232 MET cc_start: 0.7285 (ttt) cc_final: 0.7060 (ttp) REVERT: HF 266 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6579 (mm-30) REVERT: HF 295 GLU cc_start: 0.6606 (tt0) cc_final: 0.6280 (pt0) REVERT: HF 307 GLU cc_start: 0.6912 (tt0) cc_final: 0.6501 (tt0) REVERT: HG 88 LYS cc_start: 0.7763 (mttt) cc_final: 0.7347 (mttt) REVERT: HH 16 GLU cc_start: 0.6855 (pt0) cc_final: 0.6630 (pt0) REVERT: HH 59 GLU cc_start: 0.7088 (tp30) cc_final: 0.6801 (mm-30) REVERT: HH 60 MET cc_start: 0.6585 (ttp) cc_final: 0.6098 (mmp) REVERT: HI 32 GLU cc_start: 0.7185 (tp30) cc_final: 0.6767 (tp30) REVERT: HI 42 MET cc_start: 0.8570 (mmm) cc_final: 0.8261 (mmm) REVERT: HI 51 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5888 (mmp) REVERT: HI 109 LYS cc_start: 0.7430 (mmtm) cc_final: 0.6849 (mmtm) REVERT: HI 125 GLN cc_start: 0.6383 (tm-30) cc_final: 0.5954 (pp30) REVERT: HI 129 LYS cc_start: 0.7296 (mttt) cc_final: 0.7063 (mttt) REVERT: HJ 153 GLU cc_start: 0.6848 (mp0) cc_final: 0.6643 (mp0) REVERT: HJ 167 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.7960 (mtp85) REVERT: HJ 177 ASP cc_start: 0.6489 (t0) cc_final: 0.6197 (t0) REVERT: HJ 202 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6576 (mm-30) REVERT: HJ 244 SER cc_start: 0.8073 (m) cc_final: 0.7584 (t) REVERT: HJ 272 LEU cc_start: 0.6917 (mp) cc_final: 0.6707 (mp) REVERT: HJ 277 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6330 (tt) REVERT: HJ 281 PHE cc_start: 0.5818 (p90) cc_final: 0.4969 (p90) REVERT: HJ 296 ARG cc_start: 0.6659 (mtt-85) cc_final: 0.6282 (mtt-85) REVERT: HJ 300 ARG cc_start: 0.7064 (mtm180) cc_final: 0.6769 (mtm180) REVERT: HJ 326 GLU cc_start: 0.6214 (tp30) cc_final: 0.5933 (tp30) REVERT: HJ 331 ASN cc_start: 0.7608 (m-40) cc_final: 0.7261 (m-40) REVERT: HJ 374 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7681 (tm-30) REVERT: HJ 393 ARG cc_start: 0.7543 (ttp80) cc_final: 0.6669 (ttp80) REVERT: HJ 399 PHE cc_start: 0.7444 (m-80) cc_final: 0.7048 (m-80) REVERT: HJ 425 ASP cc_start: 0.6143 (t70) cc_final: 0.5893 (t0) REVERT: HJ 433 MET cc_start: 0.8251 (mmt) cc_final: 0.7743 (mmt) REVERT: HJ 467 LYS cc_start: 0.7165 (tptt) cc_final: 0.6883 (tptt) REVERT: HJ 557 GLU cc_start: 0.6925 (tp30) cc_final: 0.6613 (tp30) REVERT: HK 34 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7260 (ttmt) REVERT: HK 77 ARG cc_start: 0.3764 (tpt170) cc_final: 0.3394 (tpt170) REVERT: HK 103 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6458 (mm-30) REVERT: HL 38 GLN cc_start: 0.6862 (pp30) cc_final: 0.6498 (pt0) REVERT: HM 21 ARG cc_start: 0.6664 (ptp-110) cc_final: 0.6107 (mtp-110) REVERT: HM 95 LEU cc_start: 0.8288 (tp) cc_final: 0.8061 (tp) REVERT: HM 144 LEU cc_start: 0.7412 (tt) cc_final: 0.7151 (tp) REVERT: HM 203 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6690 (tm-30) REVERT: HM 205 LEU cc_start: 0.6736 (tp) cc_final: 0.6501 (tt) REVERT: HM 310 THR cc_start: 0.7666 (t) cc_final: 0.7395 (p) REVERT: HM 353 GLN cc_start: 0.6368 (mt0) cc_final: 0.6014 (tt0) REVERT: HM 361 VAL cc_start: 0.7831 (m) cc_final: 0.7598 (p) REVERT: HM 363 PHE cc_start: 0.6611 (t80) cc_final: 0.6378 (t80) REVERT: HM 581 GLN cc_start: 0.7496 (mm-40) cc_final: 0.7206 (mm-40) REVERT: HN 2 MET cc_start: 0.5773 (mmm) cc_final: 0.4810 (mmm) REVERT: HN 3 ASN cc_start: 0.7573 (p0) cc_final: 0.7270 (p0) REVERT: HN 6 ASN cc_start: 0.7136 (m-40) cc_final: 0.6856 (m110) REVERT: HO 14 ARG cc_start: 0.6741 (ttp80) cc_final: 0.6074 (ttt180) REVERT: HO 129 PHE cc_start: 0.6018 (m-80) cc_final: 0.5459 (m-80) REVERT: HP 69 LEU cc_start: 0.7310 (tp) cc_final: 0.7107 (tp) REVERT: HP 71 ARG cc_start: 0.7126 (mmm-85) cc_final: 0.6906 (mmm-85) REVERT: HP 243 GLU cc_start: 0.6391 (mp0) cc_final: 0.6187 (mp0) REVERT: HQ 17 LYS cc_start: 0.6032 (mmtm) cc_final: 0.5763 (mmtm) REVERT: HQ 32 ARG cc_start: 0.6979 (ptp-110) cc_final: 0.6658 (ptp90) REVERT: HQ 179 ASN cc_start: 0.7386 (m-40) cc_final: 0.7095 (m-40) REVERT: HQ 186 LYS cc_start: 0.7534 (mtmm) cc_final: 0.7260 (mtmm) REVERT: HQ 209 ASP cc_start: 0.7424 (m-30) cc_final: 0.5239 (t0) REVERT: HQ 216 LEU cc_start: 0.8322 (mt) cc_final: 0.8118 (mt) REVERT: HQ 232 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.7120 (ttmm) REVERT: HQ 249 PHE cc_start: 0.6327 (t80) cc_final: 0.6065 (t80) REVERT: HQ 252 LEU cc_start: 0.7977 (tp) cc_final: 0.7633 (tp) REVERT: HQ 253 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7791 (mm) REVERT: HQ 261 LYS cc_start: 0.6830 (ttmm) cc_final: 0.6416 (ttmm) REVERT: HQ 312 ARG cc_start: 0.6458 (ptp90) cc_final: 0.5522 (ptp90) REVERT: HQ 371 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6391 (mp0) REVERT: HQ 411 THR cc_start: 0.6947 (m) cc_final: 0.6365 (p) REVERT: HQ 431 PHE cc_start: 0.5197 (m-80) cc_final: 0.4917 (m-80) REVERT: HQ 465 ARG cc_start: 0.6745 (ttp80) cc_final: 0.6333 (tpp80) REVERT: HQ 531 PHE cc_start: 0.7180 (t80) cc_final: 0.6900 (t80) REVERT: HQ 630 GLN cc_start: 0.7497 (tm130) cc_final: 0.6973 (tm130) REVERT: HQ 631 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6996 (tt) REVERT: HQ 685 PHE cc_start: 0.6373 (OUTLIER) cc_final: 0.5504 (t80) REVERT: HQ 693 ARG cc_start: 0.7607 (ttm110) cc_final: 0.6963 (mmm-85) REVERT: HQ 707 LYS cc_start: 0.7895 (tttt) cc_final: 0.7610 (ttpt) REVERT: HQ 731 ARG cc_start: 0.6838 (ptt90) cc_final: 0.6567 (ptt90) REVERT: HQ 738 ARG cc_start: 0.6661 (ttp80) cc_final: 0.6352 (ttp80) REVERT: HR 28 ASP cc_start: 0.7825 (t0) cc_final: 0.7402 (t0) REVERT: HR 29 GLN cc_start: 0.6535 (tm-30) cc_final: 0.6252 (tp40) REVERT: HR 33 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7320 (mtm180) REVERT: HR 114 PHE cc_start: 0.8156 (t80) cc_final: 0.7367 (t80) REVERT: HR 124 THR cc_start: 0.7516 (m) cc_final: 0.7240 (p) REVERT: HR 156 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7050 (tm-30) REVERT: HS 131 LYS cc_start: 0.7777 (tptt) cc_final: 0.7550 (tptt) REVERT: HS 153 ARG cc_start: 0.7428 (tpt90) cc_final: 0.7187 (mmm160) REVERT: HS 166 VAL cc_start: 0.8821 (t) cc_final: 0.8274 (p) REVERT: HS 187 ASN cc_start: 0.6748 (t0) cc_final: 0.6468 (t0) REVERT: HT 26 VAL cc_start: 0.7634 (t) cc_final: 0.7329 (m) REVERT: HT 36 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6505 (t80) REVERT: HT 45 GLN cc_start: 0.7894 (mp10) cc_final: 0.7529 (mp10) REVERT: HT 50 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6451 (mt) REVERT: HT 57 LYS cc_start: 0.7527 (mttt) cc_final: 0.7159 (ttmm) REVERT: HT 68 ASP cc_start: 0.6566 (t0) cc_final: 0.6318 (t0) REVERT: HT 92 THR cc_start: 0.7309 (OUTLIER) cc_final: 0.6880 (p) REVERT: HT 105 ARG cc_start: 0.7344 (ttp80) cc_final: 0.6998 (ttp-110) REVERT: HT 113 GLN cc_start: 0.7241 (mt0) cc_final: 0.6909 (mt0) REVERT: HT 118 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7549 (mmmt) outliers start: 138 outliers final: 110 residues processed: 1135 average time/residue: 0.2943 time to fit residues: 514.1111 Evaluate side-chains 1185 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1061 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 16 ARG Chi-restraints excluded: chain HA residue 17 LEU Chi-restraints excluded: chain HA residue 146 PHE Chi-restraints excluded: chain HA residue 208 LEU Chi-restraints excluded: chain HA residue 239 ARG Chi-restraints excluded: chain HA residue 338 THR Chi-restraints excluded: chain HA residue 410 LEU Chi-restraints excluded: chain HA residue 426 ARG Chi-restraints excluded: chain HA residue 470 ASP Chi-restraints excluded: chain HB residue 47 VAL Chi-restraints excluded: chain HB residue 53 THR Chi-restraints excluded: chain HB residue 77 VAL Chi-restraints excluded: chain HC residue 10 LEU Chi-restraints excluded: chain HC residue 42 SER Chi-restraints excluded: chain HC residue 46 SER Chi-restraints excluded: chain HC residue 57 SER Chi-restraints excluded: chain HC residue 100 TYR Chi-restraints excluded: chain HC residue 149 LEU Chi-restraints excluded: chain HC residue 194 LEU Chi-restraints excluded: chain HC residue 225 LYS Chi-restraints excluded: chain HD residue 20 LEU Chi-restraints excluded: chain HD residue 42 LEU Chi-restraints excluded: chain HD residue 84 LEU Chi-restraints excluded: chain HE residue 27 SER Chi-restraints excluded: chain HE residue 110 LEU Chi-restraints excluded: chain HE residue 127 LEU Chi-restraints excluded: chain HE residue 163 VAL Chi-restraints excluded: chain HE residue 176 GLU Chi-restraints excluded: chain HF residue 102 CYS Chi-restraints excluded: chain HF residue 135 LEU Chi-restraints excluded: chain HF residue 197 LEU Chi-restraints excluded: chain HF residue 226 VAL Chi-restraints excluded: chain HF residue 322 MET Chi-restraints excluded: chain HG residue 15 LEU Chi-restraints excluded: chain HG residue 18 LEU Chi-restraints excluded: chain HG residue 70 LEU Chi-restraints excluded: chain HG residue 74 THR Chi-restraints excluded: chain HH residue 22 VAL Chi-restraints excluded: chain HH residue 54 VAL Chi-restraints excluded: chain HH residue 68 PHE Chi-restraints excluded: chain HI residue 11 THR Chi-restraints excluded: chain HI residue 51 MET Chi-restraints excluded: chain HI residue 66 LEU Chi-restraints excluded: chain HI residue 83 PHE Chi-restraints excluded: chain HI residue 132 VAL Chi-restraints excluded: chain HJ residue 165 LEU Chi-restraints excluded: chain HJ residue 171 LEU Chi-restraints excluded: chain HJ residue 238 LEU Chi-restraints excluded: chain HJ residue 277 LEU Chi-restraints excluded: chain HJ residue 411 ASP Chi-restraints excluded: chain HJ residue 413 VAL Chi-restraints excluded: chain HJ residue 459 LEU Chi-restraints excluded: chain HK residue 34 LYS Chi-restraints excluded: chain HK residue 40 ARG Chi-restraints excluded: chain HK residue 98 VAL Chi-restraints excluded: chain HL residue 42 ILE Chi-restraints excluded: chain HL residue 62 VAL Chi-restraints excluded: chain HL residue 75 GLN Chi-restraints excluded: chain HL residue 80 VAL Chi-restraints excluded: chain HM residue 75 SER Chi-restraints excluded: chain HM residue 198 LEU Chi-restraints excluded: chain HM residue 267 THR Chi-restraints excluded: chain HM residue 362 LEU Chi-restraints excluded: chain HM residue 394 LEU Chi-restraints excluded: chain HM residue 412 LEU Chi-restraints excluded: chain HM residue 418 LEU Chi-restraints excluded: chain HM residue 591 LEU Chi-restraints excluded: chain HM residue 607 ILE Chi-restraints excluded: chain HO residue 17 VAL Chi-restraints excluded: chain HO residue 62 ARG Chi-restraints excluded: chain HO residue 96 LEU Chi-restraints excluded: chain HO residue 115 VAL Chi-restraints excluded: chain HO residue 166 THR Chi-restraints excluded: chain HP residue 40 VAL Chi-restraints excluded: chain HP residue 57 THR Chi-restraints excluded: chain HP residue 171 GLN Chi-restraints excluded: chain HP residue 172 VAL Chi-restraints excluded: chain HP residue 197 GLU Chi-restraints excluded: chain HP residue 213 THR Chi-restraints excluded: chain HQ residue 124 VAL Chi-restraints excluded: chain HQ residue 126 LEU Chi-restraints excluded: chain HQ residue 187 GLU Chi-restraints excluded: chain HQ residue 192 HIS Chi-restraints excluded: chain HQ residue 202 MET Chi-restraints excluded: chain HQ residue 223 SER Chi-restraints excluded: chain HQ residue 232 LYS Chi-restraints excluded: chain HQ residue 238 ILE Chi-restraints excluded: chain HQ residue 253 ILE Chi-restraints excluded: chain HQ residue 259 SER Chi-restraints excluded: chain HQ residue 345 HIS Chi-restraints excluded: chain HQ residue 353 LEU Chi-restraints excluded: chain HQ residue 409 SER Chi-restraints excluded: chain HQ residue 421 VAL Chi-restraints excluded: chain HQ residue 535 LEU Chi-restraints excluded: chain HQ residue 586 VAL Chi-restraints excluded: chain HQ residue 626 GLU Chi-restraints excluded: chain HQ residue 631 LEU Chi-restraints excluded: chain HQ residue 685 PHE Chi-restraints excluded: chain HQ residue 702 LEU Chi-restraints excluded: chain HQ residue 710 ILE Chi-restraints excluded: chain HQ residue 723 VAL Chi-restraints excluded: chain HR residue 6 TRP Chi-restraints excluded: chain HR residue 13 THR Chi-restraints excluded: chain HR residue 17 LEU Chi-restraints excluded: chain HR residue 21 SER Chi-restraints excluded: chain HR residue 33 ARG Chi-restraints excluded: chain HR residue 36 CYS Chi-restraints excluded: chain HR residue 96 LEU Chi-restraints excluded: chain HR residue 125 TRP Chi-restraints excluded: chain HR residue 126 ASN Chi-restraints excluded: chain HS residue 83 VAL Chi-restraints excluded: chain HS residue 102 LEU Chi-restraints excluded: chain HS residue 117 LEU Chi-restraints excluded: chain HS residue 130 VAL Chi-restraints excluded: chain HS residue 149 SER Chi-restraints excluded: chain HS residue 156 GLU Chi-restraints excluded: chain HT residue 21 MET Chi-restraints excluded: chain HT residue 36 TYR Chi-restraints excluded: chain HT residue 47 VAL Chi-restraints excluded: chain HT residue 50 LEU Chi-restraints excluded: chain HT residue 89 VAL Chi-restraints excluded: chain HT residue 92 THR Chi-restraints excluded: chain HT residue 361 PHE Chi-restraints excluded: chain HT residue 378 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 370 optimal weight: 0.0570 chunk 9 optimal weight: 0.6980 chunk 408 optimal weight: 0.5980 chunk 279 optimal weight: 0.8980 chunk 369 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 200 optimal weight: 0.0970 chunk 293 optimal weight: 0.0770 chunk 89 optimal weight: 1.9990 chunk 431 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... HA 200 GLN ** HA 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 383 ASN HC 31 ASN ** HH 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HI 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HJ 416 GLN HJ 419 ASN ** HL 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HL 49 GLN ** HM 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HM 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HP 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HP 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HQ 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HQ 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HR 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HT 299 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.184222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.155387 restraints weight = 62933.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.159809 restraints weight = 38719.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.159827 restraints weight = 21953.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.159999 restraints weight = 21386.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.160276 restraints weight = 18731.789| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42419 Z= 0.132 Angle : 0.656 14.642 58628 Z= 0.331 Chirality : 0.040 0.242 6660 Planarity : 0.005 0.102 6558 Dihedral : 18.031 179.173 9203 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.45 % Favored : 92.53 % Rotamer: Outliers : 3.14 % Allowed : 25.36 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.13), residues: 4268 helix: 0.26 (0.13), residues: 1817 sheet: -1.60 (0.37), residues: 189 loop : -2.19 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARGHQ 311 TYR 0.034 0.001 TYRHH 18 PHE 0.034 0.001 PHEHJ 560 TRP 0.049 0.002 TRPHF 297 HIS 0.035 0.001 HISHQ 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (42419) covalent geometry : angle 0.65554 / 0.33 (58628) hydrogen bonds : bond 0.04570 / 2.98 ( 1057) hydrogen bonds : angle 4.28472 / 3.02 ( 2968) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 1069 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: HA 10 ARG cc_start: 0.7301 (ptm160) cc_final: 0.6300 (mmm160) REVERT: HA 46 MET cc_start: 0.3466 (ttm) cc_final: 0.3022 (pmm) REVERT: HA 56 MET cc_start: 0.7151 (mpp) cc_final: 0.6902 (mpp) REVERT: HA 59 GLU cc_start: 0.7633 (tt0) cc_final: 0.7419 (tt0) REVERT: HA 172 TRP cc_start: 0.7150 (m100) cc_final: 0.6161 (m100) REVERT: HA 174 VAL cc_start: 0.7783 (t) cc_final: 0.7525 (m) REVERT: HA 182 ARG cc_start: 0.6945 (ptm-80) cc_final: 0.6578 (ptm-80) REVERT: HA 185 ARG cc_start: 0.7308 (mtp85) cc_final: 0.7069 (mtp85) REVERT: HA 301 TRP cc_start: 0.8022 (m100) cc_final: 0.7631 (m100) REVERT: HA 313 MET cc_start: 0.5177 (ttm) cc_final: 0.4690 (ttm) REVERT: HA 339 GLN cc_start: 0.7322 (tt0) cc_final: 0.6625 (tt0) REVERT: HA 347 GLN cc_start: 0.7935 (tp40) cc_final: 0.7604 (tp40) REVERT: HA 399 ARG cc_start: 0.7441 (mtm180) cc_final: 0.7197 (mtm-85) REVERT: HA 402 ASP cc_start: 0.6457 (t70) cc_final: 0.5989 (t70) REVERT: HA 405 GLN cc_start: 0.6906 (mp10) cc_final: 0.6687 (mp10) REVERT: HA 426 ARG cc_start: 0.5952 (OUTLIER) cc_final: 0.3106 (ptt-90) REVERT: HA 466 ARG cc_start: 0.6929 (mpt180) cc_final: 0.6390 (mmt-90) REVERT: HB 51 ARG cc_start: 0.7884 (tmt90) cc_final: 0.7457 (ttt180) REVERT: HB 82 PHE cc_start: 0.7962 (t80) cc_final: 0.7682 (t80) REVERT: HB 109 ARG cc_start: 0.7696 (ttt180) cc_final: 0.7341 (ttt-90) REVERT: HB 148 MET cc_start: 0.7006 (mtm) cc_final: 0.6725 (mtt) REVERT: HB 153 MET cc_start: 0.7292 (tpp) cc_final: 0.6667 (tpp) REVERT: HC 2 LEU cc_start: 0.7453 (tt) cc_final: 0.7139 (tp) REVERT: HC 205 ILE cc_start: 0.8396 (mm) cc_final: 0.8163 (mm) REVERT: HC 221 LYS cc_start: 0.7018 (ptpp) cc_final: 0.6542 (ptpp) REVERT: HD 18 ASP cc_start: 0.7945 (t70) cc_final: 0.7658 (t0) REVERT: HD 20 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7724 (tp) REVERT: HD 40 GLN cc_start: 0.7203 (mt0) cc_final: 0.6846 (mt0) REVERT: HD 95 TYR cc_start: 0.8398 (m-80) cc_final: 0.7714 (m-80) REVERT: HE 122 ARG cc_start: 0.6107 (mtm-85) cc_final: 0.5893 (mtm-85) REVERT: HE 154 MET cc_start: 0.7500 (tpp) cc_final: 0.7253 (tpp) REVERT: HE 162 CYS cc_start: 0.7711 (m) cc_final: 0.7343 (t) REVERT: HF 63 ASP cc_start: 0.6832 (m-30) cc_final: 0.6534 (t0) REVERT: HF 108 THR cc_start: 0.7873 (m) cc_final: 0.7573 (t) REVERT: HF 141 ILE cc_start: 0.8014 (pt) cc_final: 0.7715 (pt) REVERT: HF 204 ASP cc_start: 0.6971 (t0) cc_final: 0.6715 (m-30) REVERT: HF 266 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6584 (mm-30) REVERT: HF 307 GLU cc_start: 0.6914 (tt0) cc_final: 0.6506 (tt0) REVERT: HG 88 LYS cc_start: 0.7767 (mttt) cc_final: 0.7335 (mttt) REVERT: HH 16 GLU cc_start: 0.6852 (pt0) cc_final: 0.6646 (pt0) REVERT: HH 26 TYR cc_start: 0.7694 (t80) cc_final: 0.7068 (t80) REVERT: HH 59 GLU cc_start: 0.7058 (tp30) cc_final: 0.6754 (mm-30) REVERT: HH 60 MET cc_start: 0.6536 (ttp) cc_final: 0.6092 (mmp) REVERT: HI 32 GLU cc_start: 0.7016 (tp30) cc_final: 0.6717 (tp30) REVERT: HI 42 MET cc_start: 0.8549 (mmm) cc_final: 0.8271 (mmm) REVERT: HI 51 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5837 (mmp) REVERT: HI 125 GLN cc_start: 0.6326 (tm-30) cc_final: 0.5928 (pp30) REVERT: HI 129 LYS cc_start: 0.7290 (mttt) cc_final: 0.7068 (mttt) REVERT: HJ 167 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.7797 (mtp85) REVERT: HJ 177 ASP cc_start: 0.6457 (t0) cc_final: 0.6153 (t0) REVERT: HJ 202 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6472 (mm-30) REVERT: HJ 244 SER cc_start: 0.8056 (OUTLIER) cc_final: 0.7585 (t) REVERT: HJ 272 LEU cc_start: 0.6944 (mp) cc_final: 0.6708 (mp) REVERT: HJ 277 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6299 (tt) REVERT: HJ 281 PHE cc_start: 0.5814 (p90) cc_final: 0.4976 (p90) REVERT: HJ 296 ARG cc_start: 0.6636 (mtt-85) cc_final: 0.6262 (mtt-85) REVERT: HJ 300 ARG cc_start: 0.7065 (mtm180) cc_final: 0.6760 (mtm180) REVERT: HJ 326 GLU cc_start: 0.6230 (tp30) cc_final: 0.5948 (tp30) REVERT: HJ 331 ASN cc_start: 0.7573 (m-40) cc_final: 0.7242 (m-40) REVERT: HJ 374 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7631 (tm-30) REVERT: HJ 393 ARG cc_start: 0.7590 (ttp80) cc_final: 0.6613 (ttp80) REVERT: HJ 399 PHE cc_start: 0.7402 (m-80) cc_final: 0.7095 (m-80) REVERT: HJ 425 ASP cc_start: 0.6128 (t70) cc_final: 0.5890 (t0) REVERT: HJ 433 MET cc_start: 0.8237 (mmt) cc_final: 0.7961 (mmt) REVERT: HJ 467 LYS cc_start: 0.7146 (tptt) cc_final: 0.6858 (tptt) REVERT: HJ 557 GLU cc_start: 0.6972 (tp30) cc_final: 0.6559 (tp30) REVERT: HK 77 ARG cc_start: 0.3735 (tpt170) cc_final: 0.3359 (tpt170) REVERT: HK 103 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6420 (mm-30) REVERT: HL 38 GLN cc_start: 0.6859 (pp30) cc_final: 0.6470 (pt0) REVERT: HM 21 ARG cc_start: 0.6648 (ptp-110) cc_final: 0.6057 (mtp-110) REVERT: HM 77 PHE cc_start: 0.5993 (m-80) cc_final: 0.5472 (m-80) REVERT: HM 95 LEU cc_start: 0.8308 (tp) cc_final: 0.8082 (tp) REVERT: HM 144 LEU cc_start: 0.7419 (tt) cc_final: 0.7155 (tp) REVERT: HM 203 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6610 (tm-30) REVERT: HM 205 LEU cc_start: 0.6671 (tp) cc_final: 0.6383 (tt) REVERT: HM 310 THR cc_start: 0.7657 (t) cc_final: 0.7404 (p) REVERT: HM 353 GLN cc_start: 0.6295 (mt0) cc_final: 0.5984 (tt0) REVERT: HM 361 VAL cc_start: 0.7836 (m) cc_final: 0.7601 (p) REVERT: HM 363 PHE cc_start: 0.6611 (t80) cc_final: 0.6374 (t80) REVERT: HM 409 ARG cc_start: 0.7233 (mtp85) cc_final: 0.6962 (ttm170) REVERT: HM 581 GLN cc_start: 0.7427 (mm-40) cc_final: 0.7139 (mm-40) REVERT: HN 2 MET cc_start: 0.5784 (mmm) cc_final: 0.4732 (mmm) REVERT: HN 3 ASN cc_start: 0.7538 (p0) cc_final: 0.7221 (p0) REVERT: HN 6 ASN cc_start: 0.6991 (m-40) cc_final: 0.6715 (m110) REVERT: HO 14 ARG cc_start: 0.6688 (ttp80) cc_final: 0.5989 (ttt180) REVERT: HO 129 PHE cc_start: 0.5994 (m-80) cc_final: 0.5424 (m-80) REVERT: HP 49 SER cc_start: 0.7592 (t) cc_final: 0.7143 (p) REVERT: HP 59 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7629 (mtp85) REVERT: HP 71 ARG cc_start: 0.7130 (mmm-85) cc_final: 0.6890 (mmm-85) REVERT: HP 207 GLU cc_start: 0.8005 (tp30) cc_final: 0.7775 (tp30) REVERT: HQ 32 ARG cc_start: 0.6945 (ptp-110) cc_final: 0.6612 (ptp90) REVERT: HQ 178 TRP cc_start: 0.8293 (t60) cc_final: 0.7680 (t-100) REVERT: HQ 179 ASN cc_start: 0.7394 (m-40) cc_final: 0.7062 (m-40) REVERT: HQ 186 LYS cc_start: 0.7513 (mtmm) cc_final: 0.7230 (mtmm) REVERT: HQ 209 ASP cc_start: 0.7422 (m-30) cc_final: 0.5206 (t0) REVERT: HQ 216 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8095 (mt) REVERT: HQ 249 PHE cc_start: 0.6369 (t80) cc_final: 0.6118 (t80) REVERT: HQ 252 LEU cc_start: 0.8022 (tp) cc_final: 0.7652 (tp) REVERT: HQ 253 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7808 (mm) REVERT: HQ 261 LYS cc_start: 0.6831 (ttmm) cc_final: 0.6391 (ttmm) REVERT: HQ 303 MET cc_start: 0.7991 (mmm) cc_final: 0.6671 (mtt) REVERT: HQ 411 THR cc_start: 0.6904 (m) cc_final: 0.6322 (p) REVERT: HQ 431 PHE cc_start: 0.5201 (m-80) cc_final: 0.4940 (m-80) REVERT: HQ 465 ARG cc_start: 0.6719 (ttp80) cc_final: 0.6317 (tpp80) REVERT: HQ 531 PHE cc_start: 0.7192 (t80) cc_final: 0.6895 (t80) REVERT: HQ 630 GLN cc_start: 0.7475 (tm130) cc_final: 0.6975 (tm130) REVERT: HQ 631 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6982 (tt) REVERT: HQ 693 ARG cc_start: 0.7605 (ttm110) cc_final: 0.6948 (mmm-85) REVERT: HQ 707 LYS cc_start: 0.7864 (tttt) cc_final: 0.7596 (ttpt) REVERT: HQ 731 ARG cc_start: 0.6825 (ptt90) cc_final: 0.6537 (ptt90) REVERT: HQ 738 ARG cc_start: 0.6660 (ttp80) cc_final: 0.6332 (ttp80) REVERT: HR 28 ASP cc_start: 0.7811 (t0) cc_final: 0.7411 (t0) REVERT: HR 29 GLN cc_start: 0.6429 (tm-30) cc_final: 0.6115 (tp40) REVERT: HR 33 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7295 (mtm180) REVERT: HR 114 PHE cc_start: 0.8127 (t80) cc_final: 0.7335 (t80) REVERT: HR 124 THR cc_start: 0.7440 (m) cc_final: 0.7164 (p) REVERT: HR 156 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7034 (tm-30) REVERT: HS 153 ARG cc_start: 0.7386 (tpt90) cc_final: 0.7145 (mmm160) REVERT: HS 166 VAL cc_start: 0.8803 (t) cc_final: 0.8260 (p) REVERT: HS 187 ASN cc_start: 0.6732 (t0) cc_final: 0.6461 (t0) REVERT: HT 26 VAL cc_start: 0.7576 (t) cc_final: 0.7285 (m) REVERT: HT 45 GLN cc_start: 0.7904 (mp10) cc_final: 0.7582 (mp10) REVERT: HT 50 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6354 (mt) REVERT: HT 57 LYS cc_start: 0.7534 (mttt) cc_final: 0.7183 (ttmm) REVERT: HT 68 ASP cc_start: 0.6546 (t0) cc_final: 0.6298 (t0) REVERT: HT 113 GLN cc_start: 0.7235 (mt0) cc_final: 0.6905 (mt0) REVERT: HT 118 LYS cc_start: 0.7895 (mmtt) cc_final: 0.7548 (mmmt) REVERT: HT 362 ASP cc_start: 0.7285 (t0) cc_final: 0.6871 (t70) outliers start: 117 outliers final: 95 residues processed: 1113 average time/residue: 0.2825 time to fit residues: 483.0497 Evaluate side-chains 1170 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 1065 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 17 LEU Chi-restraints excluded: chain HA residue 146 PHE Chi-restraints excluded: chain HA residue 239 ARG Chi-restraints excluded: chain HA residue 338 THR Chi-restraints excluded: chain HA residue 410 LEU Chi-restraints excluded: chain HA residue 426 ARG Chi-restraints excluded: chain HB residue 47 VAL Chi-restraints excluded: chain HB residue 53 THR Chi-restraints excluded: chain HC residue 10 LEU Chi-restraints excluded: chain HC residue 42 SER Chi-restraints excluded: chain HC residue 46 SER Chi-restraints excluded: chain HC residue 57 SER Chi-restraints excluded: chain HC residue 100 TYR Chi-restraints excluded: chain HC residue 149 LEU Chi-restraints excluded: chain HC residue 194 LEU Chi-restraints excluded: chain HC residue 225 LYS Chi-restraints excluded: chain HD residue 20 LEU Chi-restraints excluded: chain HD residue 84 LEU Chi-restraints excluded: chain HE residue 110 LEU Chi-restraints excluded: chain HE residue 127 LEU Chi-restraints excluded: chain HE residue 163 VAL Chi-restraints excluded: chain HE residue 176 GLU Chi-restraints excluded: chain HF residue 33 LEU Chi-restraints excluded: chain HF residue 135 LEU Chi-restraints excluded: chain HF residue 197 LEU Chi-restraints excluded: chain HF residue 226 VAL Chi-restraints excluded: chain HF residue 322 MET Chi-restraints excluded: chain HG residue 18 LEU Chi-restraints excluded: chain HG residue 70 LEU Chi-restraints excluded: chain HG residue 74 THR Chi-restraints excluded: chain HH residue 22 VAL Chi-restraints excluded: chain HH residue 54 VAL Chi-restraints excluded: chain HH residue 68 PHE Chi-restraints excluded: chain HI residue 11 THR Chi-restraints excluded: chain HI residue 51 MET Chi-restraints excluded: chain HI residue 66 LEU Chi-restraints excluded: chain HI residue 83 PHE Chi-restraints excluded: chain HI residue 132 VAL Chi-restraints excluded: chain HJ residue 165 LEU Chi-restraints excluded: chain HJ residue 171 LEU Chi-restraints excluded: chain HJ residue 244 SER Chi-restraints excluded: chain HJ residue 277 LEU Chi-restraints excluded: chain HJ residue 411 ASP Chi-restraints excluded: chain HJ residue 413 VAL Chi-restraints excluded: chain HJ residue 435 MET Chi-restraints excluded: chain HJ residue 459 LEU Chi-restraints excluded: chain HK residue 40 ARG Chi-restraints excluded: chain HK residue 98 VAL Chi-restraints excluded: chain HL residue 42 ILE Chi-restraints excluded: chain HL residue 62 VAL Chi-restraints excluded: chain HL residue 75 GLN Chi-restraints excluded: chain HL residue 80 VAL Chi-restraints excluded: chain HM residue 198 LEU Chi-restraints excluded: chain HM residue 267 THR Chi-restraints excluded: chain HM residue 362 LEU Chi-restraints excluded: chain HM residue 394 LEU Chi-restraints excluded: chain HM residue 412 LEU Chi-restraints excluded: chain HM residue 418 LEU Chi-restraints excluded: chain HO residue 17 VAL Chi-restraints excluded: chain HO residue 62 ARG Chi-restraints excluded: chain HO residue 96 LEU Chi-restraints excluded: chain HO residue 166 THR Chi-restraints excluded: chain HP residue 35 GLU Chi-restraints excluded: chain HP residue 40 VAL Chi-restraints excluded: chain HP residue 57 THR Chi-restraints excluded: chain HP residue 172 VAL Chi-restraints excluded: chain HP residue 197 GLU Chi-restraints excluded: chain HP residue 213 THR Chi-restraints excluded: chain HQ residue 124 VAL Chi-restraints excluded: chain HQ residue 126 LEU Chi-restraints excluded: chain HQ residue 187 GLU Chi-restraints excluded: chain HQ residue 192 HIS Chi-restraints excluded: chain HQ residue 216 LEU Chi-restraints excluded: chain HQ residue 238 ILE Chi-restraints excluded: chain HQ residue 253 ILE Chi-restraints excluded: chain HQ residue 259 SER Chi-restraints excluded: chain HQ residue 344 ILE Chi-restraints excluded: chain HQ residue 353 LEU Chi-restraints excluded: chain HQ residue 421 VAL Chi-restraints excluded: chain HQ residue 535 LEU Chi-restraints excluded: chain HQ residue 586 VAL Chi-restraints excluded: chain HQ residue 626 GLU Chi-restraints excluded: chain HQ residue 631 LEU Chi-restraints excluded: chain HQ residue 710 ILE Chi-restraints excluded: chain HQ residue 723 VAL Chi-restraints excluded: chain HR residue 13 THR Chi-restraints excluded: chain HR residue 17 LEU Chi-restraints excluded: chain HR residue 21 SER Chi-restraints excluded: chain HR residue 33 ARG Chi-restraints excluded: chain HR residue 36 CYS Chi-restraints excluded: chain HR residue 96 LEU Chi-restraints excluded: chain HR residue 125 TRP Chi-restraints excluded: chain HR residue 126 ASN Chi-restraints excluded: chain HS residue 83 VAL Chi-restraints excluded: chain HS residue 102 LEU Chi-restraints excluded: chain HS residue 117 LEU Chi-restraints excluded: chain HS residue 130 VAL Chi-restraints excluded: chain HS residue 149 SER Chi-restraints excluded: chain HS residue 156 GLU Chi-restraints excluded: chain HT residue 36 TYR Chi-restraints excluded: chain HT residue 47 VAL Chi-restraints excluded: chain HT residue 50 LEU Chi-restraints excluded: chain HT residue 89 VAL Chi-restraints excluded: chain HT residue 361 PHE Chi-restraints excluded: chain HT residue 378 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 279 optimal weight: 0.2980 chunk 434 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 175 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 chunk 263 optimal weight: 0.0050 chunk 348 optimal weight: 3.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... HA 200 GLN ** HA 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 383 ASN HC 31 ASN ** HI 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HJ 419 ASN ** HL 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HM 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HM 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HP 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HQ 342 GLN ** HQ 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HQ 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HR 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.183226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.154593 restraints weight = 63416.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.157902 restraints weight = 36297.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.159650 restraints weight = 23621.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.159980 restraints weight = 19893.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.160107 restraints weight = 16902.852| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 42419 Z= 0.147 Angle : 0.668 13.872 58628 Z= 0.336 Chirality : 0.041 0.247 6660 Planarity : 0.005 0.068 6558 Dihedral : 18.060 178.687 9203 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.90 % Favored : 92.08 % Rotamer: Outliers : 3.17 % Allowed : 25.31 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.13), residues: 4268 helix: 0.27 (0.13), residues: 1817 sheet: -1.51 (0.38), residues: 185 loop : -2.19 (0.12), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGHQ 311 TYR 0.035 0.002 TYRHH 18 PHE 0.034 0.001 PHEHJ 560 TRP 0.032 0.002 TRPHF 297 HIS 0.016 0.001 HISHQ 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (42419) covalent geometry : angle 0.66776 / 0.34 (58628) hydrogen bonds : bond 0.04732 / 3.10 ( 1057) hydrogen bonds : angle 4.30299 / 3.03 ( 2968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9579.47 seconds wall clock time: 164 minutes 44.85 seconds (9884.85 seconds total)