Starting phenix.real_space_refine on Sun Aug 9 00:55:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twa_41664/08_2026/8twa_41664.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twa_41664/08_2026/8twa_41664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8twa_41664/08_2026/8twa_41664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twa_41664/08_2026/8twa_41664.map" model { file = "/net/cci-nas-00/data/ceres_data/8twa_41664/08_2026/8twa_41664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twa_41664/08_2026/8twa_41664.cif" } resolution = 4.1 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= 0.005 sd= 0.037 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 34 5.49 5 Mg 3 5.21 5 S 149 5.16 5 C 20144 2.51 5 N 5406 2.21 5 O 6174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 213 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31914 Number of models: 1 Model: "" Number of chains: 19 Chain: "C" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 206 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 183 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 8868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 8868 Classifications: {'peptide': 1123} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PCIS': 2, 'PTRANS': 50, 'TRANS': 1070} Chain breaks: 3 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 260 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'TYR:plan': 5, 'PHE:plan': 5, 'ASP:plan': 4, 'GLU:plan': 5, 'HIS:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 160 Chain: "D" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1014 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1362 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 3, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "4" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2457 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 309} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "3" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2563 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "2" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 327} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "5" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2613 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "1" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3576 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 434} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "X" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2003 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Y" Number of atoms: 1997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1997 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1963 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 245} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5484 SG CYS E 665 108.383 50.219 73.824 1.00 81.51 S ATOM 5572 SG CYS E 677 107.466 44.740 76.899 1.00 87.54 S ATOM 6301 SG CYS E 763 103.037 47.893 77.715 1.00 94.87 S ATOM 5501 SG CYS E 668 108.028 50.100 80.375 1.00 78.76 S Time building chain proxies: 5.53, per 1000 atoms: 0.17 Number of scatterers: 31914 At special positions: 0 Unit cell: (127.512, 192.924, 134.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 149 16.00 P 34 15.00 Mg 3 11.99 O 6174 8.00 N 5406 7.00 C 20144 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: 2.00 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 E2301 " pdb="FE4 SF4 E2301 " - pdb=" SG CYS E 668 " pdb="FE1 SF4 E2301 " - pdb=" SG CYS E 665 " pdb="FE2 SF4 E2301 " - pdb=" SG CYS E 677 " pdb="FE3 SF4 E2301 " - pdb=" SG CYS E 763 " Number of angles added : 12 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7634 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 31 sheets defined 49.8% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'C' and resid 735 through 740 removed outlier: 3.647A pdb=" N LEU C 739 " --> pdb=" O THR C 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 50 removed outlier: 4.244A pdb=" N SER E 27 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN E 29 " --> pdb=" O THR E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 69 removed outlier: 3.548A pdb=" N ILE E 69 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 147 No H-bonds generated for 'chain 'E' and resid 145 through 147' Processing helix chain 'E' and resid 148 through 160 Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 195 through 216 Proline residue: E 208 - end of helix Processing helix chain 'E' and resid 234 through 237 Processing helix chain 'E' and resid 248 through 257 Processing helix chain 'E' and resid 354 through 370 Processing helix chain 'E' and resid 382 through 394 Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 422 through 429 Processing helix chain 'E' and resid 433 through 437 removed outlier: 3.773A pdb=" N GLN E 437 " --> pdb=" O GLN E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 447 Processing helix chain 'E' and resid 455 through 466 removed outlier: 4.670A pdb=" N THR E 460 " --> pdb=" O PRO E 456 " (cutoff:3.500A) Proline residue: E 461 - end of helix removed outlier: 4.164A pdb=" N PHE E 464 " --> pdb=" O THR E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 488 Processing helix chain 'E' and resid 488 through 498 removed outlier: 3.517A pdb=" N PHE E 492 " --> pdb=" O TYR E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 510 Processing helix chain 'E' and resid 511 through 527 Processing helix chain 'E' and resid 577 through 598 Proline residue: E 589 - end of helix Processing helix chain 'E' and resid 603 through 607 Processing helix chain 'E' and resid 609 through 627 Processing helix chain 'E' and resid 643 through 653 Processing helix chain 'E' and resid 661 through 668 Processing helix chain 'E' and resid 693 through 706 removed outlier: 3.770A pdb=" N ASN E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 727 through 747 Processing helix chain 'E' and resid 769 through 798 removed outlier: 3.975A pdb=" N ILE E 798 " --> pdb=" O ASN E 794 " (cutoff:3.500A) Processing helix chain 'E' and resid 806 through 834 removed outlier: 3.524A pdb=" N LYS E 810 " --> pdb=" O ARG E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 843 through 869 removed outlier: 3.634A pdb=" N ILE E 849 " --> pdb=" O GLU E 845 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG E 867 " --> pdb=" O ALA E 863 " (cutoff:3.500A) Processing helix chain 'E' and resid 905 through 919 removed outlier: 3.966A pdb=" N LEU E 910 " --> pdb=" O PRO E 906 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 913 " --> pdb=" O MET E 909 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR E 919 " --> pdb=" O HIS E 915 " (cutoff:3.500A) Processing helix chain 'E' and resid 993 through 1006 removed outlier: 4.685A pdb=" N LYS E1004 " --> pdb=" O SER E1000 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL E1005 " --> pdb=" O ASP E1001 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE E1006 " --> pdb=" O ILE E1002 " (cutoff:3.500A) Processing helix chain 'E' and resid 1011 through 1032 removed outlier: 3.542A pdb=" N VAL E1022 " --> pdb=" O ALA E1018 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU E1030 " --> pdb=" O TRP E1026 " (cutoff:3.500A) Processing helix chain 'E' and resid 1038 through 1047 Processing helix chain 'E' and resid 1055 through 1062 removed outlier: 3.501A pdb=" N GLN E1062 " --> pdb=" O GLU E1058 " (cutoff:3.500A) Processing helix chain 'E' and resid 1064 through 1077 Processing helix chain 'E' and resid 1101 through 1104 Processing helix chain 'E' and resid 1110 through 1112 No H-bonds generated for 'chain 'E' and resid 1110 through 1112' Processing helix chain 'E' and resid 1115 through 1128 Processing helix chain 'E' and resid 1136 through 1141 removed outlier: 3.521A pdb=" N ILE E1140 " --> pdb=" O ASP E1136 " (cutoff:3.500A) Processing helix chain 'E' and resid 1142 through 1158 Processing helix chain 'E' and resid 1158 through 1166 Processing helix chain 'E' and resid 1177 through 1189 Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 45 through 51 removed outlier: 3.758A pdb=" N ARG D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.896A pdb=" N LEU B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 357 through 363 Processing helix chain '4' and resid 10 through 15 Processing helix chain '4' and resid 19 through 23 removed outlier: 3.598A pdb=" N ILE 4 23 " --> pdb=" O LEU 4 20 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 40 Processing helix chain '4' and resid 55 through 68 Processing helix chain '4' and resid 70 through 74 Processing helix chain '4' and resid 85 through 99 removed outlier: 4.073A pdb=" N ILE 4 93 " --> pdb=" O VAL 4 89 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS 4 94 " --> pdb=" O ARG 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 116 through 119 Processing helix chain '4' and resid 120 through 134 removed outlier: 3.782A pdb=" N ARG 4 128 " --> pdb=" O GLN 4 124 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG 4 129 " --> pdb=" O GLN 4 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR 4 130 " --> pdb=" O ALA 4 126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR 4 134 " --> pdb=" O THR 4 130 " (cutoff:3.500A) Processing helix chain '4' and resid 146 through 150 Processing helix chain '4' and resid 151 through 157 removed outlier: 3.678A pdb=" N ARG 4 157 " --> pdb=" O PRO 4 153 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 183 Processing helix chain '4' and resid 187 through 199 Processing helix chain '4' and resid 201 through 217 Processing helix chain '4' and resid 220 through 228 Processing helix chain '4' and resid 231 through 241 removed outlier: 3.738A pdb=" N ILE 4 235 " --> pdb=" O PRO 4 231 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 255 Processing helix chain '4' and resid 262 through 276 Processing helix chain '4' and resid 281 through 300 Processing helix chain '4' and resid 305 through 321 removed outlier: 3.725A pdb=" N LEU 4 309 " --> pdb=" O THR 4 305 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 13 Processing helix chain '3' and resid 14 through 19 Processing helix chain '3' and resid 23 through 27 removed outlier: 3.735A pdb=" N VAL 3 27 " --> pdb=" O LEU 3 24 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 44 removed outlier: 3.518A pdb=" N THR 3 36 " --> pdb=" O GLU 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 58 through 72 Processing helix chain '3' and resid 74 through 78 removed outlier: 3.514A pdb=" N MET 3 78 " --> pdb=" O ASN 3 74 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 74 through 78' Processing helix chain '3' and resid 89 through 103 removed outlier: 4.012A pdb=" N LYS 3 98 " --> pdb=" O ARG 3 94 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 122 removed outlier: 3.549A pdb=" N ALA 3 121 " --> pdb=" O GLU 3 118 " (cutoff:3.500A) Processing helix chain '3' and resid 123 through 137 removed outlier: 4.379A pdb=" N ARG 3 132 " --> pdb=" O ASN 3 128 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL 3 133 " --> pdb=" O ALA 3 129 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU 3 135 " --> pdb=" O ARG 3 131 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 160 removed outlier: 3.550A pdb=" N ARG 3 160 " --> pdb=" O ALA 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 170 through 185 Processing helix chain '3' and resid 190 through 200 Processing helix chain '3' and resid 204 through 219 Processing helix chain '3' and resid 228 through 237 Processing helix chain '3' and resid 240 through 253 Processing helix chain '3' and resid 255 through 270 removed outlier: 3.801A pdb=" N LYS 3 270 " --> pdb=" O VAL 3 266 " (cutoff:3.500A) Processing helix chain '3' and resid 273 through 286 Processing helix chain '3' and resid 293 through 311 Processing helix chain '3' and resid 315 through 332 Processing helix chain '2' and resid 15 through 24 Processing helix chain '2' and resid 26 through 31 Processing helix chain '2' and resid 42 through 55 removed outlier: 3.620A pdb=" N VAL 2 46 " --> pdb=" O GLN 2 42 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL 2 48 " --> pdb=" O HIS 2 44 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS 2 54 " --> pdb=" O LYS 2 50 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER 2 55 " --> pdb=" O LYS 2 51 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 88 Proline residue: 2 85 - end of helix Processing helix chain '2' and resid 102 through 116 removed outlier: 3.894A pdb=" N VAL 2 110 " --> pdb=" O VAL 2 106 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS 2 111 " --> pdb=" O ARG 2 107 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 129 removed outlier: 3.634A pdb=" N LEU 2 126 " --> pdb=" O SER 2 122 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN 2 128 " --> pdb=" O HIS 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 141 through 145 removed outlier: 3.634A pdb=" N SER 2 144 " --> pdb=" O GLU 2 141 " (cutoff:3.500A) Processing helix chain '2' and resid 146 through 160 removed outlier: 3.556A pdb=" N LEU 2 153 " --> pdb=" O ALA 2 149 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG 2 154 " --> pdb=" O GLN 2 150 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG 2 155 " --> pdb=" O SER 2 151 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR 2 156 " --> pdb=" O ALA 2 152 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR 2 160 " --> pdb=" O THR 2 156 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 176 Processing helix chain '2' and resid 177 through 184 Processing helix chain '2' and resid 193 through 208 removed outlier: 5.160A pdb=" N ASP 2 199 " --> pdb=" O SER 2 195 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG 2 200 " --> pdb=" O ASN 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 216 through 225 Processing helix chain '2' and resid 227 through 246 removed outlier: 3.639A pdb=" N LEU 2 245 " --> pdb=" O GLY 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 252 through 260 removed outlier: 3.580A pdb=" N LEU 2 259 " --> pdb=" O GLN 2 255 " (cutoff:3.500A) Processing helix chain '2' and resid 264 through 277 Processing helix chain '2' and resid 279 through 291 Processing helix chain '2' and resid 296 through 311 Processing helix chain '2' and resid 315 through 334 removed outlier: 3.504A pdb=" N GLN 2 321 " --> pdb=" O ASN 2 317 " (cutoff:3.500A) Processing helix chain '2' and resid 338 through 352 Processing helix chain '5' and resid 19 through 32 removed outlier: 4.417A pdb=" N GLN 5 32 " --> pdb=" O SER 5 28 " (cutoff:3.500A) Processing helix chain '5' and resid 48 through 61 Processing helix chain '5' and resid 62 through 66 removed outlier: 3.516A pdb=" N VAL 5 65 " --> pdb=" O GLY 5 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR 5 66 " --> pdb=" O PRO 5 63 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 62 through 66' Processing helix chain '5' and resid 97 through 101 removed outlier: 3.964A pdb=" N MET 5 101 " --> pdb=" O PRO 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 104 through 117 removed outlier: 3.692A pdb=" N VAL 5 108 " --> pdb=" O ASN 5 104 " (cutoff:3.500A) Processing helix chain '5' and resid 143 through 146 Processing helix chain '5' and resid 147 through 161 removed outlier: 4.059A pdb=" N ARG 5 156 " --> pdb=" O ALA 5 152 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR 5 157 " --> pdb=" O ALA 5 153 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU 5 159 " --> pdb=" O ARG 5 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR 5 161 " --> pdb=" O THR 5 157 " (cutoff:3.500A) Processing helix chain '5' and resid 178 through 185 Processing helix chain '5' and resid 194 through 209 Processing helix chain '5' and resid 216 through 227 removed outlier: 4.021A pdb=" N LYS 5 220 " --> pdb=" O LYS 5 216 " (cutoff:3.500A) Processing helix chain '5' and resid 229 through 244 removed outlier: 3.530A pdb=" N ASN 5 243 " --> pdb=" O SER 5 239 " (cutoff:3.500A) Processing helix chain '5' and resid 257 through 273 Processing helix chain '5' and resid 275 through 291 removed outlier: 3.654A pdb=" N GLU 5 281 " --> pdb=" O ASN 5 277 " (cutoff:3.500A) Processing helix chain '5' and resid 295 through 309 Processing helix chain '5' and resid 314 through 335 Processing helix chain '5' and resid 337 through 353 removed outlier: 3.737A pdb=" N HIS 5 341 " --> pdb=" O LYS 5 337 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY 5 344 " --> pdb=" O PHE 5 340 " (cutoff:3.500A) Processing helix chain '1' and resid 132 through 145 removed outlier: 3.792A pdb=" N TRP 1 145 " --> pdb=" O TRP 1 141 " (cutoff:3.500A) Processing helix chain '1' and resid 145 through 150 Processing helix chain '1' and resid 188 through 200 Processing helix chain '1' and resid 214 through 228 removed outlier: 4.496A pdb=" N GLU 1 220 " --> pdb=" O PRO 1 216 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS 1 221 " --> pdb=" O MET 1 217 " (cutoff:3.500A) Processing helix chain '1' and resid 249 through 272 Processing helix chain '1' and resid 302 through 306 Processing helix chain '1' and resid 308 through 310 No H-bonds generated for 'chain '1' and resid 308 through 310' Processing helix chain '1' and resid 324 through 336 Processing helix chain '1' and resid 341 through 353 Processing helix chain '1' and resid 355 through 369 Processing helix chain '1' and resid 398 through 407 Processing helix chain '1' and resid 414 through 430 removed outlier: 3.638A pdb=" N GLY 1 430 " --> pdb=" O VAL 1 426 " (cutoff:3.500A) Processing helix chain '1' and resid 431 through 443 Processing helix chain '1' and resid 453 through 476 removed outlier: 4.088A pdb=" N ALA 1 457 " --> pdb=" O ILE 1 453 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP 1 461 " --> pdb=" O ALA 1 457 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR 1 474 " --> pdb=" O TYR 1 470 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA 1 475 " --> pdb=" O GLN 1 471 " (cutoff:3.500A) Processing helix chain '1' and resid 477 through 479 No H-bonds generated for 'chain '1' and resid 477 through 479' Processing helix chain '1' and resid 480 through 485 removed outlier: 3.859A pdb=" N SER 1 484 " --> pdb=" O LEU 1 480 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA 1 485 " --> pdb=" O LEU 1 481 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 480 through 485' Processing helix chain '1' and resid 485 through 496 removed outlier: 3.872A pdb=" N LEU 1 489 " --> pdb=" O ALA 1 485 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE 1 491 " --> pdb=" O VAL 1 487 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE 1 492 " --> pdb=" O PRO 1 488 " (cutoff:3.500A) Processing helix chain '1' and resid 508 through 534 removed outlier: 3.655A pdb=" N GLU 1 512 " --> pdb=" O ASN 1 508 " (cutoff:3.500A) Processing helix chain '1' and resid 537 through 542 removed outlier: 3.766A pdb=" N PHE 1 541 " --> pdb=" O LEU 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 543 through 550 Processing helix chain '1' and resid 550 through 561 removed outlier: 3.558A pdb=" N TYR 1 554 " --> pdb=" O GLU 1 550 " (cutoff:3.500A) Processing helix chain '1' and resid 562 through 566 Processing helix chain '1' and resid 568 through 586 Processing helix chain '1' and resid 610 through 615 Processing helix chain '1' and resid 617 through 643 removed outlier: 3.675A pdb=" N ASN 1 622 " --> pdb=" O PRO 1 618 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU 1 623 " --> pdb=" O LYS 1 619 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN 1 630 " --> pdb=" O HIS 1 626 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 20 removed outlier: 4.309A pdb=" N PHE X 12 " --> pdb=" O GLU X 8 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE X 19 " --> pdb=" O ILE X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 55 through 57 No H-bonds generated for 'chain 'X' and resid 55 through 57' Processing helix chain 'X' and resid 72 through 79 Processing helix chain 'X' and resid 141 through 153 removed outlier: 4.111A pdb=" N GLN X 153 " --> pdb=" O ARG X 149 " (cutoff:3.500A) Processing helix chain 'X' and resid 190 through 194 Processing helix chain 'X' and resid 209 through 216 Processing helix chain 'X' and resid 217 through 221 Processing helix chain 'Y' and resid 8 through 20 removed outlier: 4.309A pdb=" N PHE Y 12 " --> pdb=" O GLU Y 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE Y 19 " --> pdb=" O ILE Y 15 " (cutoff:3.500A) Processing helix chain 'Y' and resid 55 through 57 No H-bonds generated for 'chain 'Y' and resid 55 through 57' Processing helix chain 'Y' and resid 72 through 79 Processing helix chain 'Y' and resid 141 through 153 removed outlier: 4.108A pdb=" N GLN Y 153 " --> pdb=" O ARG Y 149 " (cutoff:3.500A) Processing helix chain 'Y' and resid 190 through 194 Processing helix chain 'Y' and resid 209 through 216 Processing helix chain 'Y' and resid 217 through 221 Processing helix chain 'Z' and resid 8 through 20 removed outlier: 4.309A pdb=" N PHE Z 12 " --> pdb=" O GLU Z 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE Z 19 " --> pdb=" O ILE Z 15 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 57 No H-bonds generated for 'chain 'Z' and resid 55 through 57' Processing helix chain 'Z' and resid 72 through 79 Processing helix chain 'Z' and resid 141 through 153 removed outlier: 4.106A pdb=" N GLN Z 153 " --> pdb=" O ARG Z 149 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 194 Processing helix chain 'Z' and resid 209 through 216 Processing helix chain 'Z' and resid 217 through 221 Processing sheet with id=AA1, first strand: chain 'C' and resid 719 through 722 Processing sheet with id=AA2, first strand: chain 'C' and resid 728 through 733 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 728 through 733 current: chain 'D' and resid 65 through 76 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 88 through 96 current: chain 'D' and resid 112 through 118 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 112 through 118 current: chain 'B' and resid 49 through 52 removed outlier: 5.399A pdb=" N VAL B 49 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LYS B 61 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ARG B 111 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ARG B 63 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLU B 109 " --> pdb=" O ARG B 63 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N HIS B 65 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU B 107 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN B 67 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLU B 105 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 69 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS B 103 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU B 71 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 97 " --> pdb=" O PHE B 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 75 through 78 removed outlier: 3.745A pdb=" N ARG E 75 " --> pdb=" O VAL E 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 81 through 87 removed outlier: 3.525A pdb=" N PHE E 129 " --> pdb=" O PHE E 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 166 through 172 removed outlier: 6.889A pdb=" N THR E 187 " --> pdb=" O CYS E 143 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS E 143 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP E 241 " --> pdb=" O ALA E 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 335 through 336 removed outlier: 6.869A pdb=" N GLY E 319 " --> pdb=" O THR E 348 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE E 350 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU E 321 " --> pdb=" O PHE E 350 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLU E 352 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N THR E 323 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET E 309 " --> pdb=" O ASN E 324 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU E 292 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE E 311 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP E 290 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR E 313 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA E 288 " --> pdb=" O TYR E 313 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE E 315 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL E 286 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N MET E 287 " --> pdb=" O SER E 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE E 374 " --> pdb=" O MET E 420 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 405 through 406 Processing sheet with id=AA8, first strand: chain 'E' and resid 542 through 543 Processing sheet with id=AA9, first strand: chain 'E' and resid 558 through 560 removed outlier: 6.925A pdb=" N TRP E 880 " --> pdb=" O LEU E 872 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU E 874 " --> pdb=" O GLY E 878 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLY E 878 " --> pdb=" O LEU E 874 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE E 636 " --> pdb=" O PRO E 949 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 564 through 567 removed outlier: 3.531A pdb=" N ALA E 952 " --> pdb=" O PHE E 972 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 572 through 575 Processing sheet with id=AB3, first strand: chain 'E' and resid 708 through 710 Processing sheet with id=AB4, first strand: chain 'E' and resid 890 through 894 Processing sheet with id=AB5, first strand: chain 'E' and resid 920 through 928 removed outlier: 4.044A pdb=" N GLN E 922 " --> pdb=" O HIS E 937 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N HIS E 937 " --> pdb=" O GLN E 922 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN E 924 " --> pdb=" O GLU E 935 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU E 935 " --> pdb=" O GLN E 924 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU E 926 " --> pdb=" O ILE E 933 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE E 933 " --> pdb=" O LEU E 926 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 991 through 992 Processing sheet with id=AB7, first strand: chain 'B' and resid 368 through 370 Processing sheet with id=AB8, first strand: chain '4' and resid 75 through 78 removed outlier: 6.286A pdb=" N LYS 4 109 " --> pdb=" O ARG 4 139 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA 4 141 " --> pdb=" O LYS 4 109 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL 4 111 " --> pdb=" O ALA 4 141 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA 4 143 " --> pdb=" O VAL 4 111 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU 4 113 " --> pdb=" O ALA 4 143 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE 4 46 " --> pdb=" O LEU 4 161 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 185 through 186 removed outlier: 7.489A pdb=" N LYS 4 185 " --> pdb=" O VAL 4 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain '3' and resid 79 through 82 removed outlier: 6.604A pdb=" N LEU 3 49 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA 3 147 " --> pdb=" O LEU 3 49 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE 3 51 " --> pdb=" O ALA 3 147 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU 3 50 " --> pdb=" O PHE 3 164 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '2' and resid 92 through 95 removed outlier: 6.221A pdb=" N LEU 2 62 " --> pdb=" O PHE 2 187 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '5' and resid 69 through 76 removed outlier: 6.875A pdb=" N LEU 5 94 " --> pdb=" O ILE 5 139 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASN 5 141 " --> pdb=" O LEU 5 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE 5 96 " --> pdb=" O ASN 5 141 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS 5 136 " --> pdb=" O ARG 5 166 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE 5 168 " --> pdb=" O LYS 5 136 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL 5 138 " --> pdb=" O ILE 5 168 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL 5 170 " --> pdb=" O VAL 5 138 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE 5 140 " --> pdb=" O VAL 5 170 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU 5 40 " --> pdb=" O ILE 5 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '5' and resid 212 through 213 removed outlier: 5.835A pdb=" N GLN 5 212 " --> pdb=" O LEU 5 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain '1' and resid 203 through 208 removed outlier: 6.245A pdb=" N SER 1 203 " --> pdb=" O CYS 1 237 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL 1 239 " --> pdb=" O SER 1 203 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER 1 205 " --> pdb=" O VAL 1 239 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASP 1 241 " --> pdb=" O SER 1 205 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE 1 207 " --> pdb=" O ASP 1 241 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N ILE 1 294 " --> pdb=" O VAL 1 236 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU 1 238 " --> pdb=" O ILE 1 294 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE 1 296 " --> pdb=" O LEU 1 238 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA 1 240 " --> pdb=" O ILE 1 296 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU 1 179 " --> pdb=" O CYS 1 295 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N CYS 1 297 " --> pdb=" O LEU 1 179 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU 1 181 " --> pdb=" O CYS 1 297 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '1' and resid 589 through 592 Processing sheet with id=AC7, first strand: chain 'X' and resid 59 through 60 removed outlier: 3.524A pdb=" N GLU X 59 " --> pdb=" O LYS X 5 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 66 through 71 removed outlier: 5.537A pdb=" N LEU X 25 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL X 40 " --> pdb=" O LEU X 25 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY X 244 " --> pdb=" O LEU X 241 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASP X 240 " --> pdb=" O ARG X 224 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG X 224 " --> pdb=" O ASP X 240 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 203 through 208 removed outlier: 6.289A pdb=" N SER X 157 " --> pdb=" O ASP X 172 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP X 172 " --> pdb=" O SER X 157 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER X 177 " --> pdb=" O SER Z 115 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE X 181 " --> pdb=" O ILE Z 111 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE Z 111 " --> pdb=" O ILE X 181 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU Z 59 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Y' and resid 59 through 60 removed outlier: 3.524A pdb=" N GLU Y 59 " --> pdb=" O LYS Y 5 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP Z 172 " --> pdb=" O SER Z 157 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER Z 157 " --> pdb=" O ASP Z 172 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Y' and resid 66 through 71 removed outlier: 5.539A pdb=" N LEU Y 25 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL Y 40 " --> pdb=" O LEU Y 25 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY Y 244 " --> pdb=" O LEU Y 241 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASP Y 240 " --> pdb=" O ARG Y 224 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG Y 224 " --> pdb=" O ASP Y 240 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Y' and resid 177 through 182 removed outlier: 4.662A pdb=" N ASP Y 172 " --> pdb=" O SER Y 157 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER Y 157 " --> pdb=" O ASP Y 172 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 66 through 71 removed outlier: 5.538A pdb=" N LEU Z 25 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL Z 40 " --> pdb=" O LEU Z 25 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY Z 244 " --> pdb=" O LEU Z 241 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASP Z 240 " --> pdb=" O ARG Z 224 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG Z 224 " --> pdb=" O ASP Z 240 " (cutoff:3.500A) 1668 hydrogen bonds defined for protein. 4734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.51 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.33: 6583 1.33 - 1.56: 25618 1.56 - 1.80: 154 1.80 - 2.04: 162 2.04 - 2.27: 12 Bond restraints: 32529 Sorted by residual: bond pdb=" C ARG B 354 " pdb=" N GLY B 355 " ideal model delta sigma weight residual 1.331 1.538 -0.208 1.46e-02 4.69e+03 2.03e+02 bond pdb=" C GLU E 766 " pdb=" N ASN E 767 " ideal model delta sigma weight residual 1.331 1.558 -0.227 2.07e-02 2.33e+03 1.20e+02 bond pdb=" C1' DG P 2 " pdb=" N9 DG P 2 " ideal model delta sigma weight residual 1.468 1.360 0.108 1.40e-02 5.10e+03 5.93e+01 bond pdb=" C GLY B 355 " pdb=" N MET B 356 " ideal model delta sigma weight residual 1.328 1.206 0.122 1.62e-02 3.81e+03 5.64e+01 bond pdb=" C1' DG P 8 " pdb=" N9 DG P 8 " ideal model delta sigma weight residual 1.468 1.364 0.104 1.40e-02 5.10e+03 5.50e+01 ... (remaining 32524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.44: 44105 10.44 - 20.88: 27 20.88 - 31.33: 1 31.33 - 41.77: 0 41.77 - 52.21: 1 Bond angle restraints: 44134 Sorted by residual: angle pdb=" O ARG B 334 " pdb=" C ARG B 334 " pdb=" N LEU B 335 " ideal model delta sigma weight residual 122.59 70.38 52.21 1.33e+00 5.65e-01 1.54e+03 angle pdb=" CA ARG B 334 " pdb=" C ARG B 334 " pdb=" N LEU B 335 " ideal model delta sigma weight residual 116.84 142.10 -25.26 1.71e+00 3.42e-01 2.18e+02 angle pdb=" N GLU Y 257 " pdb=" CA GLU Y 257 " pdb=" C GLU Y 257 " ideal model delta sigma weight residual 110.41 122.92 -12.51 1.18e+00 7.18e-01 1.12e+02 angle pdb=" N GLU X 257 " pdb=" CA GLU X 257 " pdb=" C GLU X 257 " ideal model delta sigma weight residual 110.41 122.90 -12.49 1.18e+00 7.18e-01 1.12e+02 angle pdb=" O GLU E 766 " pdb=" C GLU E 766 " pdb=" N ASN E 767 " ideal model delta sigma weight residual 122.95 111.66 11.29 1.24e+00 6.50e-01 8.29e+01 ... (remaining 44129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.97: 19425 33.97 - 67.94: 430 67.94 - 101.91: 51 101.91 - 135.88: 5 135.88 - 169.85: 4 Dihedral angle restraints: 19915 sinusoidal: 8190 harmonic: 11725 Sorted by residual: dihedral pdb=" O2A ADP 5 401 " pdb=" O3A ADP 5 401 " pdb=" PA ADP 5 401 " pdb=" PB ADP 5 401 " ideal model delta sinusoidal sigma weight residual -60.00 60.68 -120.68 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" O1B ADP 5 401 " pdb=" O3A ADP 5 401 " pdb=" PB ADP 5 401 " pdb=" PA ADP 5 401 " ideal model delta sinusoidal sigma weight residual -60.00 48.61 -108.61 1 2.00e+01 2.50e-03 3.17e+01 dihedral pdb=" CA ARG E 672 " pdb=" C ARG E 672 " pdb=" N PRO E 673 " pdb=" CA PRO E 673 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 19912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 4327 0.119 - 0.239: 631 0.239 - 0.358: 92 0.358 - 0.477: 14 0.477 - 0.596: 5 Chirality restraints: 5069 Sorted by residual: chirality pdb=" CA GLU X 257 " pdb=" N GLU X 257 " pdb=" C GLU X 257 " pdb=" CB GLU X 257 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.89e+00 chirality pdb=" CA GLU Y 257 " pdb=" N GLU Y 257 " pdb=" C GLU Y 257 " pdb=" CB GLU Y 257 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.82e+00 chirality pdb=" CA CYS Z 22 " pdb=" N CYS Z 22 " pdb=" C CYS Z 22 " pdb=" CB CYS Z 22 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.82e+00 ... (remaining 5066 not shown) Planarity restraints: 5582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 334 " 0.119 2.00e-02 2.50e+03 1.63e-01 2.66e+02 pdb=" C ARG B 334 " -0.280 2.00e-02 2.50e+03 pdb=" O ARG B 334 " 0.058 2.00e-02 2.50e+03 pdb=" N LEU B 335 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 355 " 0.055 2.00e-02 2.50e+03 1.19e-01 1.43e+02 pdb=" C GLY B 355 " -0.206 2.00e-02 2.50e+03 pdb=" O GLY B 355 " 0.079 2.00e-02 2.50e+03 pdb=" N MET B 356 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 81 " -0.052 2.00e-02 2.50e+03 1.03e-01 1.07e+02 pdb=" C ASN E 81 " 0.179 2.00e-02 2.50e+03 pdb=" O ASN E 81 " -0.070 2.00e-02 2.50e+03 pdb=" N MET E 82 " -0.056 2.00e-02 2.50e+03 ... (remaining 5579 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 4 1.89 - 2.64: 487 2.64 - 3.40: 41992 3.40 - 4.15: 77154 4.15 - 4.90: 137366 Nonbonded interactions: 257003 Sorted by model distance: nonbonded pdb=" CZ PHE B 333 " pdb=" CB ALA B 366 " model vdw 1.141 3.760 nonbonded pdb=" CD1 ILE E 700 " pdb=" CE2 TYR E 742 " model vdw 1.707 3.760 nonbonded pdb=" SD MET E1052 " pdb=" CE2 TYR E1059 " model vdw 1.733 3.700 nonbonded pdb=" O ASP X 109 " pdb=" O ILE Y 181 " model vdw 1.772 3.040 nonbonded pdb=" CE2 PHE B 333 " pdb=" CB ALA B 366 " model vdw 1.938 3.760 ... (remaining 256998 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 'X' and (resid 1 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 69 or (resid 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 83 or (resid 84 and (n \ ame N or name CA or name C or name O or name CB )) or resid 85 or (resid 86 and \ (name N or name CA or name C or name O or name CB )) or resid 87 through 96 or ( \ resid 97 and (name N or name CA or name C or name O or name CB )) or resid 98 th \ rough 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) \ or resid 118 or (resid 119 and (name N or name CA or name C or name O or name C \ B )) or resid 120 through 125 or (resid 126 and (name N or name CA or name C or \ name O or name CB )) or resid 127 through 173 or (resid 174 and (name N or name \ CA or name C or name O or name CB )) or resid 175 through 235 or (resid 236 and \ (name N or name CA or name C or name O or name CB )) or resid 237 through 253 or \ (resid 254 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'Y' and (resid 1 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 43 or (resid 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 67 or (resid 68 and (n \ ame N or name CA or name C or name O or name CB )) or resid 69 through 78 or (re \ sid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 thro \ ugh 85 or (resid 86 and (name N or name CA or name C or name O or name CB )) or \ resid 87 through 109 or (resid 110 and (name N or name CA or name C or name O or \ name CB )) or resid 111 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )) or resid 127 through 173 or (resid 174 and (name N o \ r name CA or name C or name O or name CB )) or resid 175 through 235 or (resid 2 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 237 through \ 254)) selection = (chain 'Z' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 or (resid 72 and (name N or name CA or na \ me C or name O or name CB )) or resid 73 through 78 or (resid 79 and (name N or \ name CA or name C or name O or name CB )) or resid 80 through 109 or (resid 110 \ and (name N or name CA or name C or name O or name CB )) or resid 111 through 11 \ 8 or (resid 119 and (name N or name CA or name C or name O or name CB )) or resi \ d 120 through 252 or (resid 253 through 254 and (name N or name CA or name C or \ name O or name CB )))) } 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: 3.140 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 28.540 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 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 0.534 32533 Z= 0.659 Angle : 1.514 52.211 44146 Z= 0.967 Chirality : 0.089 0.596 5069 Planarity : 0.012 0.184 5582 Dihedral : 14.592 169.850 12281 Min Nonbonded Distance : 1.141 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.99 % Allowed : 3.94 % Favored : 95.07 % Rotamer: Outliers : 0.61 % Allowed : 5.64 % Favored : 93.75 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.89 % 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 (0.12), residues: 3958 helix: -0.49 (0.11), residues: 1707 sheet: -0.12 (0.17), residues: 812 loop : -1.63 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG Y 224 TYR 0.119 0.012 TYR E 485 PHE 0.086 0.010 PHE 1 563 TRP 0.107 0.010 TRP E 384 HIS 0.021 0.003 HIS E 388 Details of bonding type rmsd/Z covalent geometry : bond 0.01083 / 0.65 (32529) covalent geometry : angle 1.47726 / 0.97 (44134) hydrogen bonds : bond 0.15924 / 13.59 ( 1668) hydrogen bonds : angle 6.71614 / 5.75 ( 4734) metal coordination : bond 0.32341 / 15.86 ( 4) metal coordination : angle 20.24604 / 11.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 520 time to evaluate : 0.790 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: C 716 VAL cc_start: 0.8486 (t) cc_final: 0.8271 (p) REVERT: E 43 ILE cc_start: 0.8274 (mt) cc_final: 0.8008 (mm) REVERT: E 177 MET cc_start: 0.8586 (ttm) cc_final: 0.8166 (tpp) REVERT: E 308 ILE cc_start: 0.5924 (mt) cc_final: 0.5608 (mt) REVERT: E 427 LYS cc_start: 0.7373 (mtmt) cc_final: 0.7102 (ttmm) REVERT: E 459 MET cc_start: 0.5922 (mtp) cc_final: 0.5709 (mtm) REVERT: E 486 MET cc_start: 0.8408 (mmm) cc_final: 0.8050 (mpp) REVERT: E 738 ARG cc_start: 0.6736 (mmt90) cc_final: 0.4790 (mmt90) REVERT: E 825 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7577 (p) REVERT: E 846 MET cc_start: 0.8902 (ttt) cc_final: 0.8594 (ttp) REVERT: E 1056 LEU cc_start: 0.7073 (mm) cc_final: 0.6669 (mt) REVERT: E 1091 TYR cc_start: 0.6671 (p90) cc_final: 0.6356 (p90) REVERT: D 74 GLN cc_start: 0.8437 (tp40) cc_final: 0.7911 (tp40) REVERT: D 119 MET cc_start: 0.8065 (mmp) cc_final: 0.7800 (mmm) REVERT: B 6 HIS cc_start: 0.8183 (m-70) cc_final: 0.7163 (m-70) REVERT: B 43 ASP cc_start: 0.7868 (p0) cc_final: 0.7432 (p0) REVERT: B 68 THR cc_start: 0.8655 (p) cc_final: 0.8241 (p) REVERT: B 72 MET cc_start: 0.5408 (mpp) cc_final: 0.4835 (mpp) REVERT: B 113 THR cc_start: 0.8358 (m) cc_final: 0.7908 (p) REVERT: 4 111 VAL cc_start: 0.5461 (t) cc_final: 0.5235 (t) REVERT: 4 231 PRO cc_start: 0.8674 (OUTLIER) cc_final: 0.8344 (Cg_endo) REVERT: 4 294 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7355 (tp) REVERT: 2 116 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5765 (mt) REVERT: 2 263 VAL cc_start: 0.8128 (t) cc_final: 0.7884 (t) REVERT: 1 190 THR cc_start: 0.7693 (m) cc_final: 0.7467 (m) REVERT: X 44 ARG cc_start: 0.7224 (mtt180) cc_final: 0.7017 (ttt-90) REVERT: Y 68 LEU cc_start: 0.6977 (pp) cc_final: 0.6659 (pp) REVERT: Y 184 PRO cc_start: 0.8189 (Cg_exo) cc_final: 0.7868 (Cg_endo) REVERT: Z 70 MET cc_start: 0.6794 (ptt) cc_final: 0.6563 (ptt) REVERT: Z 199 MET cc_start: 0.7827 (ttp) cc_final: 0.7317 (tmm) outliers start: 21 outliers final: 3 residues processed: 537 average time/residue: 0.1814 time to fit residues: 155.5375 Evaluate side-chains 279 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 272 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0020 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 619 GLN E 638 HIS E 828 ASN ** E 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 18 GLN 4 60 HIS 4 177 GLN 4 220 ASN 4 244 ASN 3 180 ASN 3 317 GLN ** 2 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 303 GLN 2 352 GLN 5 244 ASN 5 341 HIS 1 429 ASN 1 534 GLN X 64 HIS Y 64 HIS Y 83 ASN Z 64 HIS Z 83 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.111657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.102499 restraints weight = 160492.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.103521 restraints weight = 102305.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.104231 restraints weight = 70574.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.104853 restraints weight = 52657.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.105307 restraints weight = 42146.527| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32533 Z= 0.167 Angle : 0.708 35.419 44146 Z= 0.349 Chirality : 0.044 0.252 5069 Planarity : 0.005 0.079 5582 Dihedral : 11.320 175.055 4652 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.54 % Rotamer: Outliers : 0.12 % Allowed : 2.51 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.07 (0.13), residues: 3958 helix: 0.87 (0.12), residues: 1750 sheet: 0.17 (0.17), residues: 818 loop : -0.98 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Y 224 TYR 0.032 0.002 TYR E1059 PHE 0.035 0.002 PHE B 333 TRP 0.014 0.002 TRP 1 399 HIS 0.006 0.001 HIS E 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (32529) covalent geometry : angle 0.66548 / 0.35 (44134) hydrogen bonds : bond 0.04800 / 4.13 ( 1668) hydrogen bonds : angle 5.10840 / 4.20 ( 4734) metal coordination : bond 0.01649 / 0.80 ( 4) metal coordination : angle 14.70499 / 8.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 357 time to evaluate : 1.180 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: E 43 ILE cc_start: 0.8396 (mt) cc_final: 0.8127 (mm) REVERT: E 177 MET cc_start: 0.8918 (ttm) cc_final: 0.8294 (tpp) REVERT: E 308 ILE cc_start: 0.4961 (mt) cc_final: 0.4649 (mt) REVERT: E 427 LYS cc_start: 0.7779 (mtmt) cc_final: 0.7525 (ttmm) REVERT: E 738 ARG cc_start: 0.6274 (mmt90) cc_final: 0.4614 (mmt90) REVERT: E 742 TYR cc_start: 0.6869 (m-80) cc_final: 0.5694 (m-10) REVERT: E 846 MET cc_start: 0.8548 (ttt) cc_final: 0.8235 (ttp) REVERT: E 1091 TYR cc_start: 0.6802 (p90) cc_final: 0.6533 (p90) REVERT: D 132 ILE cc_start: 0.8201 (pt) cc_final: 0.7853 (mt) REVERT: B 3 ILE cc_start: 0.5584 (mm) cc_final: 0.5211 (mm) REVERT: B 6 HIS cc_start: 0.7743 (m-70) cc_final: 0.6951 (m-70) REVERT: B 46 LYS cc_start: 0.8795 (pttt) cc_final: 0.8505 (pttp) REVERT: B 68 THR cc_start: 0.8227 (p) cc_final: 0.7930 (p) REVERT: B 96 MET cc_start: 0.4474 (ptt) cc_final: 0.4021 (ptt) REVERT: B 113 THR cc_start: 0.7536 (m) cc_final: 0.6948 (p) REVERT: B 323 MET cc_start: 0.2408 (mmm) cc_final: 0.1773 (mmm) REVERT: 4 111 VAL cc_start: 0.5947 (t) cc_final: 0.5414 (t) REVERT: 3 306 ILE cc_start: 0.7129 (mm) cc_final: 0.6733 (mm) REVERT: 2 263 VAL cc_start: 0.8296 (t) cc_final: 0.8070 (t) REVERT: 2 331 SER cc_start: 0.8258 (m) cc_final: 0.7832 (p) REVERT: 5 142 GLU cc_start: 0.6956 (tm-30) cc_final: 0.6722 (tm-30) REVERT: 5 174 MET cc_start: 0.7467 (mtm) cc_final: 0.7121 (mtm) REVERT: 1 469 MET cc_start: 0.6303 (ttp) cc_final: 0.5901 (mtt) REVERT: X 193 THR cc_start: 0.6623 (t) cc_final: 0.6399 (t) REVERT: Y 184 PRO cc_start: 0.8227 (Cg_exo) cc_final: 0.7984 (Cg_endo) REVERT: Y 204 ASP cc_start: 0.8028 (t70) cc_final: 0.7431 (t0) REVERT: Z 199 MET cc_start: 0.7802 (ttp) cc_final: 0.7446 (tmm) outliers start: 4 outliers final: 1 residues processed: 360 average time/residue: 0.1727 time to fit residues: 102.2236 Evaluate side-chains 260 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 383 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 274 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 278 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 294 optimal weight: 20.0000 chunk 264 optimal weight: 8.9990 chunk 370 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 54 HIS 4 91 ASN ** 4 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 98 GLN 4 145 ASN 4 204 GLN 4 216 HIS 4 317 HIS 3 184 HIS ** 2 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 171 ASN 2 236 GLN 5 18 HIS 5 19 ASN 5 74 GLN 5 244 ASN 1 437 GLN 1 534 GLN X 83 ASN X 94 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.101535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.092291 restraints weight = 164123.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.092965 restraints weight = 111001.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.093543 restraints weight = 76350.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.093762 restraints weight = 62756.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.093782 restraints weight = 54099.067| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.129 32533 Z= 0.340 Angle : 0.928 31.068 44146 Z= 0.464 Chirality : 0.051 0.222 5069 Planarity : 0.007 0.064 5582 Dihedral : 11.464 179.259 4652 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.78 % Favored : 95.12 % Rotamer: Outliers : 0.26 % Allowed : 4.65 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.62 (0.13), residues: 3958 helix: 0.13 (0.12), residues: 1748 sheet: -0.02 (0.18), residues: 789 loop : -1.18 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG X 44 TYR 0.046 0.003 TYR 5 161 PHE 0.031 0.003 PHE E 139 TRP 0.032 0.003 TRP B 58 HIS 0.012 0.002 HIS 3 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00757 / 0.34 (32529) covalent geometry : angle 0.90769 / 0.46 (44134) hydrogen bonds : bond 0.05603 / 4.68 ( 1668) hydrogen bonds : angle 5.62122 / 4.50 ( 4734) metal coordination : bond 0.01219 / 0.60 ( 4) metal coordination : angle 11.78565 / 6.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 296 time to evaluate : 1.248 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: E 43 ILE cc_start: 0.8566 (mt) cc_final: 0.8329 (mm) REVERT: E 177 MET cc_start: 0.9079 (ttm) cc_final: 0.8418 (tpp) REVERT: E 314 MET cc_start: 0.7359 (ttm) cc_final: 0.7153 (tpp) REVERT: E 868 VAL cc_start: 0.8989 (m) cc_final: 0.8585 (p) REVERT: E 876 THR cc_start: 0.8144 (p) cc_final: 0.7866 (p) REVERT: D 119 MET cc_start: 0.8205 (mmm) cc_final: 0.7588 (mmt) REVERT: D 132 ILE cc_start: 0.8655 (pt) cc_final: 0.8159 (tp) REVERT: B 3 ILE cc_start: 0.7444 (mm) cc_final: 0.6953 (mm) REVERT: B 6 HIS cc_start: 0.8153 (m-70) cc_final: 0.6799 (m-70) REVERT: B 96 MET cc_start: 0.4768 (ptt) cc_final: 0.4447 (ptt) REVERT: B 113 THR cc_start: 0.8496 (m) cc_final: 0.8087 (p) REVERT: B 323 MET cc_start: 0.2346 (mmm) cc_final: 0.1596 (mmm) REVERT: 4 183 ASP cc_start: 0.8223 (t70) cc_final: 0.7989 (t70) REVERT: 3 62 THR cc_start: 0.8122 (m) cc_final: 0.7904 (m) REVERT: 3 306 ILE cc_start: 0.7610 (mm) cc_final: 0.7304 (mm) REVERT: 2 88 MET cc_start: 0.7563 (mmm) cc_final: 0.6944 (tmm) REVERT: 2 192 LEU cc_start: 0.7892 (mt) cc_final: 0.7645 (mp) REVERT: 5 85 LEU cc_start: 0.6849 (tt) cc_final: 0.6565 (tp) REVERT: 5 142 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7025 (tm-30) REVERT: 5 299 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6426 (mm) REVERT: 1 402 ILE cc_start: 0.5943 (OUTLIER) cc_final: 0.5629 (mt) REVERT: 1 425 GLN cc_start: 0.8066 (mt0) cc_final: 0.7820 (mt0) REVERT: 1 437 GLN cc_start: 0.7431 (mt0) cc_final: 0.7126 (mt0) REVERT: X 188 MET cc_start: 0.7499 (mmp) cc_final: 0.7183 (mmp) REVERT: Y 188 MET cc_start: 0.6696 (mmm) cc_final: 0.6462 (mmm) outliers start: 9 outliers final: 2 residues processed: 303 average time/residue: 0.1648 time to fit residues: 83.3885 Evaluate side-chains 231 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 227 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 27 optimal weight: 6.9990 chunk 366 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 375 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 394 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 363 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 171 GLN ** 2 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 534 GLN 1 593 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.103310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.093819 restraints weight = 161283.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.094715 restraints weight = 100935.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.095346 restraints weight = 70241.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.095898 restraints weight = 53426.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.096318 restraints weight = 43486.501| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32533 Z= 0.168 Angle : 0.648 29.224 44146 Z= 0.322 Chirality : 0.043 0.228 5069 Planarity : 0.004 0.060 5582 Dihedral : 11.115 173.145 4652 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.21 % Rotamer: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.20 (0.13), residues: 3958 helix: 0.67 (0.12), residues: 1758 sheet: -0.12 (0.17), residues: 811 loop : -1.05 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 2 188 TYR 0.023 0.002 TYR E1059 PHE 0.021 0.002 PHE E 139 TRP 0.017 0.002 TRP E 841 HIS 0.005 0.001 HIS E 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (32529) covalent geometry : angle 0.62109 / 0.32 (44134) hydrogen bonds : bond 0.04223 / 3.58 ( 1668) hydrogen bonds : angle 5.17790 / 4.18 ( 4734) metal coordination : bond 0.00735 / 0.37 ( 4) metal coordination : angle 11.19783 / 6.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 43 ILE cc_start: 0.8612 (mt) cc_final: 0.8382 (mm) REVERT: E 177 MET cc_start: 0.9056 (ttm) cc_final: 0.8397 (tpp) REVERT: E 242 ILE cc_start: 0.5518 (mm) cc_final: 0.4822 (mt) REVERT: E 314 MET cc_start: 0.7618 (ttm) cc_final: 0.5998 (tpp) REVERT: E 325 ARG cc_start: 0.7460 (ttm-80) cc_final: 0.7218 (mmp80) REVERT: E 868 VAL cc_start: 0.8945 (m) cc_final: 0.8630 (p) REVERT: E 1052 MET cc_start: 0.5110 (ttm) cc_final: 0.4807 (ttm) REVERT: E 1056 LEU cc_start: 0.7040 (mp) cc_final: 0.6472 (mt) REVERT: D 119 MET cc_start: 0.7731 (mmm) cc_final: 0.7139 (mmt) REVERT: D 132 ILE cc_start: 0.8323 (pt) cc_final: 0.8103 (pt) REVERT: B 3 ILE cc_start: 0.6092 (mm) cc_final: 0.5846 (mm) REVERT: B 6 HIS cc_start: 0.7722 (m-70) cc_final: 0.6772 (m-70) REVERT: B 96 MET cc_start: 0.4458 (ptt) cc_final: 0.4074 (ptt) REVERT: B 113 THR cc_start: 0.8280 (m) cc_final: 0.7886 (p) REVERT: B 323 MET cc_start: 0.2664 (mmm) cc_final: 0.1810 (mmm) REVERT: 4 183 ASP cc_start: 0.7887 (t70) cc_final: 0.7678 (t70) REVERT: 3 158 LEU cc_start: 0.6871 (mt) cc_final: 0.6618 (mt) REVERT: 3 306 ILE cc_start: 0.7587 (mm) cc_final: 0.7296 (mm) REVERT: 2 88 MET cc_start: 0.7660 (tpt) cc_final: 0.7231 (tmm) REVERT: 5 85 LEU cc_start: 0.6667 (tt) cc_final: 0.6249 (tp) REVERT: 5 142 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6858 (tm-30) REVERT: 5 174 MET cc_start: 0.7565 (mtp) cc_final: 0.6516 (mtm) REVERT: Y 184 PRO cc_start: 0.8442 (Cg_exo) cc_final: 0.8108 (Cg_endo) REVERT: Y 188 MET cc_start: 0.6682 (mmm) cc_final: 0.6424 (mmm) REVERT: Y 204 ASP cc_start: 0.8258 (t0) cc_final: 0.7951 (t0) REVERT: Z 188 MET cc_start: 0.8856 (mmm) cc_final: 0.8624 (mmm) outliers start: 1 outliers final: 0 residues processed: 306 average time/residue: 0.1811 time to fit residues: 90.8638 Evaluate side-chains 235 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 318 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 chunk 298 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 384 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** E 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 859 GLN ** E 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 60 HIS 4 64 HIS ** 4 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 95 ASN ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 229 ASN 1 425 GLN 1 534 GLN Y 190 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.099535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.090276 restraints weight = 165561.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.091108 restraints weight = 107235.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.091888 restraints weight = 68184.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.091959 restraints weight = 63548.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.091956 restraints weight = 50813.093| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 32533 Z= 0.289 Angle : 0.807 30.058 44146 Z= 0.403 Chirality : 0.048 0.205 5069 Planarity : 0.006 0.146 5582 Dihedral : 11.216 168.992 4652 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.36 % Favored : 94.54 % Rotamer: Outliers : 0.15 % Allowed : 3.62 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.69 (0.13), residues: 3958 helix: 0.32 (0.12), residues: 1749 sheet: -0.47 (0.17), residues: 799 loop : -1.30 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 2 101 TYR 0.037 0.003 TYR 5 161 PHE 0.026 0.003 PHE E 139 TRP 0.018 0.002 TRP 4 257 HIS 0.012 0.002 HIS Z 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.29 (32529) covalent geometry : angle 0.78197 / 0.40 (44134) hydrogen bonds : bond 0.04989 / 4.17 ( 1668) hydrogen bonds : angle 5.57661 / 4.46 ( 4734) metal coordination : bond 0.04042 / 2.01 ( 4) metal coordination : angle 12.09038 / 6.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 266 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 43 ILE cc_start: 0.8659 (mt) cc_final: 0.8421 (mm) REVERT: E 349 ILE cc_start: 0.8023 (mm) cc_final: 0.7761 (mm) REVERT: E 458 LEU cc_start: 0.9297 (mm) cc_final: 0.8599 (mm) REVERT: E 486 MET cc_start: 0.8987 (mmm) cc_final: 0.8758 (mmm) REVERT: E 868 VAL cc_start: 0.9009 (m) cc_final: 0.8662 (p) REVERT: E 953 MET cc_start: 0.6627 (mtp) cc_final: 0.6353 (mtm) REVERT: E 1052 MET cc_start: 0.5430 (ttm) cc_final: 0.5185 (ttm) REVERT: D 119 MET cc_start: 0.8318 (mmm) cc_final: 0.8009 (mmm) REVERT: B 3 ILE cc_start: 0.7719 (mm) cc_final: 0.7297 (mm) REVERT: B 6 HIS cc_start: 0.8384 (m-70) cc_final: 0.7421 (m-70) REVERT: B 33 GLN cc_start: 0.6760 (mt0) cc_final: 0.6503 (mt0) REVERT: B 96 MET cc_start: 0.4668 (ptt) cc_final: 0.4370 (ptt) REVERT: B 113 THR cc_start: 0.8729 (m) cc_final: 0.8400 (p) REVERT: 4 183 ASP cc_start: 0.8205 (t70) cc_final: 0.7899 (t70) REVERT: 4 288 MET cc_start: 0.7641 (mtt) cc_final: 0.7429 (mtp) REVERT: 3 151 HIS cc_start: 0.7961 (p-80) cc_final: 0.7657 (p-80) REVERT: 3 174 ILE cc_start: 0.8391 (mm) cc_final: 0.8185 (mm) REVERT: 3 306 ILE cc_start: 0.7786 (mm) cc_final: 0.7351 (mm) REVERT: 5 142 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7090 (tm-30) REVERT: 1 239 VAL cc_start: 0.8232 (t) cc_final: 0.8029 (p) REVERT: Y 188 MET cc_start: 0.7355 (mmm) cc_final: 0.7065 (mmm) REVERT: Y 204 ASP cc_start: 0.8331 (t0) cc_final: 0.8116 (t0) outliers start: 5 outliers final: 2 residues processed: 271 average time/residue: 0.1619 time to fit residues: 74.6142 Evaluate side-chains 218 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 385 optimal weight: 9.9990 chunk 377 optimal weight: 5.9990 chunk 272 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 360 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 198 optimal weight: 0.4980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 859 GLN ** E 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 60 HIS ** 4 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 321 ASN ** 2 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 534 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.101639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.092368 restraints weight = 161972.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.093229 restraints weight = 107518.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.093878 restraints weight = 72762.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.094118 restraints weight = 58079.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.094158 restraints weight = 48503.143| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 32533 Z= 0.155 Angle : 0.640 26.544 44146 Z= 0.317 Chirality : 0.043 0.235 5069 Planarity : 0.004 0.074 5582 Dihedral : 10.979 167.667 4652 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.07 % Favored : 95.83 % Rotamer: Outliers : 0.03 % Allowed : 1.67 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.31 (0.13), residues: 3958 helix: 0.68 (0.12), residues: 1755 sheet: -0.36 (0.17), residues: 803 loop : -1.11 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 154 TYR 0.029 0.001 TYR Y 211 PHE 0.024 0.002 PHE 1 443 TRP 0.012 0.001 TRP 1 141 HIS 0.006 0.001 HIS 4 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (32529) covalent geometry : angle 0.61255 / 0.32 (44134) hydrogen bonds : bond 0.04142 / 3.50 ( 1668) hydrogen bonds : angle 5.21249 / 4.21 ( 4734) metal coordination : bond 0.01141 / 0.57 ( 4) metal coordination : angle 11.33280 / 6.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 458 LEU cc_start: 0.9246 (mm) cc_final: 0.8213 (mm) REVERT: E 459 MET cc_start: 0.6043 (mtm) cc_final: 0.5790 (mtm) REVERT: E 486 MET cc_start: 0.8941 (mmm) cc_final: 0.8724 (mmm) REVERT: E 506 GLU cc_start: 0.8337 (pt0) cc_final: 0.8030 (pt0) REVERT: E 851 CYS cc_start: 0.8112 (m) cc_final: 0.7883 (m) REVERT: E 868 VAL cc_start: 0.8963 (m) cc_final: 0.8693 (p) REVERT: E 1052 MET cc_start: 0.5417 (ttm) cc_final: 0.5137 (ttm) REVERT: E 1056 LEU cc_start: 0.7586 (mm) cc_final: 0.7367 (mm) REVERT: D 104 MET cc_start: 0.7131 (ptp) cc_final: 0.6830 (ptt) REVERT: B 3 ILE cc_start: 0.7504 (mm) cc_final: 0.7132 (mm) REVERT: B 6 HIS cc_start: 0.8105 (m-70) cc_final: 0.6955 (m-70) REVERT: B 33 GLN cc_start: 0.6682 (mt0) cc_final: 0.6376 (mt0) REVERT: B 88 LEU cc_start: 0.9299 (mt) cc_final: 0.9070 (mt) REVERT: B 96 MET cc_start: 0.4677 (ptt) cc_final: 0.4383 (ptt) REVERT: B 113 THR cc_start: 0.8753 (m) cc_final: 0.8419 (p) REVERT: 4 288 MET cc_start: 0.7671 (mtt) cc_final: 0.7461 (mtp) REVERT: 3 151 HIS cc_start: 0.7847 (p-80) cc_final: 0.7542 (p-80) REVERT: 3 306 ILE cc_start: 0.7656 (mm) cc_final: 0.7387 (mm) REVERT: 5 142 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6785 (tm-30) REVERT: 1 338 MET cc_start: 0.4832 (mmm) cc_final: 0.4392 (mmm) REVERT: Y 184 PRO cc_start: 0.8516 (Cg_exo) cc_final: 0.8150 (Cg_endo) REVERT: Y 188 MET cc_start: 0.7229 (mmm) cc_final: 0.7020 (mmm) REVERT: Y 204 ASP cc_start: 0.8289 (t0) cc_final: 0.7883 (t0) REVERT: Z 119 MET cc_start: 0.6403 (mmm) cc_final: 0.6191 (mmm) REVERT: Z 153 GLN cc_start: 0.7204 (mt0) cc_final: 0.6949 (mt0) outliers start: 1 outliers final: 0 residues processed: 286 average time/residue: 0.1666 time to fit residues: 80.9316 Evaluate side-chains 225 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 324 optimal weight: 0.5980 chunk 279 optimal weight: 5.9990 chunk 362 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 282 optimal weight: 0.0970 chunk 92 optimal weight: 9.9990 chunk 283 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 overall best weight: 3.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 698 ASN ** E 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 26 ASN 4 64 HIS ** 2 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 534 GLN ** Y 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.100863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.091538 restraints weight = 163223.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.092630 restraints weight = 105964.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.093435 restraints weight = 66886.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.093545 restraints weight = 57962.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.093557 restraints weight = 46198.543| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32533 Z= 0.178 Angle : 0.651 23.395 44146 Z= 0.322 Chirality : 0.044 0.239 5069 Planarity : 0.004 0.058 5582 Dihedral : 10.920 171.469 4652 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 0.03 % Allowed : 1.14 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.23 (0.13), residues: 3958 helix: 0.75 (0.12), residues: 1744 sheet: -0.37 (0.17), residues: 802 loop : -1.04 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 3 20 TYR 0.034 0.002 TYR Y 211 PHE 0.022 0.002 PHE E 139 TRP 0.011 0.001 TRP 4 257 HIS 0.013 0.001 HIS 4 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (32529) covalent geometry : angle 0.62612 / 0.32 (44134) hydrogen bonds : bond 0.04108 / 3.47 ( 1668) hydrogen bonds : angle 5.20975 / 4.22 ( 4734) metal coordination : bond 0.00834 / 0.42 ( 4) metal coordination : angle 10.76892 / 5.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 263 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 458 LEU cc_start: 0.9288 (mm) cc_final: 0.8986 (mt) REVERT: E 459 MET cc_start: 0.6317 (mtm) cc_final: 0.6022 (mtm) REVERT: E 486 MET cc_start: 0.8995 (mmm) cc_final: 0.8772 (mmm) REVERT: E 851 CYS cc_start: 0.8103 (m) cc_final: 0.7867 (m) REVERT: E 868 VAL cc_start: 0.8929 (m) cc_final: 0.8604 (p) REVERT: E 1052 MET cc_start: 0.4957 (ttm) cc_final: 0.4700 (ttm) REVERT: D 119 MET cc_start: 0.8231 (mmm) cc_final: 0.7901 (mmm) REVERT: B 3 ILE cc_start: 0.7579 (mm) cc_final: 0.7189 (mm) REVERT: B 6 HIS cc_start: 0.8265 (m-70) cc_final: 0.7289 (m-70) REVERT: B 33 GLN cc_start: 0.6748 (mt0) cc_final: 0.6375 (mt0) REVERT: B 88 LEU cc_start: 0.9234 (mt) cc_final: 0.9002 (mt) REVERT: B 96 MET cc_start: 0.4695 (ptt) cc_final: 0.4352 (ptt) REVERT: B 113 THR cc_start: 0.8838 (m) cc_final: 0.8539 (p) REVERT: 3 151 HIS cc_start: 0.8012 (p-80) cc_final: 0.7733 (p-80) REVERT: 3 306 ILE cc_start: 0.7676 (mm) cc_final: 0.7339 (mm) REVERT: Y 187 ASP cc_start: 0.7359 (t0) cc_final: 0.7103 (t0) REVERT: Y 204 ASP cc_start: 0.8221 (t0) cc_final: 0.7987 (t0) REVERT: Z 119 MET cc_start: 0.6343 (mmm) cc_final: 0.6141 (mmm) REVERT: Z 153 GLN cc_start: 0.7289 (mt0) cc_final: 0.7045 (mt0) outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.1664 time to fit residues: 75.1287 Evaluate side-chains 224 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 38 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 351 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 151 HIS ** 2 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 534 GLN ** Y 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.101107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.091895 restraints weight = 162871.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.092810 restraints weight = 108397.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.093170 restraints weight = 69448.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.093410 restraints weight = 60435.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.093433 restraints weight = 54169.060| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 32533 Z= 0.169 Angle : 0.635 21.899 44146 Z= 0.314 Chirality : 0.043 0.248 5069 Planarity : 0.004 0.066 5582 Dihedral : 10.856 177.660 4652 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.19 % Favored : 95.70 % Rotamer: Outliers : 0.03 % Allowed : 0.88 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.16 (0.13), residues: 3958 helix: 0.79 (0.12), residues: 1745 sheet: -0.35 (0.18), residues: 804 loop : -0.98 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 80 TYR 0.025 0.002 TYR E 462 PHE 0.020 0.002 PHE E 139 TRP 0.011 0.001 TRP 1 141 HIS 0.004 0.001 HIS 4 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (32529) covalent geometry : angle 0.61070 / 0.31 (44134) hydrogen bonds : bond 0.04011 / 3.39 ( 1668) hydrogen bonds : angle 5.16190 / 4.18 ( 4734) metal coordination : bond 0.00730 / 0.36 ( 4) metal coordination : angle 10.67025 / 5.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 458 LEU cc_start: 0.9125 (mm) cc_final: 0.8719 (mt) REVERT: E 459 MET cc_start: 0.6601 (mtm) cc_final: 0.6290 (mtm) REVERT: E 486 MET cc_start: 0.8964 (mmm) cc_final: 0.8746 (mmm) REVERT: E 851 CYS cc_start: 0.8121 (m) cc_final: 0.7903 (m) REVERT: E 1052 MET cc_start: 0.5126 (ttm) cc_final: 0.4862 (ttm) REVERT: E 1056 LEU cc_start: 0.7544 (mm) cc_final: 0.7333 (mm) REVERT: D 62 GLN cc_start: 0.8190 (mp10) cc_final: 0.7526 (mp10) REVERT: D 104 MET cc_start: 0.7634 (ptp) cc_final: 0.6967 (ptt) REVERT: D 119 MET cc_start: 0.8199 (mmm) cc_final: 0.7220 (mmt) REVERT: B 3 ILE cc_start: 0.7761 (mm) cc_final: 0.7372 (mm) REVERT: B 6 HIS cc_start: 0.8117 (m-70) cc_final: 0.6985 (m-70) REVERT: B 33 GLN cc_start: 0.6816 (mt0) cc_final: 0.6394 (mt0) REVERT: B 88 LEU cc_start: 0.9177 (mt) cc_final: 0.8962 (mt) REVERT: B 96 MET cc_start: 0.4808 (ptt) cc_final: 0.4501 (ptt) REVERT: B 113 THR cc_start: 0.8852 (m) cc_final: 0.8586 (p) REVERT: 3 151 HIS cc_start: 0.8025 (p90) cc_final: 0.7725 (p-80) REVERT: 3 306 ILE cc_start: 0.7708 (mm) cc_final: 0.7385 (mm) REVERT: 2 88 MET cc_start: 0.6901 (ttp) cc_final: 0.6685 (ttp) REVERT: 1 338 MET cc_start: 0.5039 (mmm) cc_final: 0.4566 (mmm) REVERT: Y 187 ASP cc_start: 0.7357 (t0) cc_final: 0.7118 (t0) REVERT: Y 204 ASP cc_start: 0.8190 (t0) cc_final: 0.7939 (t0) REVERT: Z 153 GLN cc_start: 0.7232 (mt0) cc_final: 0.6961 (mt0) REVERT: Z 199 MET cc_start: 0.7863 (tmm) cc_final: 0.6886 (tmm) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.1627 time to fit residues: 73.7049 Evaluate side-chains 222 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 304 optimal weight: 6.9990 chunk 268 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 chunk 317 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 376 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 64 HIS 4 124 GLN ** 2 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 534 GLN ** 1 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.100237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.091001 restraints weight = 162890.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.091962 restraints weight = 107753.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.092674 restraints weight = 69050.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.092868 restraints weight = 60363.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.092835 restraints weight = 47622.608| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32533 Z= 0.197 Angle : 0.671 21.327 44146 Z= 0.333 Chirality : 0.044 0.256 5069 Planarity : 0.005 0.070 5582 Dihedral : 10.889 178.558 4652 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 0.03 % Allowed : 0.53 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.31 (0.13), residues: 3958 helix: 0.66 (0.12), residues: 1748 sheet: -0.39 (0.18), residues: 806 loop : -1.06 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 3 20 TYR 0.023 0.002 TYR E 462 PHE 0.023 0.002 PHE Z 239 TRP 0.013 0.002 TRP E 791 HIS 0.015 0.001 HIS 4 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (32529) covalent geometry : angle 0.64746 / 0.33 (44134) hydrogen bonds : bond 0.04183 / 3.50 ( 1668) hydrogen bonds : angle 5.26806 / 4.25 ( 4734) metal coordination : bond 0.00852 / 0.43 ( 4) metal coordination : angle 10.72774 / 5.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 458 LEU cc_start: 0.9129 (mm) cc_final: 0.8695 (mt) REVERT: E 459 MET cc_start: 0.6612 (mtm) cc_final: 0.6362 (mtm) REVERT: E 486 MET cc_start: 0.8995 (mmm) cc_final: 0.8757 (mmm) REVERT: E 1052 MET cc_start: 0.4899 (ttm) cc_final: 0.4638 (ttm) REVERT: D 62 GLN cc_start: 0.8021 (mp10) cc_final: 0.7413 (mp10) REVERT: D 101 MET cc_start: 0.8356 (mmm) cc_final: 0.7928 (mmm) REVERT: D 104 MET cc_start: 0.7375 (ptp) cc_final: 0.6758 (ptt) REVERT: B 3 ILE cc_start: 0.7528 (mm) cc_final: 0.7167 (mm) REVERT: B 6 HIS cc_start: 0.8228 (m-70) cc_final: 0.7190 (m-70) REVERT: B 33 GLN cc_start: 0.6746 (mt0) cc_final: 0.6332 (mt0) REVERT: B 96 MET cc_start: 0.4830 (ptt) cc_final: 0.4515 (ptt) REVERT: B 113 THR cc_start: 0.8868 (m) cc_final: 0.8590 (p) REVERT: 4 288 MET cc_start: 0.7727 (mtt) cc_final: 0.7482 (mtp) REVERT: 3 151 HIS cc_start: 0.8222 (p90) cc_final: 0.7946 (p-80) REVERT: 3 306 ILE cc_start: 0.7690 (mm) cc_final: 0.7383 (mm) REVERT: 2 88 MET cc_start: 0.6976 (ttp) cc_final: 0.6688 (ttp) REVERT: 1 338 MET cc_start: 0.4963 (mmm) cc_final: 0.4562 (mmm) REVERT: Y 187 ASP cc_start: 0.7237 (t0) cc_final: 0.6986 (t0) REVERT: Y 204 ASP cc_start: 0.8195 (t0) cc_final: 0.7959 (t0) REVERT: Z 153 GLN cc_start: 0.7263 (mt0) cc_final: 0.6996 (mt0) outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.1676 time to fit residues: 72.2632 Evaluate side-chains 215 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 313 optimal weight: 0.9980 chunk 390 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 293 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 859 GLN ** E 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 534 GLN ** 1 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.100148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.090824 restraints weight = 164064.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.091787 restraints weight = 106982.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.092764 restraints weight = 66983.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.092809 restraints weight = 56493.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.092836 restraints weight = 44851.419| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32533 Z= 0.195 Angle : 0.664 19.380 44146 Z= 0.330 Chirality : 0.044 0.254 5069 Planarity : 0.004 0.060 5582 Dihedral : 10.870 177.967 4652 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.67 % Favored : 95.22 % Rotamer: Outliers : 0.03 % Allowed : 0.29 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.31 (0.13), residues: 3958 helix: 0.66 (0.12), residues: 1743 sheet: -0.35 (0.18), residues: 800 loop : -1.08 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 101 TYR 0.023 0.002 TYR 3 52 PHE 0.023 0.002 PHE Z 19 TRP 0.012 0.002 TRP 1 141 HIS 0.005 0.001 HIS 4 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (32529) covalent geometry : angle 0.64047 / 0.33 (44134) hydrogen bonds : bond 0.04144 / 3.48 ( 1668) hydrogen bonds : angle 5.25883 / 4.24 ( 4734) metal coordination : bond 0.00939 / 0.47 ( 4) metal coordination : angle 10.68696 / 5.90 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7916 Ramachandran restraints generated. 3958 Oldfield, 0 Emsley, 3958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 458 LEU cc_start: 0.9124 (mm) cc_final: 0.8662 (mt) REVERT: E 459 MET cc_start: 0.6801 (mtm) cc_final: 0.6560 (mtm) REVERT: E 486 MET cc_start: 0.8997 (mmm) cc_final: 0.8744 (mmm) REVERT: E 953 MET cc_start: 0.6331 (mtp) cc_final: 0.6056 (mtm) REVERT: E 1052 MET cc_start: 0.4877 (ttm) cc_final: 0.4610 (ttm) REVERT: D 62 GLN cc_start: 0.8174 (mp10) cc_final: 0.7608 (mp10) REVERT: D 101 MET cc_start: 0.8409 (mmm) cc_final: 0.8003 (mmm) REVERT: D 104 MET cc_start: 0.7556 (ptp) cc_final: 0.6896 (ptt) REVERT: B 3 ILE cc_start: 0.7693 (mm) cc_final: 0.7315 (mm) REVERT: B 6 HIS cc_start: 0.8010 (m-70) cc_final: 0.6968 (m-70) REVERT: B 33 GLN cc_start: 0.6783 (mt0) cc_final: 0.6362 (mt0) REVERT: B 88 LEU cc_start: 0.9131 (mt) cc_final: 0.8811 (mt) REVERT: B 96 MET cc_start: 0.4753 (ptt) cc_final: 0.4410 (ptt) REVERT: B 113 THR cc_start: 0.8928 (m) cc_final: 0.8664 (p) REVERT: 3 122 MET cc_start: 0.6792 (mmt) cc_final: 0.6505 (mmt) REVERT: 3 306 ILE cc_start: 0.7709 (mm) cc_final: 0.7400 (mm) REVERT: 2 88 MET cc_start: 0.7032 (ttp) cc_final: 0.6770 (ttp) REVERT: 5 142 GLU cc_start: 0.6509 (tm-30) cc_final: 0.5994 (pp20) REVERT: 5 174 MET cc_start: 0.7554 (mtm) cc_final: 0.7025 (mtm) REVERT: 1 338 MET cc_start: 0.5024 (mmm) cc_final: 0.4682 (mmm) REVERT: Y 187 ASP cc_start: 0.7217 (t0) cc_final: 0.6954 (t0) REVERT: Y 204 ASP cc_start: 0.8208 (t0) cc_final: 0.7941 (t0) REVERT: Z 119 MET cc_start: 0.6405 (mmm) cc_final: 0.6142 (mmm) REVERT: Z 153 GLN cc_start: 0.7318 (mt0) cc_final: 0.7098 (mt0) REVERT: Z 199 MET cc_start: 0.7957 (tmm) cc_final: 0.7009 (tmm) outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.1649 time to fit residues: 70.1054 Evaluate side-chains 214 residues out of total 3605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 278 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 310 optimal weight: 9.9990 chunk 306 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 357 optimal weight: 8.9990 chunk 386 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 370 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 38 HIS 5 229 ASN 5 317 ASN 1 534 GLN ** 1 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.097657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.087981 restraints weight = 166688.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088909 restraints weight = 115381.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089046 restraints weight = 75119.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.089241 restraints weight = 69679.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.089304 restraints weight = 62016.857| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 32533 Z= 0.290 Angle : 0.786 19.561 44146 Z= 0.393 Chirality : 0.048 0.276 5069 Planarity : 0.006 0.065 5582 Dihedral : 11.011 174.008 4652 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.19 % Favored : 93.71 % Rotamer: Outliers : 0.03 % Allowed : 0.29 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.76 (0.13), residues: 3958 helix: 0.22 (0.12), residues: 1745 sheet: -0.48 (0.18), residues: 806 loop : -1.30 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 3 20 TYR 0.026 0.002 TYR 5 161 PHE 0.030 0.003 PHE Z 19 TRP 0.017 0.002 TRP 1 141 HIS 0.009 0.002 HIS 5 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.29 (32529) covalent geometry : angle 0.76474 / 0.39 (44134) hydrogen bonds : bond 0.04752 / 3.96 ( 1668) hydrogen bonds : angle 5.60607 / 4.49 ( 4734) metal coordination : bond 0.01128 / 0.56 ( 4) metal coordination : angle 11.14954 / 6.15 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3914.03 seconds wall clock time: 69 minutes 13.16 seconds (4153.16 seconds total)