Starting phenix.real_space_refine on Tue Sep 15 10:51:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6q9b_4479/09_2026/6q9b_4479.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q9b_4479/09_2026/6q9b_4479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6q9b_4479/09_2026/6q9b_4479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q9b_4479/09_2026/6q9b_4479.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6q9b_4479/09_2026/6q9b_4479.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6q9b_4479/09_2026/6q9b_4479.cif" model { file = "/net/cci-nas-00/data/ceres_data/6q9b_4479/09_2026/6q9b_4479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q9b_4479/09_2026/6q9b_4479.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 276 5.16 5 C 24847 2.51 5 N 6172 2.21 5 O 6700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.07s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38012 Number of models: 1 Model: "" Number of chains: 37 Chain: "S2" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 325 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 7, 'TRANS': 31} Chain: "D3" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 728 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "D1" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2400 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 278} Chain breaks: 1 Chain: "D6" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1308 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 164} Chain breaks: 1 Chain: "4L" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain: "D5" Number of atoms: 4805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4805 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Chain: "D4" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3646 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 437} Chain: "D2" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2724 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 326} Chain: "AK" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1025 Classifications: {'peptide': 140} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain: "B5" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1156 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "AB" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "A8" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1404 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 156} Chain: "BJ" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "AJ" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2583 Classifications: {'peptide': 319} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 299} Chain: "S5" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "A3" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 62} Chain: "B3" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 578 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C2" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 997 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 107} Chain: "B4" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 117} Chain: "AM" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 945 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "B6" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 804 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 12, 'TRANS': 82} Chain breaks: 1 Chain: "B7" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1026 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "B9" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1515 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 16, 'TRANS': 159} Chain: "B2" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "B8" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1324 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 135} Chain: "BK" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 853 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 93} Chain: "C1" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 391 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 3, 'TRANS': 42} Chain: "B1" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 449 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "A1" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 577 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "D6" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "D5" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 200 Unusual residues: {'3PE': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 102 Chain: "D4" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'3PE': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 71 Chain: "AK" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "B5" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "AB" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "A8" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "B4" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 23 Time building chain proxies: 7.40, per 1000 atoms: 0.19 Number of scatterers: 38012 At special positions: 0 Unit cell: (221.2, 134.4, 151.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 276 16.00 P 17 15.00 O 6700 8.00 N 6172 7.00 C 24847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYSAK 17 " - pdb=" SG CYSAK 74 " distance=2.03 Simple disulfide: pdb=" SG CYSAK 94 " - pdb=" SG CYSAK 114 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 35 " - pdb=" SG CYSA8 65 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 45 " - pdb=" SG CYSA8 55 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 77 " - pdb=" SG CYSA8 109 " distance=2.02 Simple disulfide: pdb=" SG CYSA8 87 " - pdb=" SG CYSA8 99 " distance=2.03 Simple disulfide: pdb=" SG CYSBJ 76 " - pdb=" SG CYSBJ 83 " distance=2.04 Simple disulfide: pdb=" SG CYSBJ 112 " - pdb=" SG CYSBJ 124 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 32 " - pdb=" SG CYSS5 65 " distance=2.04 Simple disulfide: pdb=" SG CYSS5 42 " - pdb=" SG CYSS5 55 " distance=2.04 Simple disulfide: pdb=" SG CYSB7 58 " - pdb=" SG CYSB7 89 " distance=2.03 Simple disulfide: pdb=" SG CYSB7 68 " - pdb=" SG CYSB7 79 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.3 seconds 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8772 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 4 sheets defined 64.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'S2' and resid 7 through 13 removed outlier: 3.600A pdb=" N ALAS2 11 " --> pdb=" O ASPS2 7 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLNS2 13 " --> pdb=" O GLUS2 9 " (cutoff:3.500A) Processing helix chain 'D3' and resid 2 through 24 Processing helix chain 'D3' and resid 52 through 73 removed outlier: 4.238A pdb=" N VALD3 58 " --> pdb=" O LYSD3 54 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALAD3 59 " --> pdb=" O PHED3 55 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILED3 60 " --> pdb=" O PHED3 56 " (cutoff:3.500A) Processing helix chain 'D3' and resid 74 through 79 Processing helix chain 'D3' and resid 83 through 108 removed outlier: 3.748A pdb=" N METD3 87 " --> pdb=" O ASND3 83 " (cutoff:3.500A) Processing helix chain 'D1' and resid 2 through 32 Proline residue: D1 12 - end of helix removed outlier: 3.931A pdb=" N LEUD1 15 " --> pdb=" O ILED1 11 " (cutoff:3.500A) Processing helix chain 'D1' and resid 45 through 58 Processing helix chain 'D1' and resid 67 through 85 Proline residue: D1 75 - end of helix Processing helix chain 'D1' and resid 101 through 123 Processing helix chain 'D1' and resid 126 through 141 Processing helix chain 'D1' and resid 142 through 155 removed outlier: 3.545A pdb=" N ALAD1 147 " --> pdb=" O GLUD1 143 " (cutoff:3.500A) Processing helix chain 'D1' and resid 162 through 169 Processing helix chain 'D1' and resid 178 through 193 removed outlier: 3.527A pdb=" N ALAD1 182 " --> pdb=" O ALAD1 178 " (cutoff:3.500A) Processing helix chain 'D1' and resid 219 through 242 Processing helix chain 'D1' and resid 251 through 276 removed outlier: 4.547A pdb=" N TYRD1 255 " --> pdb=" O METD1 251 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SERD1 276 " --> pdb=" O TRPD1 272 " (cutoff:3.500A) Processing helix chain 'D1' and resid 281 through 307 Proline residue: D1 295 - end of helix Processing helix chain 'D1' and resid 307 through 312 Processing helix chain 'D6' and resid 4 through 22 Processing helix chain 'D6' and resid 25 through 48 Processing helix chain 'D6' and resid 50 through 61 removed outlier: 4.316A pdb=" N LEUD6 54 " --> pdb=" O SERD6 50 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHED6 57 " --> pdb=" O GLYD6 53 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILED6 59 " --> pdb=" O METD6 55 " (cutoff:3.500A) Processing helix chain 'D6' and resid 64 through 76 removed outlier: 3.619A pdb=" N ALAD6 75 " --> pdb=" O THRD6 71 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THRD6 76 " --> pdb=" O THRD6 72 " (cutoff:3.500A) Processing helix chain 'D6' and resid 86 through 109 Processing helix chain 'D6' and resid 137 through 144 Processing helix chain 'D6' and resid 150 through 172 removed outlier: 3.892A pdb=" N VALD6 154 " --> pdb=" O GLYD6 150 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILED6 155 " --> pdb=" O THRD6 151 " (cutoff:3.500A) Processing helix chain '4L' and resid 3 through 21 removed outlier: 3.625A pdb=" N ASN4L 7 " --> pdb=" O LEU4L 3 " (cutoff:3.500A) Processing helix chain '4L' and resid 26 through 52 Processing helix chain '4L' and resid 57 through 84 removed outlier: 4.614A pdb=" N ILE4L 61 " --> pdb=" O SER4L 57 " (cutoff:3.500A) Processing helix chain 'D5' and resid 2 through 14 Processing helix chain 'D5' and resid 16 through 24 Processing helix chain 'D5' and resid 31 through 58 removed outlier: 4.732A pdb=" N ILED5 49 " --> pdb=" O ILED5 45 " (cutoff:3.500A) Proline residue: D5 50 - end of helix Processing helix chain 'D5' and resid 83 through 89 Processing helix chain 'D5' and resid 89 through 108 removed outlier: 3.762A pdb=" N METD5 108 " --> pdb=" O SERD5 104 " (cutoff:3.500A) Processing helix chain 'D5' and resid 113 through 134 removed outlier: 3.528A pdb=" N PHED5 117 " --> pdb=" O ASND5 113 " (cutoff:3.500A) Processing helix chain 'D5' and resid 136 through 156 Processing helix chain 'D5' and resid 161 through 194 removed outlier: 3.573A pdb=" N ASND5 165 " --> pdb=" O ARGD5 161 " (cutoff:3.500A) Processing helix chain 'D5' and resid 197 through 204 Processing helix chain 'D5' and resid 209 through 224 removed outlier: 3.693A pdb=" N LEUD5 213 " --> pdb=" O SERD5 209 " (cutoff:3.500A) Processing helix chain 'D5' and resid 232 through 238 Processing helix chain 'D5' and resid 240 through 250 removed outlier: 4.045A pdb=" N SERD5 250 " --> pdb=" O LEUD5 246 " (cutoff:3.500A) Processing helix chain 'D5' and resid 256 through 263 removed outlier: 4.126A pdb=" N LEUD5 260 " --> pdb=" O GLYD5 256 " (cutoff:3.500A) Processing helix chain 'D5' and resid 270 through 293 removed outlier: 3.552A pdb=" N LEUD5 293 " --> pdb=" O ALAD5 289 " (cutoff:3.500A) Processing helix chain 'D5' and resid 297 through 319 removed outlier: 3.605A pdb=" N ILED5 301 " --> pdb=" O ASPD5 297 " (cutoff:3.500A) Processing helix chain 'D5' and resid 321 through 350 removed outlier: 3.724A pdb=" N ALAD5 325 " --> pdb=" O GLND5 321 " (cutoff:3.500A) Processing helix chain 'D5' and resid 367 through 380 Processing helix chain 'D5' and resid 386 through 401 removed outlier: 4.081A pdb=" N TYRD5 390 " --> pdb=" O LEUD5 386 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SERD5 391 " --> pdb=" O THRD5 387 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYSD5 392 " --> pdb=" O GLYD5 388 " (cutoff:3.500A) Processing helix chain 'D5' and resid 407 through 432 Processing helix chain 'D5' and resid 447 through 471 removed outlier: 3.658A pdb=" N ILED5 451 " --> pdb=" O ASND5 447 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLYD5 465 " --> pdb=" O SERD5 461 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N PHED5 466 " --> pdb=" O LEUD5 462 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASND5 471 " --> pdb=" O ILED5 467 " (cutoff:3.500A) Processing helix chain 'D5' and resid 488 through 509 Processing helix chain 'D5' and resid 518 through 525 Processing helix chain 'D5' and resid 528 through 547 Proline residue: D5 538 - end of helix removed outlier: 3.673A pdb=" N LEUD5 542 " --> pdb=" O PROD5 538 " (cutoff:3.500A) Processing helix chain 'D5' and resid 554 through 562 Processing helix chain 'D5' and resid 562 through 578 removed outlier: 4.068A pdb=" N ILED5 566 " --> pdb=" O LEUD5 562 " (cutoff:3.500A) Processing helix chain 'D5' and resid 583 through 600 removed outlier: 3.816A pdb=" N TYRD5 587 " --> pdb=" O LEUD5 583 " (cutoff:3.500A) Processing helix chain 'D4' and resid 2 through 17 Proline residue: D4 7 - end of helix removed outlier: 3.820A pdb=" N METD4 12 " --> pdb=" O THRD4 8 " (cutoff:3.500A) Proline residue: D4 13 - end of helix removed outlier: 3.652A pdb=" N TRPD4 16 " --> pdb=" O METD4 12 " (cutoff:3.500A) Processing helix chain 'D4' and resid 22 through 40 Processing helix chain 'D4' and resid 61 through 80 removed outlier: 4.140A pdb=" N LEUD4 65 " --> pdb=" O LEUD4 61 " (cutoff:3.500A) Proline residue: D4 74 - end of helix Processing helix chain 'D4' and resid 88 through 111 Processing helix chain 'D4' and resid 114 through 136 Proline residue: D4 128 - end of helix removed outlier: 4.036A pdb=" N ILED4 131 " --> pdb=" O VALD4 127 " (cutoff:3.500A) Processing helix chain 'D4' and resid 141 through 158 Processing helix chain 'D4' and resid 158 through 169 removed outlier: 4.009A pdb=" N VALD4 162 " --> pdb=" O LEUD4 158 " (cutoff:3.500A) Processing helix chain 'D4' and resid 175 through 180 Processing helix chain 'D4' and resid 190 through 207 Processing helix chain 'D4' and resid 209 through 213 removed outlier: 3.616A pdb=" N HISD4 213 " --> pdb=" O TYRD4 210 " (cutoff:3.500A) Processing helix chain 'D4' and resid 214 through 222 removed outlier: 4.535A pdb=" N LYSD4 218 " --> pdb=" O LEUD4 214 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALAD4 219 " --> pdb=" O TRPD4 215 " (cutoff:3.500A) Processing helix chain 'D4' and resid 224 through 247 Processing helix chain 'D4' and resid 252 through 258 removed outlier: 4.082A pdb=" N PHED4 256 " --> pdb=" O PROD4 252 " (cutoff:3.500A) Processing helix chain 'D4' and resid 258 through 276 removed outlier: 3.826A pdb=" N ILED4 262 " --> pdb=" O ALAD4 258 " (cutoff:3.500A) Processing helix chain 'D4' and resid 282 through 303 removed outlier: 4.257A pdb=" N ILED4 286 " --> pdb=" O LEUD4 282 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALAD4 287 " --> pdb=" O LYSD4 283 " (cutoff:3.500A) Processing helix chain 'D4' and resid 305 through 337 Processing helix chain 'D4' and resid 354 through 367 removed outlier: 3.856A pdb=" N TRPD4 358 " --> pdb=" O LEUD4 354 " (cutoff:3.500A) Processing helix chain 'D4' and resid 372 through 389 removed outlier: 3.527A pdb=" N ILED4 376 " --> pdb=" O SERD4 372 " (cutoff:3.500A) Processing helix chain 'D4' and resid 392 through 415 removed outlier: 3.557A pdb=" N METD4 396 " --> pdb=" O THRD4 392 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THRD4 414 " --> pdb=" O METD4 410 " (cutoff:3.500A) Processing helix chain 'D4' and resid 430 through 450 removed outlier: 3.748A pdb=" N ASND4 434 " --> pdb=" O PHED4 430 " (cutoff:3.500A) Proline residue: D4 443 - end of helix removed outlier: 3.546A pdb=" N ASND4 450 " --> pdb=" O LEUD4 446 " (cutoff:3.500A) Processing helix chain 'D2' and resid 2 through 23 removed outlier: 3.782A pdb=" N SERD2 23 " --> pdb=" O ILED2 19 " (cutoff:3.500A) Processing helix chain 'D2' and resid 25 through 41 Processing helix chain 'D2' and resid 49 through 80 removed outlier: 3.594A pdb=" N THRD2 53 " --> pdb=" O ASND2 49 " (cutoff:3.500A) Processing helix chain 'D2' and resid 91 through 107 Processing helix chain 'D2' and resid 111 through 113 No H-bonds generated for 'chain 'D2' and resid 111 through 113' Processing helix chain 'D2' and resid 114 through 121 removed outlier: 3.682A pdb=" N GLYD2 121 " --> pdb=" O GLUD2 117 " (cutoff:3.500A) Processing helix chain 'D2' and resid 123 through 146 Proline residue: D2 138 - end of helix removed outlier: 3.897A pdb=" N VALD2 141 " --> pdb=" O ALAD2 137 " (cutoff:3.500A) Processing helix chain 'D2' and resid 147 through 149 No H-bonds generated for 'chain 'D2' and resid 147 through 149' Processing helix chain 'D2' and resid 150 through 168 removed outlier: 3.934A pdb=" N ILED2 154 " --> pdb=" O ASND2 150 " (cutoff:3.500A) Processing helix chain 'D2' and resid 174 through 192 removed outlier: 3.852A pdb=" N ILED2 178 " --> pdb=" O GLND2 174 " (cutoff:3.500A) Processing helix chain 'D2' and resid 197 through 221 removed outlier: 4.033A pdb=" N THRD2 201 " --> pdb=" O ASND2 197 " (cutoff:3.500A) Processing helix chain 'D2' and resid 226 through 237 removed outlier: 3.588A pdb=" N ALAD2 237 " --> pdb=" O THRD2 233 " (cutoff:3.500A) Processing helix chain 'D2' and resid 238 through 253 removed outlier: 3.564A pdb=" N ILED2 242 " --> pdb=" O PROD2 238 " (cutoff:3.500A) Processing helix chain 'D2' and resid 260 through 272 removed outlier: 3.595A pdb=" N METD2 265 " --> pdb=" O METD2 261 " (cutoff:3.500A) Processing helix chain 'D2' and resid 276 through 289 Processing helix chain 'D2' and resid 290 through 301 Processing helix chain 'D2' and resid 310 through 315 Processing helix chain 'D2' and resid 326 through 335 Processing helix chain 'D2' and resid 339 through 346 removed outlier: 3.973A pdb=" N SERD2 344 " --> pdb=" O PROD2 341 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEUD2 346 " --> pdb=" O LEUD2 343 " (cutoff:3.500A) Processing helix chain 'AK' and resid 2 through 9 Processing helix chain 'AK' and resid 18 through 42 Processing helix chain 'AK' and resid 47 through 81 Processing helix chain 'AK' and resid 86 through 105 Processing helix chain 'AK' and resid 106 through 131 Processing helix chain 'B5' and resid 14 through 31 removed outlier: 4.477A pdb=" N ASPB5 18 " --> pdb=" O SERB5 14 " (cutoff:3.500A) Processing helix chain 'B5' and resid 33 through 47 Processing helix chain 'B5' and resid 69 through 79 Processing helix chain 'B5' and resid 82 through 118 Processing helix chain 'B5' and resid 129 through 133 removed outlier: 3.930A pdb=" N LEUB5 132 " --> pdb=" O ASPB5 129 " (cutoff:3.500A) Processing helix chain 'AB' and resid 7 through 21 Processing helix chain 'AB' and resid 43 through 59 Processing helix chain 'AB' and resid 72 through 85 Processing helix chain 'A8' and resid 20 through 27 removed outlier: 3.503A pdb=" N LEUA8 24 " --> pdb=" O SERA8 20 " (cutoff:3.500A) Processing helix chain 'A8' and resid 27 through 34 removed outlier: 3.535A pdb=" N TYRA8 31 " --> pdb=" O ALAA8 27 " (cutoff:3.500A) Processing helix chain 'A8' and resid 38 through 49 removed outlier: 3.979A pdb=" N PHEA8 42 " --> pdb=" O PROA8 38 " (cutoff:3.500A) Processing helix chain 'A8' and resid 55 through 76 Processing helix chain 'A8' and resid 79 through 90 removed outlier: 4.073A pdb=" N GLUA8 83 " --> pdb=" O GLUA8 79 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYRA8 90 " --> pdb=" O THRA8 86 " (cutoff:3.500A) Processing helix chain 'A8' and resid 100 through 114 Processing helix chain 'BJ' and resid 27 through 56 removed outlier: 3.877A pdb=" N TYRBJ 31 " --> pdb=" O ASNBJ 27 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARGBJ 42 " --> pdb=" O LEUBJ 38 " (cutoff:3.500A) Proline residue: BJ 43 - end of helix Processing helix chain 'BJ' and resid 80 through 117 removed outlier: 5.135A pdb=" N GLUBJ 86 " --> pdb=" O LEUBJ 82 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLYBJ 117 " --> pdb=" O GLNBJ 113 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 124 through 142 Processing helix chain 'BJ' and resid 151 through 173 Processing helix chain 'AJ' and resid 4 through 11 Processing helix chain 'AJ' and resid 35 through 47 removed outlier: 3.900A pdb=" N ALAAJ 39 " --> pdb=" O LYSAJ 35 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLYAJ 47 " --> pdb=" O ALAAJ 43 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 57 through 62 Processing helix chain 'AJ' and resid 78 through 85 Processing helix chain 'AJ' and resid 92 through 117 removed outlier: 3.854A pdb=" N LEUAJ 96 " --> pdb=" O ASNAJ 92 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 127 through 141 Processing helix chain 'AJ' and resid 145 through 160 Processing helix chain 'AJ' and resid 161 through 163 No H-bonds generated for 'chain 'AJ' and resid 161 through 163' Processing helix chain 'AJ' and resid 175 through 187 removed outlier: 3.557A pdb=" N VALAJ 179 " --> pdb=" O PROAJ 175 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLYAJ 187 " --> pdb=" O ILEAJ 183 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 188 through 193 Processing helix chain 'AJ' and resid 196 through 209 Processing helix chain 'AJ' and resid 230 through 240 removed outlier: 3.776A pdb=" N VALAJ 234 " --> pdb=" O ASPAJ 230 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 246 through 250 removed outlier: 4.208A pdb=" N LEUAJ 249 " --> pdb=" O GLYAJ 246 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASPAJ 250 " --> pdb=" O PROAJ 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'AJ' and resid 246 through 250' Processing helix chain 'AJ' and resid 253 through 264 removed outlier: 3.520A pdb=" N GLNAJ 264 " --> pdb=" O ARGAJ 260 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 269 through 273 removed outlier: 4.191A pdb=" N TYRAJ 272 " --> pdb=" O VALAJ 269 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THRAJ 273 " --> pdb=" O LEUAJ 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'AJ' and resid 269 through 273' Processing helix chain 'AJ' and resid 285 through 298 Processing helix chain 'S5' and resid 4 through 9 Processing helix chain 'S5' and resid 32 through 43 Processing helix chain 'S5' and resid 49 through 55 Processing helix chain 'S5' and resid 55 through 67 removed outlier: 3.534A pdb=" N PHES5 59 " --> pdb=" O CYSS5 55 " (cutoff:3.500A) Processing helix chain 'S5' and resid 68 through 89 Processing helix chain 'A3' and resid 15 through 31 Processing helix chain 'A3' and resid 37 through 47 Processing helix chain 'B3' and resid 25 through 39 Processing helix chain 'B3' and resid 61 through 67 Processing helix chain 'B3' and resid 68 through 71 removed outlier: 4.069A pdb=" N LYSB3 71 " --> pdb=" O LYSB3 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 68 through 71' Processing helix chain 'B3' and resid 72 through 83 removed outlier: 3.749A pdb=" N ALAB3 76 " --> pdb=" O TRPB3 72 " (cutoff:3.500A) Processing helix chain 'C2' and resid 15 through 20 removed outlier: 3.546A pdb=" N ALAC2 18 " --> pdb=" O PROC2 15 " (cutoff:3.500A) Processing helix chain 'C2' and resid 28 through 49 removed outlier: 3.924A pdb=" N ARGC2 49 " --> pdb=" O ASPC2 45 " (cutoff:3.500A) Processing helix chain 'C2' and resid 57 through 97 removed outlier: 3.548A pdb=" N HISC2 97 " --> pdb=" O TYRC2 93 " (cutoff:3.500A) Processing helix chain 'B4' and resid 19 through 23 removed outlier: 3.507A pdb=" N TYRB4 22 " --> pdb=" O PROB4 19 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASPB4 23 " --> pdb=" O ALAB4 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B4' and resid 19 through 23' Processing helix chain 'B4' and resid 25 through 49 Processing helix chain 'B4' and resid 61 through 72 removed outlier: 3.511A pdb=" N ILEB4 65 " --> pdb=" O ASPB4 61 " (cutoff:3.500A) Processing helix chain 'B4' and resid 82 through 118 removed outlier: 3.564A pdb=" N ILEB4 94 " --> pdb=" O ALAB4 90 " (cutoff:3.500A) Proline residue: B4 96 - end of helix Processing helix chain 'AM' and resid 31 through 97 Proline residue: AM 72 - end of helix Processing helix chain 'AM' and resid 129 through 136 Processing helix chain 'B6' and resid 4 through 25 Processing helix chain 'B6' and resid 68 through 92 Proline residue: B6 77 - end of helix removed outlier: 3.680A pdb=" N TYRB6 87 " --> pdb=" O TYRB6 83 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HISB6 88 " --> pdb=" O TYRB6 84 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VALB6 89 " --> pdb=" O LEUB6 85 " (cutoff:3.500A) Processing helix chain 'B7' and resid 2 through 10 Processing helix chain 'B7' and resid 41 through 48 Processing helix chain 'B7' and resid 59 through 72 Processing helix chain 'B7' and resid 80 through 119 Processing helix chain 'B9' and resid 10 through 30 Processing helix chain 'B9' and resid 33 through 50 removed outlier: 4.370A pdb=" N HISB9 50 " --> pdb=" O ARGB9 46 " (cutoff:3.500A) Processing helix chain 'B9' and resid 56 through 72 Processing helix chain 'B9' and resid 91 through 97 removed outlier: 4.099A pdb=" N CYSB9 95 " --> pdb=" O ARGB9 92 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYRB9 96 " --> pdb=" O TYRB9 93 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYSB9 97 " --> pdb=" O GLUB9 94 " (cutoff:3.500A) Processing helix chain 'B9' and resid 107 through 114 removed outlier: 3.611A pdb=" N TYRB9 114 " --> pdb=" O GLUB9 110 " (cutoff:3.500A) Processing helix chain 'B9' and resid 114 through 131 removed outlier: 3.670A pdb=" N PHEB9 118 " --> pdb=" O TYRB9 114 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SERB9 131 " --> pdb=" O LEUB9 127 " (cutoff:3.500A) Processing helix chain 'B9' and resid 133 through 141 Processing helix chain 'B9' and resid 166 through 171 Processing helix chain 'B2' and resid 18 through 41 removed outlier: 3.731A pdb=" N VALB2 22 " --> pdb=" O THRB2 18 " (cutoff:3.500A) Processing helix chain 'B8' and resid 4 through 8 removed outlier: 3.582A pdb=" N METB8 8 " --> pdb=" O THRB8 5 " (cutoff:3.500A) Processing helix chain 'B8' and resid 17 through 27 Processing helix chain 'B8' and resid 80 through 84 Processing helix chain 'B8' and resid 98 through 122 Processing helix chain 'BK' and resid 50 through 64 removed outlier: 3.673A pdb=" N ASPBK 54 " --> pdb=" O ASPBK 50 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VALBK 55 " --> pdb=" O PROBK 51 " (cutoff:3.500A) Processing helix chain 'BK' and resid 69 through 79 removed outlier: 3.854A pdb=" N TYRBK 79 " --> pdb=" O THRBK 75 " (cutoff:3.500A) Processing helix chain 'BK' and resid 86 through 103 Processing helix chain 'BK' and resid 114 through 118 removed outlier: 3.823A pdb=" N ILEBK 118 " --> pdb=" O PROBK 115 " (cutoff:3.500A) Processing helix chain 'C1' and resid 15 through 46 Processing helix chain 'B1' and resid 14 through 34 Processing helix chain 'A1' and resid 5 through 16 Processing helix chain 'A1' and resid 17 through 30 removed outlier: 3.893A pdb=" N META1 21 " --> pdb=" O PHEA1 17 " (cutoff:3.500A) Processing helix chain 'A1' and resid 41 through 54 Processing sheet with id=AA1, first strand: chain 'D6' and resid 112 through 113 removed outlier: 3.594A pdb=" N VALD6 113 " --> pdb=" O PHED6 119 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHED6 119 " --> pdb=" O VALD6 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D5' and resid 78 through 82 Processing sheet with id=AA3, first strand: chain 'D4' and resid 50 through 51 Processing sheet with id=AA4, first strand: chain 'AJ' and resid 49 through 50 removed outlier: 6.970A pdb=" N LYSAJ 49 " --> pdb=" O VALAJ 123 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N GLUAJ 125 " --> pdb=" O LYSAJ 49 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VALAJ 169 " --> pdb=" O LEUAJ 221 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYRAJ 223 " --> pdb=" O VALAJ 169 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYRAJ 171 " --> pdb=" O TYRAJ 223 " (cutoff:3.500A) 2139 hydrogen bonds defined for protein. 6366 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: 6.39 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6994 1.33 - 1.45: 10460 1.45 - 1.58: 21036 1.58 - 1.71: 35 1.71 - 1.84: 499 Bond restraints: 39024 Sorted by residual: bond pdb=" C PROS5 94 " pdb=" N PROS5 95 " ideal model delta sigma weight residual 1.336 1.408 -0.072 1.08e-02 8.57e+03 4.46e+01 bond pdb=" O5 ZMPAB 101 " pdb=" P1 ZMPAB 101 " ideal model delta sigma weight residual 1.715 1.596 0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" OB3 CDLAK 501 " pdb=" PB2 CDLAK 501 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.00e-02 1.00e+04 2.60e+01 bond pdb=" OB3 CDLB5 201 " pdb=" PB2 CDLB5 201 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.00e-02 1.00e+04 2.58e+01 bond pdb=" OA3 CDLD5 901 " pdb=" PA1 CDLD5 901 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.53e+01 ... (remaining 39019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 51577 3.38 - 6.75: 1071 6.75 - 10.13: 196 10.13 - 13.51: 41 13.51 - 16.89: 9 Bond angle restraints: 52894 Sorted by residual: angle pdb=" C CYSAK 17 " pdb=" N HISAK 18 " pdb=" CA HISAK 18 " ideal model delta sigma weight residual 121.54 133.71 -12.17 1.91e+00 2.74e-01 4.06e+01 angle pdb=" C PROA8 52 " pdb=" N ARGA8 53 " pdb=" CA ARGA8 53 " ideal model delta sigma weight residual 121.54 133.09 -11.55 1.91e+00 2.74e-01 3.66e+01 angle pdb=" C GLYC2 4 " pdb=" N ARGC2 5 " pdb=" CA ARGC2 5 " ideal model delta sigma weight residual 121.70 132.55 -10.85 1.80e+00 3.09e-01 3.64e+01 angle pdb=" C LYSB6 99 " pdb=" N LYSB6 100 " pdb=" CA LYSB6 100 " ideal model delta sigma weight residual 121.80 136.32 -14.52 2.44e+00 1.68e-01 3.54e+01 angle pdb=" N ASPA3 58 " pdb=" CA ASPA3 58 " pdb=" C ASPA3 58 " ideal model delta sigma weight residual 111.02 118.18 -7.16 1.22e+00 6.72e-01 3.44e+01 ... (remaining 52889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.92: 22414 24.92 - 49.83: 811 49.83 - 74.75: 87 74.75 - 99.67: 8 99.67 - 124.59: 2 Dihedral angle restraints: 23322 sinusoidal: 9755 harmonic: 13567 Sorted by residual: dihedral pdb=" CA ALAD5 365 " pdb=" C ALAD5 365 " pdb=" N METD5 366 " pdb=" CA METD5 366 " ideal model delta harmonic sigma weight residual 180.00 -122.93 -57.07 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA PHEB7 30 " pdb=" C PHEB7 30 " pdb=" N PROB7 31 " pdb=" CA PROB7 31 " ideal model delta harmonic sigma weight residual -180.00 -124.06 -55.94 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA METD1 91 " pdb=" C METD1 91 " pdb=" N PROD1 92 " pdb=" CA PROD1 92 " ideal model delta harmonic sigma weight residual -180.00 -127.08 -52.92 0 5.00e+00 4.00e-02 1.12e+02 ... (remaining 23319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 5343 0.109 - 0.218: 451 0.218 - 0.328: 21 0.328 - 0.437: 3 0.437 - 0.546: 2 Chirality restraints: 5820 Sorted by residual: chirality pdb=" CG LEUAJ 135 " pdb=" CB LEUAJ 135 " pdb=" CD1 LEUAJ 135 " pdb=" CD2 LEUAJ 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.46e+00 chirality pdb=" CA4 CDLD5 904 " pdb=" CA3 CDLD5 904 " pdb=" CA6 CDLD5 904 " pdb=" OA6 CDLD5 904 " both_signs ideal model delta sigma weight residual False -2.57 -2.12 -0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CB4 CDLB5 201 " pdb=" CB3 CDLB5 201 " pdb=" CB6 CDLB5 201 " pdb=" OB6 CDLB5 201 " both_signs ideal model delta sigma weight residual False -2.57 -2.14 -0.44 2.00e-01 2.50e+01 4.75e+00 ... (remaining 5817 not shown) Planarity restraints: 6543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHED4 52 " 0.029 2.00e-02 2.50e+03 5.68e-02 3.23e+01 pdb=" C PHED4 52 " -0.098 2.00e-02 2.50e+03 pdb=" O PHED4 52 " 0.037 2.00e-02 2.50e+03 pdb=" N SERD4 53 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHEB7 30 " 0.059 5.00e-02 4.00e+02 9.03e-02 1.30e+01 pdb=" N PROB7 31 " -0.156 5.00e-02 4.00e+02 pdb=" CA PROB7 31 " 0.049 5.00e-02 4.00e+02 pdb=" CD PROB7 31 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYRAJ 206 " 0.035 2.00e-02 2.50e+03 2.53e-02 1.28e+01 pdb=" CG TYRAJ 206 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYRAJ 206 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYRAJ 206 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYRAJ 206 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYRAJ 206 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYRAJ 206 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYRAJ 206 " 0.006 2.00e-02 2.50e+03 ... (remaining 6540 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4515 2.75 - 3.29: 37244 3.29 - 3.82: 63505 3.82 - 4.36: 70749 4.36 - 4.90: 120730 Nonbonded interactions: 296743 Sorted by model distance: nonbonded pdb=" O LYSB6 86 " pdb=" OG1 THRB6 90 " model vdw 2.212 3.040 nonbonded pdb=" O LEUD4 177 " pdb=" O GLND4 180 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THRAJ 15 " pdb=" OD1 ASPAJ 253 " model vdw 2.240 3.040 nonbonded pdb=" O ALAD1 18 " pdb=" OG1 THRD1 21 " model vdw 2.252 3.040 nonbonded pdb=" OH TYRD4 4 " pdb=" O THRD4 37 " model vdw 2.261 3.040 ... (remaining 296738 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 9.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 30.870 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 : 0.008 0.605 39038 Z= 0.445 Angle : 1.243 16.887 52918 Z= 0.635 Chirality : 0.064 0.546 5820 Planarity : 0.009 0.090 6543 Dihedral : 12.595 124.586 14514 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.31 % Favored : 88.62 % Rotamer: Outliers : 0.27 % Allowed : 6.62 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.32 % Twisted Proline : 2.17 % Twisted General : 0.49 % 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: -3.94 (0.10), residues: 4561 helix: -1.81 (0.08), residues: 2795 sheet: -4.14 (0.54), residues: 38 loop : -3.89 (0.12), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARGD1 274 TYR 0.060 0.003 TYRAJ 206 PHE 0.046 0.003 PHE4L 53 TRP 0.045 0.003 TRPAM 141 HIS 0.019 0.002 HISAK 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.32 (39024) covalent geometry : angle 1.24234 / 0.63 (52894) SS BOND : bond 0.00521 / 0.35 ( 12) SS BOND : angle 2.17530 / 1.52 ( 24) hydrogen bonds : bond 0.10979 / 7.32 ( 2139) hydrogen bonds : angle 6.20511 / 4.35 ( 6366) Misc. bond : bond 0.42991 / 20.49 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1860 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 1849 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 36 VAL cc_start: 0.8814 (t) cc_final: 0.8372 (t) REVERT: D3 1 MET cc_start: 0.7021 (pp-130) cc_final: 0.6003 (ppp) REVERT: D3 11 PHE cc_start: 0.8548 (t80) cc_final: 0.8146 (t80) REVERT: D3 89 THR cc_start: 0.9232 (m) cc_final: 0.8821 (p) REVERT: D3 96 PHE cc_start: 0.8156 (t80) cc_final: 0.7850 (t80) REVERT: D1 1 MET cc_start: 0.7587 (mmm) cc_final: 0.7061 (mmm) REVERT: D1 23 VAL cc_start: 0.8511 (t) cc_final: 0.8099 (p) REVERT: D1 25 ARG cc_start: 0.8572 (ttm110) cc_final: 0.8235 (ttm-80) REVERT: D1 26 LYS cc_start: 0.8697 (mmmm) cc_final: 0.8452 (mmtt) REVERT: D1 81 LEU cc_start: 0.8795 (mt) cc_final: 0.8594 (mp) REVERT: D1 142 TYR cc_start: 0.9349 (m-80) cc_final: 0.9106 (m-10) REVERT: D1 224 PHE cc_start: 0.6982 (t80) cc_final: 0.6681 (t80) REVERT: D1 239 THR cc_start: 0.9093 (m) cc_final: 0.8738 (p) REVERT: D1 271 LEU cc_start: 0.8446 (tm) cc_final: 0.8192 (tm) REVERT: D1 272 TRP cc_start: 0.7404 (t60) cc_final: 0.6782 (t-100) REVERT: D1 279 ARG cc_start: 0.7587 (mtm180) cc_final: 0.7321 (ptt-90) REVERT: D1 281 ARG cc_start: 0.8264 (ttp-170) cc_final: 0.6854 (mpt180) REVERT: D6 15 MET cc_start: 0.7444 (mmm) cc_final: 0.7086 (mmm) REVERT: D6 60 TYR cc_start: 0.5597 (t80) cc_final: 0.5163 (t80) REVERT: D6 70 TYR cc_start: 0.8385 (t80) cc_final: 0.7316 (t80) REVERT: D6 136 PHE cc_start: 0.8543 (p90) cc_final: 0.8086 (p90) REVERT: D6 151 THR cc_start: 0.8329 (p) cc_final: 0.8113 (p) REVERT: D6 155 ILE cc_start: 0.8628 (mt) cc_final: 0.8387 (mt) REVERT: 4L 6 MET cc_start: 0.8720 (tmt) cc_final: 0.8377 (tmm) REVERT: 4L 9 MET cc_start: 0.8466 (mtp) cc_final: 0.8070 (ppp) REVERT: 4L 37 MET cc_start: 0.7334 (ttm) cc_final: 0.6738 (ttm) REVERT: 4L 79 VAL cc_start: 0.9014 (t) cc_final: 0.8712 (p) REVERT: 4L 88 ASP cc_start: 0.8305 (p0) cc_final: 0.7844 (p0) REVERT: D5 119 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8351 (tttp) REVERT: D5 150 MET cc_start: 0.8177 (mmp) cc_final: 0.7671 (mtp) REVERT: D5 279 CYS cc_start: 0.7052 (m) cc_final: 0.6446 (m) REVERT: D5 480 MET cc_start: 0.7175 (tpt) cc_final: 0.6400 (tpp) REVERT: D5 499 ILE cc_start: 0.8718 (mm) cc_final: 0.8398 (mt) REVERT: D5 533 MET cc_start: 0.8568 (mmm) cc_final: 0.8224 (mmt) REVERT: D5 596 LEU cc_start: 0.8778 (mp) cc_final: 0.8520 (tt) REVERT: D4 4 TYR cc_start: 0.6938 (m-10) cc_final: 0.6584 (m-10) REVERT: D4 25 ILE cc_start: 0.8638 (mm) cc_final: 0.8344 (mm) REVERT: D4 108 MET cc_start: 0.7975 (mmp) cc_final: 0.7173 (mmt) REVERT: D4 119 TYR cc_start: 0.8041 (t80) cc_final: 0.7812 (t80) REVERT: D4 178 ILE cc_start: 0.8240 (mt) cc_final: 0.7890 (mm) REVERT: D4 201 MET cc_start: 0.8281 (tpp) cc_final: 0.8036 (ttt) REVERT: D4 225 ILE cc_start: 0.8657 (tp) cc_final: 0.8162 (tp) REVERT: D4 331 ASN cc_start: 0.8952 (t0) cc_final: 0.8712 (t0) REVERT: D4 383 MET cc_start: 0.8828 (mmp) cc_final: 0.8491 (mmp) REVERT: D2 15 LEU cc_start: 0.9124 (tp) cc_final: 0.8905 (tp) REVERT: D2 18 ILE cc_start: 0.8819 (mt) cc_final: 0.8584 (mm) REVERT: D2 36 ASN cc_start: 0.8816 (t160) cc_final: 0.8431 (t0) REVERT: D2 91 ASN cc_start: 0.8637 (t0) cc_final: 0.7944 (t0) REVERT: D2 100 MET cc_start: 0.8894 (mtt) cc_final: 0.8489 (mtp) REVERT: D2 105 LYS cc_start: 0.9107 (tptp) cc_final: 0.8825 (mmmt) REVERT: D2 129 ILE cc_start: 0.9143 (tt) cc_final: 0.8625 (mt) REVERT: D2 154 ILE cc_start: 0.8732 (mt) cc_final: 0.8427 (tp) REVERT: D2 174 GLN cc_start: 0.8712 (mm110) cc_final: 0.8465 (mm-40) REVERT: D2 323 MET cc_start: 0.6848 (mpt) cc_final: 0.6324 (mpt) REVERT: D2 342 ILE cc_start: 0.9249 (mm) cc_final: 0.8787 (mm) REVERT: AK 8 TYR cc_start: 0.9215 (t80) cc_final: 0.8925 (t80) REVERT: AK 33 LEU cc_start: 0.8335 (tt) cc_final: 0.8109 (mt) REVERT: AK 139 LYS cc_start: 0.8298 (pptt) cc_final: 0.8019 (pptt) REVERT: B5 114 MET cc_start: 0.9080 (ttm) cc_final: 0.8831 (ttm) REVERT: AB 77 VAL cc_start: 0.9414 (t) cc_final: 0.9197 (p) REVERT: BJ 16 THR cc_start: 0.8672 (m) cc_final: 0.6709 (m) REVERT: BJ 52 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7114 (mm-30) REVERT: BJ 101 ILE cc_start: 0.9103 (mt) cc_final: 0.8769 (mt) REVERT: BJ 110 LYS cc_start: 0.9276 (mttp) cc_final: 0.8758 (mtmm) REVERT: AJ 131 ASP cc_start: 0.7855 (t0) cc_final: 0.7562 (t0) REVERT: AJ 271 ASN cc_start: 0.8252 (m-40) cc_final: 0.7757 (m110) REVERT: AJ 308 TYR cc_start: 0.8083 (m-80) cc_final: 0.7414 (m-80) REVERT: S5 13 LEU cc_start: 0.8389 (pt) cc_final: 0.8181 (pt) REVERT: S5 14 ASP cc_start: 0.8662 (m-30) cc_final: 0.8414 (m-30) REVERT: S5 16 TRP cc_start: 0.8359 (p-90) cc_final: 0.7790 (p-90) REVERT: S5 64 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7998 (mt-10) REVERT: S5 76 ASN cc_start: 0.8921 (t0) cc_final: 0.8611 (t0) REVERT: A3 45 ASN cc_start: 0.8503 (t0) cc_final: 0.8168 (t0) REVERT: C2 101 PHE cc_start: 0.8332 (m-10) cc_final: 0.8093 (m-10) REVERT: B4 43 LYS cc_start: 0.9286 (mtpm) cc_final: 0.8844 (mmmm) REVERT: B4 65 ILE cc_start: 0.9145 (mm) cc_final: 0.8914 (mt) REVERT: B4 116 GLN cc_start: 0.8586 (tp40) cc_final: 0.8363 (tp-100) REVERT: AM 81 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.8182 (tpt170) REVERT: AM 88 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8178 (mt-10) REVERT: AM 96 ILE cc_start: 0.8583 (tt) cc_final: 0.8282 (mt) REVERT: AM 119 MET cc_start: 0.8766 (ptt) cc_final: 0.8440 (ptp) REVERT: AM 136 THR cc_start: 0.8446 (p) cc_final: 0.7664 (p) REVERT: AM 137 TYR cc_start: 0.8193 (m-10) cc_final: 0.7915 (m-10) REVERT: B6 9 LEU cc_start: 0.8332 (tp) cc_final: 0.7751 (tp) REVERT: B6 107 ASP cc_start: 0.8217 (m-30) cc_final: 0.7949 (m-30) REVERT: B6 114 GLU cc_start: 0.7634 (pm20) cc_final: 0.7249 (pm20) REVERT: B7 56 ASP cc_start: 0.8265 (m-30) cc_final: 0.7966 (m-30) REVERT: B7 63 ILE cc_start: 0.9348 (mm) cc_final: 0.9123 (mm) REVERT: B7 85 ASP cc_start: 0.8105 (m-30) cc_final: 0.7829 (m-30) REVERT: B9 79 TYR cc_start: 0.8710 (t80) cc_final: 0.8488 (t80) REVERT: B2 60 THR cc_start: 0.8010 (p) cc_final: 0.7223 (t) REVERT: B8 46 ASP cc_start: 0.8676 (p0) cc_final: 0.8415 (p0) REVERT: B8 72 ASN cc_start: 0.8487 (t0) cc_final: 0.8245 (t0) REVERT: B8 80 ASP cc_start: 0.8644 (m-30) cc_final: 0.8240 (m-30) REVERT: B8 103 LYS cc_start: 0.8445 (mttt) cc_final: 0.8219 (tttp) REVERT: B8 122 TYR cc_start: 0.8318 (m-10) cc_final: 0.8095 (m-10) REVERT: B8 140 LEU cc_start: 0.9167 (mt) cc_final: 0.8623 (mp) REVERT: BK 26 TRP cc_start: 0.7709 (m100) cc_final: 0.7429 (m100) REVERT: BK 83 TYR cc_start: 0.8126 (t80) cc_final: 0.7859 (t80) REVERT: BK 84 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7103 (mmm-85) REVERT: C1 9 HIS cc_start: 0.6995 (p90) cc_final: 0.6186 (p-80) REVERT: C1 41 GLU cc_start: 0.8004 (tp30) cc_final: 0.7595 (tm-30) REVERT: B1 28 ARG cc_start: 0.7141 (mmt180) cc_final: 0.6899 (mtm180) REVERT: A1 28 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7461 (ttp80) REVERT: A1 53 ARG cc_start: 0.8764 (ttm110) cc_final: 0.7692 (ttt-90) outliers start: 11 outliers final: 4 residues processed: 1855 average time/residue: 0.2418 time to fit residues: 724.7896 Evaluate side-chains 1175 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1171 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 230 VAL Chi-restraints excluded: chain B8 residue 9 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.1980 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D3 108 GLN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 99 ASN D1 169 GLN D1 194 ASN 4L 83 ASN D5 113 ASN D5 175 ASN D5 205 ASN D5 270 ASN D5 332 HIS D5 509 HIS D4 51 ASN D4 138 ASN D4 139 GLN D4 192 ASN ** D4 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 36 ASN D2 63 GLN ** D2 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 204 ASN D2 235 ASN D2 316 GLN A8 63 ASN A8 150 ASN A8 162 HIS BJ 130 GLN AJ 21 ASN AJ 92 ASN AJ 151 HIS AJ 154 GLN AJ 251 GLN AJ 271 ASN ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 47 ASN C2 6 GLN C2 59 HIS B4 82 ASN AM 75 GLN AM 89 ASN ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B7 91 HIS B9 32 HIS B9 168 HIS B8 104 HIS BK 27 GLN BK 57 ASN A1 27 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.108993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.097970 restraints weight = 86445.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100628 restraints weight = 43888.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102356 restraints weight = 26315.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103550 restraints weight = 17632.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104365 restraints weight = 12825.724| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 39038 Z= 0.173 Angle : 0.869 12.867 52918 Z= 0.433 Chirality : 0.047 0.340 5820 Planarity : 0.006 0.079 6543 Dihedral : 9.837 90.962 5352 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.58 % Favored : 90.40 % Rotamer: Outliers : 4.45 % Allowed : 17.18 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.32 % Twisted Proline : 1.08 % Twisted General : 0.23 % 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: -1.94 (0.12), residues: 4561 helix: -0.01 (0.09), residues: 2847 sheet: -3.76 (0.71), residues: 24 loop : -3.60 (0.13), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAM 80 TYR 0.035 0.002 TYRD5 422 PHE 0.029 0.002 PHED4 122 TRP 0.029 0.002 TRPAM 141 HIS 0.037 0.001 HISB9 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (39024) covalent geometry : angle 0.86898 / 0.43 (52894) SS BOND : bond 0.00521 / 0.31 ( 12) SS BOND : angle 1.57908 / 1.13 ( 24) hydrogen bonds : bond 0.05236 / 3.40 ( 2139) hydrogen bonds : angle 4.83088 / 3.37 ( 6366) Misc. bond : bond 0.00942 / 0.45 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 1306 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D3 11 PHE cc_start: 0.8743 (t80) cc_final: 0.8473 (t80) REVERT: D3 105 GLU cc_start: 0.6595 (tp30) cc_final: 0.5786 (tp30) REVERT: D1 25 ARG cc_start: 0.8927 (ttm110) cc_final: 0.8338 (ttm-80) REVERT: D1 26 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8540 (mmtt) REVERT: D1 100 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8324 (pt) REVERT: D1 195 ARG cc_start: 0.7780 (mtp85) cc_final: 0.7233 (mtm180) REVERT: D1 233 MET cc_start: 0.8388 (tmm) cc_final: 0.7900 (tmm) REVERT: D1 234 MET cc_start: 0.8883 (mmt) cc_final: 0.8508 (mpp) REVERT: D1 239 THR cc_start: 0.9030 (m) cc_final: 0.8788 (p) REVERT: D1 251 MET cc_start: 0.7603 (ttp) cc_final: 0.7359 (ptm) REVERT: D1 266 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8499 (tt) REVERT: D1 272 TRP cc_start: 0.7131 (t60) cc_final: 0.6564 (t-100) REVERT: D1 279 ARG cc_start: 0.7549 (mtm180) cc_final: 0.7333 (ptt-90) REVERT: D1 281 ARG cc_start: 0.8279 (ttp-170) cc_final: 0.6954 (mpt180) REVERT: D1 284 GLN cc_start: 0.6835 (mt0) cc_final: 0.6456 (pt0) REVERT: D6 15 MET cc_start: 0.7206 (mmm) cc_final: 0.6811 (mmm) REVERT: D6 70 TYR cc_start: 0.8093 (t80) cc_final: 0.6994 (t80) REVERT: D6 98 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8675 (tm) REVERT: D6 100 GLU cc_start: 0.6990 (tp30) cc_final: 0.6665 (tp30) REVERT: 4L 5 TYR cc_start: 0.8339 (m-10) cc_final: 0.7696 (m-80) REVERT: 4L 6 MET cc_start: 0.8825 (tmt) cc_final: 0.8385 (tmm) REVERT: 4L 37 MET cc_start: 0.7067 (ttm) cc_final: 0.6618 (ttm) REVERT: 4L 47 MET cc_start: 0.8204 (tpp) cc_final: 0.7698 (mmm) REVERT: 4L 79 VAL cc_start: 0.8907 (t) cc_final: 0.8677 (p) REVERT: 4L 88 ASP cc_start: 0.8332 (p0) cc_final: 0.7986 (p0) REVERT: D5 60 GLU cc_start: 0.5746 (mt-10) cc_final: 0.5493 (mt-10) REVERT: D5 94 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9211 (mm) REVERT: D5 108 MET cc_start: 0.8629 (tpp) cc_final: 0.8252 (mpp) REVERT: D5 393 ASP cc_start: 0.8271 (m-30) cc_final: 0.8022 (m-30) REVERT: D5 397 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7383 (mt-10) REVERT: D5 467 ILE cc_start: 0.8726 (mt) cc_final: 0.8370 (mm) REVERT: D5 475 MET cc_start: 0.7227 (mpp) cc_final: 0.7026 (mpp) REVERT: D5 480 MET cc_start: 0.7645 (tpt) cc_final: 0.6538 (tpp) REVERT: D5 499 ILE cc_start: 0.8814 (mm) cc_final: 0.8346 (mt) REVERT: D5 533 MET cc_start: 0.8591 (mmm) cc_final: 0.8329 (mmt) REVERT: D5 604 PHE cc_start: 0.8623 (m-10) cc_final: 0.8388 (m-80) REVERT: D4 9 MET cc_start: 0.6935 (ttt) cc_final: 0.6435 (tmm) REVERT: D4 23 ILE cc_start: 0.7305 (pp) cc_final: 0.6777 (pt) REVERT: D4 26 ASN cc_start: 0.8169 (m-40) cc_final: 0.7857 (m110) REVERT: D4 44 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8169 (pp30) REVERT: D4 97 SER cc_start: 0.8938 (p) cc_final: 0.8646 (m) REVERT: D4 108 MET cc_start: 0.8302 (mmp) cc_final: 0.7953 (tpp) REVERT: D4 121 MET cc_start: 0.8262 (mmm) cc_final: 0.7787 (mmm) REVERT: D4 152 TYR cc_start: 0.8457 (m-80) cc_final: 0.8176 (m-80) REVERT: D4 168 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8456 (tm-30) REVERT: D4 200 MET cc_start: 0.8362 (mmt) cc_final: 0.8133 (mmp) REVERT: D4 201 MET cc_start: 0.8184 (tpp) cc_final: 0.7980 (ttt) REVERT: D4 221 VAL cc_start: 0.8977 (m) cc_final: 0.8717 (p) REVERT: D4 257 MET cc_start: 0.7354 (mmm) cc_final: 0.6629 (mmm) REVERT: D4 263 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7469 (mmt) REVERT: D4 278 ARG cc_start: 0.7776 (ttt-90) cc_final: 0.7418 (ttt-90) REVERT: D4 331 ASN cc_start: 0.9052 (t0) cc_final: 0.8661 (t0) REVERT: D4 379 LEU cc_start: 0.8814 (tt) cc_final: 0.8595 (tp) REVERT: D2 14 MET cc_start: 0.7287 (tmm) cc_final: 0.6878 (tmm) REVERT: D2 18 ILE cc_start: 0.8927 (mt) cc_final: 0.8578 (mm) REVERT: D2 21 MET cc_start: 0.8947 (mmt) cc_final: 0.8666 (mmt) REVERT: D2 91 ASN cc_start: 0.8474 (t0) cc_final: 0.7862 (t0) REVERT: D2 93 MET cc_start: 0.9084 (tpp) cc_final: 0.8844 (tpp) REVERT: D2 100 MET cc_start: 0.8575 (mtt) cc_final: 0.8360 (mtt) REVERT: D2 105 LYS cc_start: 0.8911 (tptp) cc_final: 0.8557 (mmmt) REVERT: D2 120 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8309 (tp-100) REVERT: D2 129 ILE cc_start: 0.9156 (tt) cc_final: 0.8822 (mt) REVERT: D2 151 LEU cc_start: 0.8556 (tt) cc_final: 0.8271 (tt) REVERT: D2 217 THR cc_start: 0.9074 (m) cc_final: 0.8749 (p) REVERT: D2 323 MET cc_start: 0.7062 (mpt) cc_final: 0.6565 (mpt) REVERT: AK 8 TYR cc_start: 0.9191 (t80) cc_final: 0.8826 (t80) REVERT: AK 114 CYS cc_start: 0.6170 (OUTLIER) cc_final: 0.5509 (t) REVERT: AK 139 LYS cc_start: 0.8370 (pptt) cc_final: 0.7840 (pptt) REVERT: B5 79 PHE cc_start: 0.8466 (m-10) cc_final: 0.7817 (m-10) REVERT: AB 37 MET cc_start: 0.7163 (mmm) cc_final: 0.6819 (mmp) REVERT: AB 75 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6319 (mt-10) REVERT: AB 83 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8687 (ttmm) REVERT: BJ 80 ASP cc_start: 0.8440 (t0) cc_final: 0.7615 (t0) REVERT: BJ 98 ASP cc_start: 0.8259 (t0) cc_final: 0.7751 (t0) REVERT: BJ 110 LYS cc_start: 0.9197 (mttp) cc_final: 0.8827 (mtmm) REVERT: AJ 18 MET cc_start: 0.7986 (mmm) cc_final: 0.7393 (mmm) REVERT: AJ 90 ASP cc_start: 0.8499 (p0) cc_final: 0.8239 (p0) REVERT: AJ 271 ASN cc_start: 0.7983 (m110) cc_final: 0.7650 (m110) REVERT: AJ 308 TYR cc_start: 0.8143 (m-80) cc_final: 0.7405 (m-80) REVERT: AJ 315 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6600 (ttpp) REVERT: S5 16 TRP cc_start: 0.8475 (p-90) cc_final: 0.7838 (p-90) REVERT: S5 41 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7526 (mt-10) REVERT: S5 60 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7599 (mt-10) REVERT: A3 45 ASN cc_start: 0.8700 (t0) cc_final: 0.8338 (t0) REVERT: B3 33 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8301 (mm-30) REVERT: C2 2 MET cc_start: 0.6287 (ttp) cc_final: 0.5838 (tmm) REVERT: B4 40 SER cc_start: 0.9631 (p) cc_final: 0.8260 (t) REVERT: B4 43 LYS cc_start: 0.9101 (mtpm) cc_final: 0.8597 (ttmm) REVERT: B4 45 GLU cc_start: 0.8239 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B4 47 GLN cc_start: 0.8654 (mt0) cc_final: 0.7999 (mt0) REVERT: B4 74 ASN cc_start: 0.8036 (t0) cc_final: 0.7753 (t0) REVERT: B4 116 GLN cc_start: 0.8756 (tp40) cc_final: 0.8547 (tp-100) REVERT: B4 117 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7030 (tm-30) REVERT: B4 119 LYS cc_start: 0.8676 (ptmm) cc_final: 0.8473 (ptpp) REVERT: B4 123 THR cc_start: 0.8772 (p) cc_final: 0.8478 (t) REVERT: AM 84 GLN cc_start: 0.7558 (tt0) cc_final: 0.6959 (tt0) REVERT: AM 85 MET cc_start: 0.8093 (mmm) cc_final: 0.7311 (mmt) REVERT: AM 93 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7819 (mt-10) REVERT: AM 136 THR cc_start: 0.8496 (p) cc_final: 0.8252 (p) REVERT: B6 9 LEU cc_start: 0.8383 (tp) cc_final: 0.8024 (tp) REVERT: B6 13 GLN cc_start: 0.7663 (mp10) cc_final: 0.7222 (mp10) REVERT: B6 107 ASP cc_start: 0.8227 (m-30) cc_final: 0.7846 (m-30) REVERT: B7 85 ASP cc_start: 0.8037 (m-30) cc_final: 0.7815 (m-30) REVERT: B9 83 GLU cc_start: 0.8073 (mp0) cc_final: 0.7780 (mp0) REVERT: B9 123 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8690 (tm-30) REVERT: B8 46 ASP cc_start: 0.8639 (p0) cc_final: 0.8393 (p0) REVERT: B8 52 ASP cc_start: 0.8333 (m-30) cc_final: 0.8112 (t70) REVERT: B8 80 ASP cc_start: 0.8891 (m-30) cc_final: 0.8533 (m-30) REVERT: B8 103 LYS cc_start: 0.8079 (mttt) cc_final: 0.7806 (tttp) REVERT: B8 112 MET cc_start: 0.8069 (mmp) cc_final: 0.7861 (mmm) REVERT: B8 122 TYR cc_start: 0.8280 (m-10) cc_final: 0.7932 (m-10) REVERT: B8 137 ASN cc_start: 0.8839 (t0) cc_final: 0.8606 (t0) REVERT: BK 84 ARG cc_start: 0.7417 (mmm-85) cc_final: 0.6913 (mmm-85) REVERT: BK 92 GLU cc_start: 0.8058 (tp30) cc_final: 0.7833 (tp30) REVERT: BK 117 LYS cc_start: 0.8312 (ptpp) cc_final: 0.8082 (ptpp) REVERT: C1 5 GLN cc_start: 0.7628 (pp30) cc_final: 0.7048 (pp30) REVERT: C1 9 HIS cc_start: 0.6775 (p90) cc_final: 0.6018 (p-80) REVERT: B1 8 ARG cc_start: 0.5536 (mmp-170) cc_final: 0.4510 (ptp-170) REVERT: B1 28 ARG cc_start: 0.7130 (mmt180) cc_final: 0.6746 (mtm180) REVERT: A1 16 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8369 (mm) REVERT: A1 28 ARG cc_start: 0.7657 (mtp180) cc_final: 0.7250 (ttp80) outliers start: 182 outliers final: 96 residues processed: 1404 average time/residue: 0.2188 time to fit residues: 515.6869 Evaluate side-chains 1200 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1093 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D3 residue 55 PHE Chi-restraints excluded: chain D3 residue 72 LEU Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 113 VAL Chi-restraints excluded: chain D1 residue 115 SER Chi-restraints excluded: chain D1 residue 129 LEU Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 56 VAL Chi-restraints excluded: chain D6 residue 76 THR Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 102 LEU Chi-restraints excluded: chain D6 residue 132 ASP Chi-restraints excluded: chain 4L residue 17 THR Chi-restraints excluded: chain 4L residue 75 LEU Chi-restraints excluded: chain D5 residue 7 LEU Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 94 LEU Chi-restraints excluded: chain D5 residue 100 ILE Chi-restraints excluded: chain D5 residue 132 VAL Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 233 LEU Chi-restraints excluded: chain D5 residue 254 VAL Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 536 LEU Chi-restraints excluded: chain D5 residue 581 LYS Chi-restraints excluded: chain D4 residue 44 GLN Chi-restraints excluded: chain D4 residue 75 LEU Chi-restraints excluded: chain D4 residue 120 ILE Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 230 VAL Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 251 ASN Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 323 SER Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 86 VAL Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 244 VAL Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 266 ILE Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain AK residue 71 LEU Chi-restraints excluded: chain AK residue 98 LEU Chi-restraints excluded: chain AK residue 114 CYS Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 41 THR Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 75 GLU Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 83 GLU Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain BJ residue 103 ASN Chi-restraints excluded: chain AJ residue 16 LYS Chi-restraints excluded: chain AJ residue 100 LEU Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 202 ILE Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 92 THR Chi-restraints excluded: chain A3 residue 24 ILE Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain B3 residue 66 LEU Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain AM residue 95 THR Chi-restraints excluded: chain AM residue 109 VAL Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 90 THR Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B7 residue 30 PHE Chi-restraints excluded: chain B7 residue 41 THR Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B2 residue 18 THR Chi-restraints excluded: chain B2 residue 57 SER Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 39 ASP Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 109 VAL Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain C1 residue 39 VAL Chi-restraints excluded: chain B1 residue 7 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain A1 residue 16 LEU Chi-restraints excluded: chain A1 residue 57 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 6 optimal weight: 0.9990 chunk 338 optimal weight: 3.9990 chunk 341 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 301 optimal weight: 0.7980 chunk 313 optimal weight: 0.9990 chunk 245 optimal weight: 0.0010 chunk 111 optimal weight: 2.9990 chunk 418 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 46 ASN ** D5 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 570 GLN D4 43 ASN D4 51 ASN D4 399 ASN D4 415 GLN ** D2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 47 ASN ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B8 72 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.108717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.097812 restraints weight = 86243.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100408 restraints weight = 43692.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102153 restraints weight = 26085.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103344 restraints weight = 17445.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104154 restraints weight = 12604.482| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 39038 Z= 0.161 Angle : 0.838 13.490 52918 Z= 0.411 Chirality : 0.046 0.307 5820 Planarity : 0.006 0.071 6543 Dihedral : 9.617 90.144 5350 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.80 % Favored : 90.18 % Rotamer: Outliers : 5.47 % Allowed : 19.84 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.32 % Twisted Proline : 1.08 % Twisted General : 0.21 % 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: -1.17 (0.12), residues: 4561 helix: 0.70 (0.10), residues: 2841 sheet: -3.32 (0.76), residues: 24 loop : -3.48 (0.13), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAM 80 TYR 0.031 0.002 TYRD5 422 PHE 0.024 0.002 PHED4 122 TRP 0.031 0.002 TRPAM 103 HIS 0.014 0.001 HISB9 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (39024) covalent geometry : angle 0.83648 / 0.41 (52894) SS BOND : bond 0.00504 / 0.24 ( 12) SS BOND : angle 2.28080 / 1.38 ( 24) hydrogen bonds : bond 0.04776 / 3.11 ( 2139) hydrogen bonds : angle 4.63763 / 3.24 ( 6366) Misc. bond : bond 0.00541 / 0.26 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1422 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 1198 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D3 11 PHE cc_start: 0.8745 (t80) cc_final: 0.8307 (t80) REVERT: D3 88 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8418 (tp) REVERT: D1 23 VAL cc_start: 0.8513 (t) cc_final: 0.8174 (p) REVERT: D1 25 ARG cc_start: 0.8817 (ttm110) cc_final: 0.8198 (ttm-80) REVERT: D1 26 LYS cc_start: 0.8893 (mmmm) cc_final: 0.8586 (mmtt) REVERT: D1 70 MET cc_start: 0.8567 (tpp) cc_final: 0.8329 (tpp) REVERT: D1 100 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8220 (pt) REVERT: D1 192 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7708 (tm-30) REVERT: D1 195 ARG cc_start: 0.7528 (mtp85) cc_final: 0.6921 (mtm180) REVERT: D1 233 MET cc_start: 0.8434 (tmm) cc_final: 0.7976 (tmm) REVERT: D1 234 MET cc_start: 0.8838 (mmt) cc_final: 0.8507 (tpp) REVERT: D1 239 THR cc_start: 0.9063 (m) cc_final: 0.8784 (p) REVERT: D1 266 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8597 (tt) REVERT: D1 271 LEU cc_start: 0.8385 (tm) cc_final: 0.7810 (tm) REVERT: D1 272 TRP cc_start: 0.7218 (t60) cc_final: 0.6525 (t-100) REVERT: D1 281 ARG cc_start: 0.8295 (ttp-170) cc_final: 0.6891 (mpt180) REVERT: D1 284 GLN cc_start: 0.6799 (mt0) cc_final: 0.6408 (pt0) REVERT: D6 15 MET cc_start: 0.7179 (mmm) cc_final: 0.6768 (mmm) REVERT: D6 17 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.7742 (t80) REVERT: D6 70 TYR cc_start: 0.7962 (t80) cc_final: 0.7005 (t80) REVERT: D6 98 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8612 (tm) REVERT: D6 136 PHE cc_start: 0.8438 (p90) cc_final: 0.7875 (p90) REVERT: 4L 1 MET cc_start: 0.7459 (ttm) cc_final: 0.6857 (ttm) REVERT: 4L 37 MET cc_start: 0.7106 (ttm) cc_final: 0.6807 (ttm) REVERT: 4L 88 ASP cc_start: 0.8381 (p0) cc_final: 0.7968 (p0) REVERT: D5 60 GLU cc_start: 0.5843 (mt-10) cc_final: 0.5460 (mt-10) REVERT: D5 94 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9178 (mm) REVERT: D5 128 MET cc_start: 0.7938 (tmm) cc_final: 0.7654 (tmm) REVERT: D5 154 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9022 (mm) REVERT: D5 204 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7188 (tp) REVERT: D5 393 ASP cc_start: 0.8441 (m-30) cc_final: 0.8184 (m-30) REVERT: D5 397 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7664 (mt-10) REVERT: D5 533 MET cc_start: 0.8477 (mmm) cc_final: 0.8259 (mmt) REVERT: D5 602 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8969 (pp) REVERT: D4 1 MET cc_start: 0.7716 (tpp) cc_final: 0.7071 (tpp) REVERT: D4 9 MET cc_start: 0.6945 (ttt) cc_final: 0.6429 (tmm) REVERT: D4 23 ILE cc_start: 0.7363 (pp) cc_final: 0.6940 (pt) REVERT: D4 26 ASN cc_start: 0.8057 (m-40) cc_final: 0.7821 (m110) REVERT: D4 108 MET cc_start: 0.8221 (mmp) cc_final: 0.7439 (ttm) REVERT: D4 119 TYR cc_start: 0.8721 (t80) cc_final: 0.8283 (t80) REVERT: D4 121 MET cc_start: 0.8044 (mmm) cc_final: 0.7381 (mmm) REVERT: D4 158 LEU cc_start: 0.9156 (tm) cc_final: 0.8841 (tp) REVERT: D4 201 MET cc_start: 0.8146 (tpp) cc_final: 0.7934 (ttt) REVERT: D4 221 VAL cc_start: 0.8986 (m) cc_final: 0.8774 (p) REVERT: D4 241 TYR cc_start: 0.8503 (t80) cc_final: 0.8238 (t80) REVERT: D4 263 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7537 (mmt) REVERT: D4 278 ARG cc_start: 0.7877 (ttt-90) cc_final: 0.7497 (ttt-90) REVERT: D4 331 ASN cc_start: 0.9101 (t0) cc_final: 0.8768 (t0) REVERT: D4 340 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7763 (ttm-80) REVERT: D2 14 MET cc_start: 0.7200 (tmm) cc_final: 0.6568 (tmm) REVERT: D2 15 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8022 (mp) REVERT: D2 18 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8583 (mm) REVERT: D2 91 ASN cc_start: 0.8378 (t0) cc_final: 0.7824 (t0) REVERT: D2 104 MET cc_start: 0.8731 (mtt) cc_final: 0.8524 (mtt) REVERT: D2 105 LYS cc_start: 0.8968 (tptp) cc_final: 0.8607 (mmmt) REVERT: D2 120 GLN cc_start: 0.8777 (tp-100) cc_final: 0.8493 (tp-100) REVERT: D2 129 ILE cc_start: 0.9037 (tt) cc_final: 0.8732 (mt) REVERT: D2 217 THR cc_start: 0.9296 (m) cc_final: 0.9084 (p) REVERT: AK 8 TYR cc_start: 0.9153 (t80) cc_final: 0.8925 (t80) REVERT: AK 11 ILE cc_start: 0.9018 (mm) cc_final: 0.8741 (mp) REVERT: AK 57 ARG cc_start: 0.6856 (ttp-110) cc_final: 0.6624 (mtp180) REVERT: AK 117 MET cc_start: 0.7996 (mmt) cc_final: 0.7554 (mmp) REVERT: AK 139 LYS cc_start: 0.8374 (pptt) cc_final: 0.7835 (pptt) REVERT: B5 112 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7710 (ptm160) REVERT: B5 133 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7920 (tt) REVERT: AB 52 MET cc_start: 0.8229 (tpp) cc_final: 0.7943 (tpt) REVERT: AB 75 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6351 (mt-10) REVERT: AB 83 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8638 (ttmm) REVERT: A8 76 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6919 (t-90) REVERT: A8 95 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8007 (mt) REVERT: BJ 80 ASP cc_start: 0.8177 (t0) cc_final: 0.7830 (t0) REVERT: BJ 110 LYS cc_start: 0.9198 (mttp) cc_final: 0.8943 (mtmm) REVERT: AJ 18 MET cc_start: 0.8001 (mmm) cc_final: 0.7553 (mmm) REVERT: AJ 271 ASN cc_start: 0.7978 (m110) cc_final: 0.7611 (m110) REVERT: AJ 308 TYR cc_start: 0.8121 (m-80) cc_final: 0.7581 (m-80) REVERT: AJ 315 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6654 (ttpp) REVERT: S5 16 TRP cc_start: 0.8492 (p-90) cc_final: 0.7810 (p-90) REVERT: A3 45 ASN cc_start: 0.8710 (t0) cc_final: 0.8418 (t0) REVERT: B3 29 GLU cc_start: 0.8474 (tt0) cc_final: 0.8274 (tt0) REVERT: C2 2 MET cc_start: 0.6521 (ttp) cc_final: 0.5787 (tmm) REVERT: C2 11 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6638 (pp) REVERT: B4 27 GLU cc_start: 0.7672 (pp20) cc_final: 0.7260 (tm-30) REVERT: B4 40 SER cc_start: 0.9616 (p) cc_final: 0.8067 (t) REVERT: B4 43 LYS cc_start: 0.9044 (mtpm) cc_final: 0.8635 (ttmm) REVERT: B4 47 GLN cc_start: 0.8627 (mt0) cc_final: 0.8146 (mt0) REVERT: B4 74 ASN cc_start: 0.7830 (t0) cc_final: 0.7386 (t0) REVERT: B4 116 GLN cc_start: 0.8546 (tp40) cc_final: 0.8141 (tp-100) REVERT: B4 117 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6989 (tm-30) REVERT: B4 119 LYS cc_start: 0.8727 (ptmm) cc_final: 0.8496 (ptpp) REVERT: B6 31 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.5660 (pp20) REVERT: B6 96 ILE cc_start: 0.8651 (pt) cc_final: 0.8382 (pt) REVERT: B6 107 ASP cc_start: 0.8042 (m-30) cc_final: 0.7681 (m-30) REVERT: B6 114 GLU cc_start: 0.7525 (pm20) cc_final: 0.7042 (pm20) REVERT: B6 121 GLU cc_start: 0.8105 (tt0) cc_final: 0.7887 (tt0) REVERT: B7 49 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7581 (tp-100) REVERT: B7 56 ASP cc_start: 0.8980 (p0) cc_final: 0.8502 (p0) REVERT: B7 85 ASP cc_start: 0.7983 (m-30) cc_final: 0.7712 (m-30) REVERT: B9 83 GLU cc_start: 0.8045 (mp0) cc_final: 0.7786 (mp0) REVERT: B9 93 TYR cc_start: 0.8014 (m-80) cc_final: 0.7664 (m-10) REVERT: B9 123 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8662 (tm-30) REVERT: B2 28 PHE cc_start: 0.8068 (m-80) cc_final: 0.7640 (t80) REVERT: B8 52 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8049 (t70) REVERT: B8 80 ASP cc_start: 0.8880 (m-30) cc_final: 0.8536 (m-30) REVERT: B8 103 LYS cc_start: 0.8139 (mttt) cc_final: 0.7908 (tttp) REVERT: B8 122 TYR cc_start: 0.8338 (m-10) cc_final: 0.7914 (m-10) REVERT: B8 137 ASN cc_start: 0.8896 (t0) cc_final: 0.8634 (t0) REVERT: BK 36 ASN cc_start: 0.8913 (t0) cc_final: 0.8675 (t0) REVERT: BK 84 ARG cc_start: 0.7181 (mmm-85) cc_final: 0.6973 (mmm-85) REVERT: BK 92 GLU cc_start: 0.8084 (tp30) cc_final: 0.7846 (tp30) REVERT: BK 117 LYS cc_start: 0.8425 (ptpp) cc_final: 0.8212 (ptpp) REVERT: C1 5 GLN cc_start: 0.7552 (pp30) cc_final: 0.7006 (pp30) REVERT: C1 9 HIS cc_start: 0.6827 (p90) cc_final: 0.6096 (p-80) REVERT: C1 37 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7571 (tm-30) REVERT: B1 8 ARG cc_start: 0.5366 (mmp-170) cc_final: 0.4494 (ptp-170) REVERT: A1 16 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8214 (mm) REVERT: A1 28 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7208 (ttp80) REVERT: A1 34 ARG cc_start: 0.8261 (mpt180) cc_final: 0.7898 (mmt90) outliers start: 224 outliers final: 119 residues processed: 1329 average time/residue: 0.2226 time to fit residues: 495.9721 Evaluate side-chains 1233 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1091 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 7 LEU Chi-restraints excluded: chain D3 residue 17 LEU Chi-restraints excluded: chain D3 residue 88 LEU Chi-restraints excluded: chain D3 residue 100 VAL Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 97 ASN Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 103 LEU Chi-restraints excluded: chain D1 residue 113 VAL Chi-restraints excluded: chain D1 residue 129 LEU Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D6 residue 17 PHE Chi-restraints excluded: chain D6 residue 46 ASN Chi-restraints excluded: chain D6 residue 76 THR Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 102 LEU Chi-restraints excluded: chain D6 residue 132 ASP Chi-restraints excluded: chain 4L residue 39 SER Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain D5 residue 7 LEU Chi-restraints excluded: chain D5 residue 12 LEU Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 69 LEU Chi-restraints excluded: chain D5 residue 78 LEU Chi-restraints excluded: chain D5 residue 94 LEU Chi-restraints excluded: chain D5 residue 100 ILE Chi-restraints excluded: chain D5 residue 130 ILE Chi-restraints excluded: chain D5 residue 132 VAL Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 204 LEU Chi-restraints excluded: chain D5 residue 246 LEU Chi-restraints excluded: chain D5 residue 254 VAL Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 536 LEU Chi-restraints excluded: chain D5 residue 590 SER Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 6 ILE Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 35 SER Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 191 SER Chi-restraints excluded: chain D4 residue 230 VAL Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 298 ILE Chi-restraints excluded: chain D4 residue 323 SER Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 15 LEU Chi-restraints excluded: chain D2 residue 18 ILE Chi-restraints excluded: chain D2 residue 86 VAL Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 239 ILE Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 281 LEU Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 288 LEU Chi-restraints excluded: chain D2 residue 294 MET Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 331 VAL Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain AK residue 98 LEU Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 41 THR Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain B5 residue 112 ARG Chi-restraints excluded: chain B5 residue 133 ILE Chi-restraints excluded: chain AB residue 11 ILE Chi-restraints excluded: chain AB residue 51 ILE Chi-restraints excluded: chain AB residue 75 GLU Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 76 HIS Chi-restraints excluded: chain A8 residue 83 GLU Chi-restraints excluded: chain A8 residue 95 LEU Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 16 THR Chi-restraints excluded: chain BJ residue 23 THR Chi-restraints excluded: chain BJ residue 70 VAL Chi-restraints excluded: chain BJ residue 103 ASN Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 100 LEU Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 279 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 25 LYS Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 65 ILE Chi-restraints excluded: chain C2 residue 69 VAL Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain AM residue 109 VAL Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 90 THR Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B9 residue 50 HIS Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B2 residue 57 SER Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 39 ASP Chi-restraints excluded: chain B8 residue 52 ASP Chi-restraints excluded: chain B8 residue 53 ARG Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 77 VAL Chi-restraints excluded: chain C1 residue 39 VAL Chi-restraints excluded: chain B1 residue 7 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 14 VAL Chi-restraints excluded: chain A1 residue 16 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 150 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 374 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 255 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 437 optimal weight: 0.6980 chunk 225 optimal weight: 0.0270 chunk 45 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 46 ASN 4L 83 ASN ** D5 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 72 GLN D5 534 HIS D5 580 GLN D4 374 ASN ** D2 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 172 GLN D2 289 ASN ** A8 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 99 GLN ** A3 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4 51 ASN B4 125 ASN ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 58 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.108746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.097791 restraints weight = 85946.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100441 restraints weight = 43435.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.102146 restraints weight = 25876.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103305 restraints weight = 17394.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104145 restraints weight = 12743.490| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 39038 Z= 0.153 Angle : 0.811 12.714 52918 Z= 0.398 Chirality : 0.045 0.239 5820 Planarity : 0.005 0.069 6543 Dihedral : 8.859 80.222 5350 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.82 % Favored : 90.16 % Rotamer: Outliers : 5.59 % Allowed : 21.67 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.32 % Twisted Proline : 1.08 % Twisted General : 0.16 % 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: -0.84 (0.13), residues: 4561 helix: 0.96 (0.10), residues: 2873 sheet: -2.84 (0.85), residues: 24 loop : -3.42 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGB9 92 TYR 0.029 0.001 TYRBK 83 PHE 0.025 0.002 PHEB6 69 TRP 0.035 0.001 TRPAM 103 HIS 0.012 0.001 HISB9 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (39024) covalent geometry : angle 0.81062 / 0.40 (52894) SS BOND : bond 0.00488 / 0.29 ( 12) SS BOND : angle 1.36447 / 0.84 ( 24) hydrogen bonds : bond 0.04582 / 2.97 ( 2139) hydrogen bonds : angle 4.51726 / 3.16 ( 6366) Misc. bond : bond 0.00451 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 1196 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 34 ASN cc_start: 0.8440 (p0) cc_final: 0.8079 (p0) REVERT: D3 11 PHE cc_start: 0.8738 (t80) cc_final: 0.8482 (t80) REVERT: D3 88 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8611 (tp) REVERT: D1 23 VAL cc_start: 0.8504 (t) cc_final: 0.8217 (p) REVERT: D1 25 ARG cc_start: 0.8843 (ttm110) cc_final: 0.8250 (ttm-80) REVERT: D1 26 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8347 (mmtt) REVERT: D1 81 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8294 (mp) REVERT: D1 85 MET cc_start: 0.8091 (mmm) cc_final: 0.7776 (mmm) REVERT: D1 100 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8142 (pt) REVERT: D1 192 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7636 (tm-30) REVERT: D1 195 ARG cc_start: 0.7509 (mtp85) cc_final: 0.7025 (mtm180) REVERT: D1 233 MET cc_start: 0.8504 (tmm) cc_final: 0.8016 (tmm) REVERT: D1 234 MET cc_start: 0.8894 (mmt) cc_final: 0.8540 (tpp) REVERT: D1 239 THR cc_start: 0.8997 (m) cc_final: 0.8742 (p) REVERT: D1 266 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8574 (tt) REVERT: D1 272 TRP cc_start: 0.7238 (t60) cc_final: 0.6529 (t-100) REVERT: D1 281 ARG cc_start: 0.8343 (ttp-170) cc_final: 0.6836 (mpt180) REVERT: D1 284 GLN cc_start: 0.6775 (mt0) cc_final: 0.6383 (pt0) REVERT: D6 15 MET cc_start: 0.7248 (mmm) cc_final: 0.6853 (mmm) REVERT: D6 17 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7759 (t80) REVERT: D6 98 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8630 (tm) REVERT: D6 120 ASN cc_start: 0.7454 (t0) cc_final: 0.6825 (t0) REVERT: D6 136 PHE cc_start: 0.8384 (p90) cc_final: 0.7770 (p90) REVERT: 4L 1 MET cc_start: 0.7688 (ttm) cc_final: 0.7341 (ttm) REVERT: 4L 6 MET cc_start: 0.8785 (ppp) cc_final: 0.8411 (ppp) REVERT: 4L 37 MET cc_start: 0.7214 (ttm) cc_final: 0.6983 (ttm) REVERT: 4L 88 ASP cc_start: 0.8342 (p0) cc_final: 0.7981 (p0) REVERT: D5 53 MET cc_start: 0.7485 (tpt) cc_final: 0.7250 (tpt) REVERT: D5 94 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9177 (mm) REVERT: D5 150 MET cc_start: 0.8160 (mmp) cc_final: 0.7713 (tpp) REVERT: D5 154 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8938 (mm) REVERT: D5 341 MET cc_start: 0.8028 (tpp) cc_final: 0.7690 (tpp) REVERT: D5 359 MET cc_start: 0.7327 (ttm) cc_final: 0.6875 (mtt) REVERT: D5 393 ASP cc_start: 0.8609 (m-30) cc_final: 0.8340 (m-30) REVERT: D5 397 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7681 (mt-10) REVERT: D5 487 LYS cc_start: 0.7494 (ttmp) cc_final: 0.6976 (ttmt) REVERT: D5 533 MET cc_start: 0.8491 (mmm) cc_final: 0.8287 (mmt) REVERT: D4 1 MET cc_start: 0.7573 (tpp) cc_final: 0.6952 (tpp) REVERT: D4 9 MET cc_start: 0.6848 (ttt) cc_final: 0.6459 (tmm) REVERT: D4 44 GLN cc_start: 0.8503 (pp30) cc_final: 0.8251 (pt0) REVERT: D4 119 TYR cc_start: 0.8874 (t80) cc_final: 0.8369 (t80) REVERT: D4 121 MET cc_start: 0.8044 (mmm) cc_final: 0.7522 (tpp) REVERT: D4 158 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8842 (tp) REVERT: D4 221 VAL cc_start: 0.9024 (m) cc_final: 0.8726 (p) REVERT: D4 241 TYR cc_start: 0.8562 (t80) cc_final: 0.8272 (t80) REVERT: D4 257 MET cc_start: 0.7522 (mmm) cc_final: 0.7218 (mmm) REVERT: D4 263 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7454 (mmt) REVERT: D4 331 ASN cc_start: 0.9138 (t0) cc_final: 0.8875 (t0) REVERT: D2 14 MET cc_start: 0.7280 (tmm) cc_final: 0.6511 (tmm) REVERT: D2 15 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7947 (mp) REVERT: D2 18 ILE cc_start: 0.8915 (mt) cc_final: 0.8608 (mm) REVERT: D2 91 ASN cc_start: 0.8434 (t0) cc_final: 0.7830 (t0) REVERT: D2 100 MET cc_start: 0.8802 (mtt) cc_final: 0.8214 (mtt) REVERT: D2 104 MET cc_start: 0.8823 (mtt) cc_final: 0.8405 (ttm) REVERT: D2 105 LYS cc_start: 0.8992 (tptp) cc_final: 0.8638 (mmmt) REVERT: D2 129 ILE cc_start: 0.9024 (tt) cc_final: 0.8707 (mt) REVERT: D2 152 ASP cc_start: 0.8599 (m-30) cc_final: 0.8394 (m-30) REVERT: D2 158 SER cc_start: 0.8779 (m) cc_final: 0.8406 (p) REVERT: D2 217 THR cc_start: 0.9288 (m) cc_final: 0.9048 (p) REVERT: D2 313 MET cc_start: 0.8190 (tmt) cc_final: 0.7821 (tmm) REVERT: AK 8 TYR cc_start: 0.9268 (t80) cc_final: 0.8973 (t80) REVERT: AK 11 ILE cc_start: 0.9040 (mm) cc_final: 0.8723 (mp) REVERT: AK 117 MET cc_start: 0.7902 (mmt) cc_final: 0.7334 (mmp) REVERT: AK 139 LYS cc_start: 0.8344 (pptt) cc_final: 0.8118 (pptt) REVERT: B5 93 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8855 (mt) REVERT: B5 114 MET cc_start: 0.9038 (ttm) cc_final: 0.8818 (ttm) REVERT: AB 52 MET cc_start: 0.8294 (tpp) cc_final: 0.7853 (tpt) REVERT: AB 83 LYS cc_start: 0.8997 (ttmm) cc_final: 0.8413 (ttmm) REVERT: A8 76 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.6910 (t-90) REVERT: A8 95 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7948 (mt) REVERT: BJ 48 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7988 (tpt-90) REVERT: BJ 60 TYR cc_start: 0.6464 (m-80) cc_final: 0.5980 (t80) REVERT: BJ 80 ASP cc_start: 0.7748 (t0) cc_final: 0.7335 (t70) REVERT: BJ 98 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8053 (t0) REVERT: BJ 118 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6774 (mt-10) REVERT: BJ 162 MET cc_start: 0.7942 (mtt) cc_final: 0.7666 (mtt) REVERT: BJ 171 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7698 (mm-30) REVERT: AJ 18 MET cc_start: 0.7996 (mmm) cc_final: 0.7542 (mmm) REVERT: AJ 267 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8352 (mt) REVERT: AJ 271 ASN cc_start: 0.8056 (m110) cc_final: 0.7646 (m110) REVERT: AJ 308 TYR cc_start: 0.8001 (m-80) cc_final: 0.7517 (m-80) REVERT: AJ 315 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6470 (ttmm) REVERT: S5 16 TRP cc_start: 0.8520 (p-90) cc_final: 0.7721 (p-90) REVERT: A3 19 VAL cc_start: 0.8888 (t) cc_final: 0.8675 (p) REVERT: A3 45 ASN cc_start: 0.8836 (t0) cc_final: 0.8522 (t0) REVERT: C2 2 MET cc_start: 0.6366 (ttp) cc_final: 0.5672 (tmm) REVERT: C2 11 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6761 (pp) REVERT: B4 27 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: B4 40 SER cc_start: 0.9566 (p) cc_final: 0.9030 (t) REVERT: B4 43 LYS cc_start: 0.9038 (mtpm) cc_final: 0.8529 (ttmm) REVERT: B4 45 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B4 47 GLN cc_start: 0.8590 (mt0) cc_final: 0.8147 (mt0) REVERT: B4 74 ASN cc_start: 0.7856 (t0) cc_final: 0.7382 (t0) REVERT: B4 116 GLN cc_start: 0.8659 (tp40) cc_final: 0.8324 (tp-100) REVERT: B4 125 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7867 (m-40) REVERT: AM 85 MET cc_start: 0.7914 (mmt) cc_final: 0.7708 (mmt) REVERT: AM 93 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8050 (mt-10) REVERT: B6 31 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5550 (pp20) REVERT: B6 96 ILE cc_start: 0.8416 (pt) cc_final: 0.8092 (pt) REVERT: B6 107 ASP cc_start: 0.7870 (m-30) cc_final: 0.7504 (m-30) REVERT: B6 114 GLU cc_start: 0.7565 (pm20) cc_final: 0.7063 (pm20) REVERT: B7 17 GLU cc_start: 0.7240 (pm20) cc_final: 0.6760 (pp20) REVERT: B7 49 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7704 (tm-30) REVERT: B7 56 ASP cc_start: 0.8851 (p0) cc_final: 0.8430 (p0) REVERT: B7 85 ASP cc_start: 0.7965 (m-30) cc_final: 0.7735 (m-30) REVERT: B9 67 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8111 (mm-30) REVERT: B9 79 TYR cc_start: 0.8815 (t80) cc_final: 0.8555 (t80) REVERT: B9 123 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8684 (tm-30) REVERT: B9 133 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B2 26 GLU cc_start: 0.8396 (tp30) cc_final: 0.7854 (tp30) REVERT: B8 52 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8067 (t70) REVERT: B8 58 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.7467 (mpp80) REVERT: B8 80 ASP cc_start: 0.8882 (m-30) cc_final: 0.8455 (m-30) REVERT: B8 103 LYS cc_start: 0.8043 (mttt) cc_final: 0.7754 (tttp) REVERT: B8 117 TRP cc_start: 0.8294 (t60) cc_final: 0.7859 (t60) REVERT: B8 122 TYR cc_start: 0.8233 (m-10) cc_final: 0.8015 (m-10) REVERT: B8 137 ASN cc_start: 0.8954 (t0) cc_final: 0.8708 (t0) REVERT: BK 36 ASN cc_start: 0.8841 (t0) cc_final: 0.7683 (t0) REVERT: BK 92 GLU cc_start: 0.8152 (tp30) cc_final: 0.7884 (tp30) REVERT: BK 108 MET cc_start: 0.7755 (ttt) cc_final: 0.7105 (ttt) REVERT: C1 5 GLN cc_start: 0.7585 (pp30) cc_final: 0.7022 (pp30) REVERT: C1 9 HIS cc_start: 0.6814 (p90) cc_final: 0.6184 (p-80) REVERT: C1 37 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7574 (tm-30) REVERT: B1 8 ARG cc_start: 0.5841 (mmp-170) cc_final: 0.4836 (ptp-170) REVERT: A1 16 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8112 (mm) REVERT: A1 28 ARG cc_start: 0.7682 (mtp180) cc_final: 0.7274 (ttp80) REVERT: A1 34 ARG cc_start: 0.8275 (mpt180) cc_final: 0.8002 (mmt90) outliers start: 229 outliers final: 144 residues processed: 1323 average time/residue: 0.2267 time to fit residues: 502.3069 Evaluate side-chains 1267 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 1098 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 1 MET Chi-restraints excluded: chain D3 residue 88 LEU Chi-restraints excluded: chain D3 residue 100 VAL Chi-restraints excluded: chain D3 residue 101 SER Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 81 LEU Chi-restraints excluded: chain D1 residue 97 ASN Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 103 LEU Chi-restraints excluded: chain D1 residue 113 VAL Chi-restraints excluded: chain D1 residue 115 SER Chi-restraints excluded: chain D1 residue 129 LEU Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D6 residue 17 PHE Chi-restraints excluded: chain D6 residue 20 PHE Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 56 VAL Chi-restraints excluded: chain D6 residue 76 THR Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 102 LEU Chi-restraints excluded: chain D6 residue 106 TYR Chi-restraints excluded: chain D6 residue 132 ASP Chi-restraints excluded: chain 4L residue 39 SER Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain 4L residue 69 CYS Chi-restraints excluded: chain D5 residue 7 LEU Chi-restraints excluded: chain D5 residue 12 LEU Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 69 LEU Chi-restraints excluded: chain D5 residue 78 LEU Chi-restraints excluded: chain D5 residue 94 LEU Chi-restraints excluded: chain D5 residue 100 ILE Chi-restraints excluded: chain D5 residue 130 ILE Chi-restraints excluded: chain D5 residue 132 VAL Chi-restraints excluded: chain D5 residue 137 LEU Chi-restraints excluded: chain D5 residue 142 ILE Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 253 VAL Chi-restraints excluded: chain D5 residue 254 VAL Chi-restraints excluded: chain D5 residue 312 LEU Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 536 LEU Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 6 ILE Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 158 LEU Chi-restraints excluded: chain D4 residue 191 SER Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 310 MET Chi-restraints excluded: chain D4 residue 323 SER Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D4 residue 403 THR Chi-restraints excluded: chain D4 residue 441 MET Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 15 LEU Chi-restraints excluded: chain D2 residue 44 MET Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 205 LEU Chi-restraints excluded: chain D2 residue 239 ILE Chi-restraints excluded: chain D2 residue 241 THR Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 281 LEU Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 288 LEU Chi-restraints excluded: chain D2 residue 289 ASN Chi-restraints excluded: chain D2 residue 294 MET Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 41 THR Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 51 ILE Chi-restraints excluded: chain AB residue 61 GLU Chi-restraints excluded: chain AB residue 86 VAL Chi-restraints excluded: chain A8 residue 15 GLN Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 36 ASP Chi-restraints excluded: chain A8 residue 65 CYS Chi-restraints excluded: chain A8 residue 76 HIS Chi-restraints excluded: chain A8 residue 83 GLU Chi-restraints excluded: chain A8 residue 95 LEU Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 144 ARG Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 16 THR Chi-restraints excluded: chain BJ residue 23 THR Chi-restraints excluded: chain BJ residue 48 ARG Chi-restraints excluded: chain BJ residue 51 ILE Chi-restraints excluded: chain BJ residue 70 VAL Chi-restraints excluded: chain BJ residue 81 VAL Chi-restraints excluded: chain BJ residue 98 ASP Chi-restraints excluded: chain BJ residue 103 ASN Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain BJ residue 163 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 77 CYS Chi-restraints excluded: chain AJ residue 106 LEU Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 259 LEU Chi-restraints excluded: chain AJ residue 267 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 5 VAL Chi-restraints excluded: chain S5 residue 36 GLU Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 65 ILE Chi-restraints excluded: chain C2 residue 69 VAL Chi-restraints excluded: chain C2 residue 119 VAL Chi-restraints excluded: chain B4 residue 27 GLU Chi-restraints excluded: chain B4 residue 64 LEU Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain B4 residue 87 LEU Chi-restraints excluded: chain B4 residue 125 ASN Chi-restraints excluded: chain AM residue 86 LEU Chi-restraints excluded: chain AM residue 109 VAL Chi-restraints excluded: chain AM residue 126 LEU Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 34 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B9 residue 50 HIS Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 39 ASP Chi-restraints excluded: chain B8 residue 52 ASP Chi-restraints excluded: chain B8 residue 53 ARG Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 71 LEU Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 131 LYS Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 71 VAL Chi-restraints excluded: chain BK residue 77 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 411 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 425 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 313 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 236 optimal weight: 6.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D3 108 GLN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 235 ASN 4L 83 ASN D5 295 GLN D4 44 GLN D4 184 GLN D4 374 ASN D4 415 GLN D2 120 GLN ** D2 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 222 ASN D2 289 ASN BJ 114 GLN ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 68 HIS A3 70 GLN AM 84 GLN ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B7 53 GLN ** B9 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 13 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.107336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096215 restraints weight = 87548.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.098844 restraints weight = 44999.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100551 restraints weight = 27158.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101710 restraints weight = 18382.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.102512 restraints weight = 13604.172| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39038 Z= 0.167 Angle : 0.820 13.566 52918 Z= 0.401 Chirality : 0.046 0.215 5820 Planarity : 0.005 0.073 6543 Dihedral : 8.550 81.680 5349 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.91 % Favored : 90.07 % Rotamer: Outliers : 5.96 % Allowed : 22.77 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 1.08 % Twisted General : 0.14 % 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: -0.61 (0.13), residues: 4561 helix: 1.14 (0.10), residues: 2873 sheet: -2.72 (0.92), residues: 24 loop : -3.33 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGBK 84 TYR 0.027 0.002 TYRD1 250 PHE 0.027 0.002 PHED6 47 TRP 0.036 0.001 TRPAM 103 HIS 0.015 0.001 HISD5 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (39024) covalent geometry : angle 0.81879 / 0.40 (52894) SS BOND : bond 0.00454 / 0.26 ( 12) SS BOND : angle 1.91180 / 1.33 ( 24) hydrogen bonds : bond 0.04600 / 2.99 ( 2139) hydrogen bonds : angle 4.47283 / 3.12 ( 6366) Misc. bond : bond 0.00430 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1397 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 1153 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 34 ASN cc_start: 0.8461 (p0) cc_final: 0.8075 (p0) REVERT: D3 11 PHE cc_start: 0.8729 (t80) cc_final: 0.8393 (t80) REVERT: D1 23 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8166 (p) REVERT: D1 25 ARG cc_start: 0.8869 (ttm110) cc_final: 0.8252 (ttm-80) REVERT: D1 26 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8484 (mmtt) REVERT: D1 70 MET cc_start: 0.8711 (tpp) cc_final: 0.8477 (tpp) REVERT: D1 81 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8114 (mp) REVERT: D1 85 MET cc_start: 0.8103 (mmm) cc_final: 0.7783 (mmm) REVERT: D1 100 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8131 (pt) REVERT: D1 192 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7654 (tm-30) REVERT: D1 195 ARG cc_start: 0.7507 (mtp85) cc_final: 0.7267 (mtp180) REVERT: D1 233 MET cc_start: 0.8359 (tmm) cc_final: 0.7780 (tmm) REVERT: D1 234 MET cc_start: 0.8938 (mmt) cc_final: 0.8567 (tpp) REVERT: D1 239 THR cc_start: 0.9024 (m) cc_final: 0.8731 (p) REVERT: D1 266 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8624 (tt) REVERT: D1 272 TRP cc_start: 0.7259 (t60) cc_final: 0.6509 (t-100) REVERT: D1 281 ARG cc_start: 0.8276 (ttp-170) cc_final: 0.6715 (mpt180) REVERT: D1 284 GLN cc_start: 0.6796 (mt0) cc_final: 0.6319 (pt0) REVERT: D6 15 MET cc_start: 0.7399 (mmm) cc_final: 0.7080 (mmm) REVERT: D6 17 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7877 (t80) REVERT: D6 98 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8621 (tm) REVERT: D6 120 ASN cc_start: 0.7204 (t0) cc_final: 0.7003 (t0) REVERT: D6 127 ILE cc_start: 0.8859 (pt) cc_final: 0.8541 (pt) REVERT: D6 136 PHE cc_start: 0.8450 (p90) cc_final: 0.7876 (p90) REVERT: 4L 6 MET cc_start: 0.8815 (ppp) cc_final: 0.8428 (ppp) REVERT: 4L 88 ASP cc_start: 0.8460 (p0) cc_final: 0.8024 (p0) REVERT: D5 53 MET cc_start: 0.7660 (tpt) cc_final: 0.7456 (tpt) REVERT: D5 94 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9172 (mm) REVERT: D5 108 MET cc_start: 0.8761 (tpp) cc_final: 0.8290 (mmt) REVERT: D5 150 MET cc_start: 0.8272 (mmp) cc_final: 0.7833 (tpp) REVERT: D5 154 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8913 (mm) REVERT: D5 235 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.7947 (t) REVERT: D5 341 MET cc_start: 0.8142 (tpp) cc_final: 0.7786 (tpp) REVERT: D5 393 ASP cc_start: 0.8502 (m-30) cc_final: 0.8182 (m-30) REVERT: D5 397 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7664 (mt-10) REVERT: D5 480 MET cc_start: 0.7886 (tpt) cc_final: 0.7588 (tpt) REVERT: D5 487 LYS cc_start: 0.7821 (ttmp) cc_final: 0.7184 (ttmt) REVERT: D5 533 MET cc_start: 0.8548 (mmm) cc_final: 0.8327 (mmt) REVERT: D5 544 MET cc_start: 0.7050 (ttt) cc_final: 0.6668 (ttt) REVERT: D5 573 MET cc_start: 0.8118 (mmm) cc_final: 0.7673 (mmm) REVERT: D4 1 MET cc_start: 0.7622 (tpp) cc_final: 0.7324 (tpp) REVERT: D4 9 MET cc_start: 0.7258 (ttt) cc_final: 0.6703 (tmm) REVERT: D4 23 ILE cc_start: 0.7659 (pp) cc_final: 0.7333 (pt) REVERT: D4 119 TYR cc_start: 0.8946 (t80) cc_final: 0.8375 (t80) REVERT: D4 152 TYR cc_start: 0.8565 (m-80) cc_final: 0.8128 (m-80) REVERT: D4 158 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8906 (tp) REVERT: D4 221 VAL cc_start: 0.9089 (m) cc_final: 0.8812 (p) REVERT: D4 241 TYR cc_start: 0.8720 (t80) cc_final: 0.8463 (t80) REVERT: D4 257 MET cc_start: 0.7386 (mmm) cc_final: 0.6803 (mmm) REVERT: D4 263 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7543 (mmt) REVERT: D4 294 MET cc_start: 0.8818 (mmp) cc_final: 0.8589 (mmm) REVERT: D4 331 ASN cc_start: 0.9189 (t0) cc_final: 0.8971 (t0) REVERT: D2 14 MET cc_start: 0.7339 (tmm) cc_final: 0.6288 (tmm) REVERT: D2 15 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7863 (mp) REVERT: D2 18 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8236 (mt) REVERT: D2 36 ASN cc_start: 0.8696 (t0) cc_final: 0.8116 (t0) REVERT: D2 91 ASN cc_start: 0.8434 (t0) cc_final: 0.7899 (t0) REVERT: D2 100 MET cc_start: 0.8793 (mtt) cc_final: 0.8544 (mtp) REVERT: D2 105 LYS cc_start: 0.9037 (tptp) cc_final: 0.8558 (mmmt) REVERT: D2 129 ILE cc_start: 0.9031 (tt) cc_final: 0.8730 (mt) REVERT: D2 130 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7667 (pp) REVERT: D2 217 THR cc_start: 0.9213 (m) cc_final: 0.8916 (p) REVERT: D2 313 MET cc_start: 0.8126 (tmt) cc_final: 0.7694 (tmm) REVERT: AK 11 ILE cc_start: 0.9099 (mm) cc_final: 0.8791 (mp) REVERT: AK 117 MET cc_start: 0.7813 (mmt) cc_final: 0.7233 (mmp) REVERT: B5 93 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8840 (mt) REVERT: B5 114 MET cc_start: 0.8977 (ttm) cc_final: 0.8760 (ttm) REVERT: AB 54 MET cc_start: 0.8945 (mmp) cc_final: 0.8704 (mmp) REVERT: AB 83 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8500 (ttmm) REVERT: A8 76 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.6832 (t-90) REVERT: BJ 48 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8461 (tpt-90) REVERT: BJ 60 TYR cc_start: 0.6521 (m-80) cc_final: 0.6105 (t80) REVERT: BJ 162 MET cc_start: 0.7932 (mtt) cc_final: 0.7633 (mtt) REVERT: AJ 18 MET cc_start: 0.7990 (mmm) cc_final: 0.7603 (mmm) REVERT: AJ 267 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8413 (mp) REVERT: AJ 271 ASN cc_start: 0.8102 (m110) cc_final: 0.7656 (m110) REVERT: AJ 308 TYR cc_start: 0.8040 (m-80) cc_final: 0.7630 (m-80) REVERT: AJ 315 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6449 (ttmm) REVERT: S5 16 TRP cc_start: 0.8572 (p-90) cc_final: 0.7772 (p-90) REVERT: A3 45 ASN cc_start: 0.8857 (t0) cc_final: 0.8482 (t0) REVERT: C2 11 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6981 (pp) REVERT: C2 80 ASP cc_start: 0.8339 (t0) cc_final: 0.8072 (t0) REVERT: B4 40 SER cc_start: 0.9476 (p) cc_final: 0.9128 (t) REVERT: B4 43 LYS cc_start: 0.9067 (mtpm) cc_final: 0.8582 (ttmm) REVERT: B4 45 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B4 47 GLN cc_start: 0.8565 (mt0) cc_final: 0.8130 (mt0) REVERT: B4 74 ASN cc_start: 0.7896 (t0) cc_final: 0.7451 (t0) REVERT: B4 116 GLN cc_start: 0.8708 (tp40) cc_final: 0.8418 (tp-100) REVERT: B4 124 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.6569 (p90) REVERT: B4 128 TYR cc_start: 0.7822 (p90) cc_final: 0.7565 (p90) REVERT: AM 85 MET cc_start: 0.7982 (mmt) cc_final: 0.7774 (mmt) REVERT: AM 93 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8150 (mt-10) REVERT: AM 137 TYR cc_start: 0.8259 (m-10) cc_final: 0.7896 (m-10) REVERT: B6 31 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.5617 (pp20) REVERT: B6 96 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8034 (pt) REVERT: B6 107 ASP cc_start: 0.7833 (m-30) cc_final: 0.7477 (m-30) REVERT: B6 114 GLU cc_start: 0.7637 (pm20) cc_final: 0.7145 (pm20) REVERT: B7 8 TYR cc_start: 0.7315 (m-80) cc_final: 0.7030 (m-80) REVERT: B7 49 GLN cc_start: 0.8247 (tp-100) cc_final: 0.7628 (tp40) REVERT: B7 56 ASP cc_start: 0.8899 (p0) cc_final: 0.8523 (p0) REVERT: B9 67 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8197 (mm-30) REVERT: B9 133 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7838 (tm-30) REVERT: B2 26 GLU cc_start: 0.8354 (tp30) cc_final: 0.7905 (tp30) REVERT: B8 52 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.7999 (t70) REVERT: B8 58 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7531 (mpp80) REVERT: B8 80 ASP cc_start: 0.8906 (m-30) cc_final: 0.8430 (m-30) REVERT: B8 103 LYS cc_start: 0.8079 (mttt) cc_final: 0.7839 (tttp) REVERT: B8 117 TRP cc_start: 0.8455 (t60) cc_final: 0.7998 (t60) REVERT: B8 122 TYR cc_start: 0.8238 (m-10) cc_final: 0.7839 (m-10) REVERT: B8 137 ASN cc_start: 0.9003 (t0) cc_final: 0.8753 (t0) REVERT: BK 39 GLU cc_start: 0.8721 (mp0) cc_final: 0.7873 (mp0) REVERT: BK 92 GLU cc_start: 0.8242 (tp30) cc_final: 0.7856 (tp30) REVERT: C1 5 GLN cc_start: 0.7526 (pp30) cc_final: 0.7014 (pp30) REVERT: C1 9 HIS cc_start: 0.6770 (p90) cc_final: 0.6227 (p-80) REVERT: C1 37 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7539 (tm-30) REVERT: B1 8 ARG cc_start: 0.5920 (mmp-170) cc_final: 0.4854 (ptp-170) REVERT: A1 4 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7058 (tt0) REVERT: A1 12 MET cc_start: 0.7777 (tmm) cc_final: 0.7526 (tmm) REVERT: A1 16 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8268 (mm) REVERT: A1 28 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7493 (ttp80) REVERT: A1 34 ARG cc_start: 0.8344 (mpt180) cc_final: 0.8087 (mmt90) outliers start: 244 outliers final: 165 residues processed: 1288 average time/residue: 0.2186 time to fit residues: 475.6402 Evaluate side-chains 1274 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 1083 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 1 MET Chi-restraints excluded: chain D3 residue 7 LEU Chi-restraints excluded: chain D3 residue 88 LEU Chi-restraints excluded: chain D3 residue 101 SER Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 23 VAL Chi-restraints excluded: chain D1 residue 81 LEU Chi-restraints excluded: chain D1 residue 97 ASN Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 103 LEU Chi-restraints excluded: chain D1 residue 129 LEU Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 235 ASN Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D6 residue 11 ILE Chi-restraints excluded: chain D6 residue 17 PHE Chi-restraints excluded: chain D6 residue 20 PHE Chi-restraints excluded: chain D6 residue 25 SER Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 56 VAL Chi-restraints excluded: chain D6 residue 76 THR Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 102 LEU Chi-restraints excluded: chain D6 residue 106 TYR Chi-restraints excluded: chain D6 residue 132 ASP Chi-restraints excluded: chain 4L residue 39 SER Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain 4L residue 48 ILE Chi-restraints excluded: chain 4L residue 69 CYS Chi-restraints excluded: chain 4L residue 76 SER Chi-restraints excluded: chain 4L residue 79 VAL Chi-restraints excluded: chain D5 residue 7 LEU Chi-restraints excluded: chain D5 residue 9 LEU Chi-restraints excluded: chain D5 residue 12 LEU Chi-restraints excluded: chain D5 residue 61 MET Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 69 LEU Chi-restraints excluded: chain D5 residue 78 LEU Chi-restraints excluded: chain D5 residue 94 LEU Chi-restraints excluded: chain D5 residue 100 ILE Chi-restraints excluded: chain D5 residue 125 LEU Chi-restraints excluded: chain D5 residue 137 LEU Chi-restraints excluded: chain D5 residue 142 ILE Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 233 LEU Chi-restraints excluded: chain D5 residue 235 SER Chi-restraints excluded: chain D5 residue 246 LEU Chi-restraints excluded: chain D5 residue 254 VAL Chi-restraints excluded: chain D5 residue 276 ILE Chi-restraints excluded: chain D5 residue 312 LEU Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 381 THR Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 500 LEU Chi-restraints excluded: chain D5 residue 536 LEU Chi-restraints excluded: chain D5 residue 590 SER Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 6 ILE Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 78 MET Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 158 LEU Chi-restraints excluded: chain D4 residue 191 SER Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 323 SER Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D4 residue 410 MET Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 15 LEU Chi-restraints excluded: chain D2 residue 18 ILE Chi-restraints excluded: chain D2 residue 44 MET Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 130 LEU Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 205 LEU Chi-restraints excluded: chain D2 residue 241 THR Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 248 LEU Chi-restraints excluded: chain D2 residue 261 MET Chi-restraints excluded: chain D2 residue 281 LEU Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 289 ASN Chi-restraints excluded: chain D2 residue 294 MET Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain D2 residue 343 LEU Chi-restraints excluded: chain AK residue 4 LEU Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain AB residue 11 ILE Chi-restraints excluded: chain AB residue 19 LEU Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 51 ILE Chi-restraints excluded: chain AB residue 86 VAL Chi-restraints excluded: chain A8 residue 15 GLN Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 65 CYS Chi-restraints excluded: chain A8 residue 76 HIS Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 144 ARG Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 16 THR Chi-restraints excluded: chain BJ residue 23 THR Chi-restraints excluded: chain BJ residue 48 ARG Chi-restraints excluded: chain BJ residue 51 ILE Chi-restraints excluded: chain BJ residue 70 VAL Chi-restraints excluded: chain BJ residue 81 VAL Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain BJ residue 150 SER Chi-restraints excluded: chain BJ residue 163 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 106 LEU Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 144 ILE Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 209 THR Chi-restraints excluded: chain AJ residue 259 LEU Chi-restraints excluded: chain AJ residue 267 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 14 ASP Chi-restraints excluded: chain S5 residue 36 GLU Chi-restraints excluded: chain A3 residue 35 SER Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 65 ILE Chi-restraints excluded: chain C2 residue 68 PHE Chi-restraints excluded: chain C2 residue 69 VAL Chi-restraints excluded: chain C2 residue 119 VAL Chi-restraints excluded: chain B4 residue 64 LEU Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain B4 residue 87 LEU Chi-restraints excluded: chain B4 residue 94 ILE Chi-restraints excluded: chain B4 residue 124 PHE Chi-restraints excluded: chain AM residue 32 TYR Chi-restraints excluded: chain AM residue 65 GLU Chi-restraints excluded: chain AM residue 68 ILE Chi-restraints excluded: chain AM residue 86 LEU Chi-restraints excluded: chain AM residue 109 VAL Chi-restraints excluded: chain AM residue 126 LEU Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 34 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 96 ILE Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B9 residue 50 HIS Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 39 ASP Chi-restraints excluded: chain B8 residue 52 ASP Chi-restraints excluded: chain B8 residue 53 ARG Chi-restraints excluded: chain B8 residue 58 ARG Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 71 LEU Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 131 LYS Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 27 GLN Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 71 VAL Chi-restraints excluded: chain BK residue 77 VAL Chi-restraints excluded: chain C1 residue 39 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 16 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 178 optimal weight: 0.6980 chunk 401 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 325 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 chunk 327 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 389 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D3 80 GLN D3 108 GLN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 235 ASN D5 270 ASN ** D4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 192 ASN D4 421 HIS ** D2 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 222 ASN D2 289 ASN ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 13 GLN B2 58 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.106976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.095986 restraints weight = 86820.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.098609 restraints weight = 44238.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100336 restraints weight = 26616.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.101534 restraints weight = 17902.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.102323 restraints weight = 12983.729| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39038 Z= 0.166 Angle : 0.823 12.417 52918 Z= 0.404 Chirality : 0.046 0.253 5820 Planarity : 0.005 0.063 6543 Dihedral : 8.380 82.719 5349 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.02 % Favored : 89.94 % Rotamer: Outliers : 5.84 % Allowed : 24.19 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 0.72 % Twisted General : 0.14 % 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: -0.49 (0.13), residues: 4561 helix: 1.24 (0.10), residues: 2867 sheet: -2.18 (0.99), residues: 22 loop : -3.30 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGBK 25 TYR 0.035 0.002 TYRD6 60 PHE 0.027 0.002 PHEB6 69 TRP 0.038 0.001 TRPAM 103 HIS 0.014 0.001 HISD5 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (39024) covalent geometry : angle 0.82258 / 0.40 (52894) SS BOND : bond 0.00478 / 0.21 ( 12) SS BOND : angle 1.92907 / 1.39 ( 24) hydrogen bonds : bond 0.04597 / 2.98 ( 2139) hydrogen bonds : angle 4.46551 / 3.12 ( 6366) Misc. bond : bond 0.00381 / 0.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1382 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 1143 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 34 ASN cc_start: 0.8447 (p0) cc_final: 0.8073 (p0) REVERT: D3 11 PHE cc_start: 0.8606 (t80) cc_final: 0.8098 (t80) REVERT: D1 23 VAL cc_start: 0.8443 (t) cc_final: 0.8186 (p) REVERT: D1 25 ARG cc_start: 0.8886 (ttm110) cc_final: 0.8261 (ttm-80) REVERT: D1 26 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8682 (mtpp) REVERT: D1 30 TYR cc_start: 0.7118 (m-80) cc_final: 0.6708 (m-80) REVERT: D1 70 MET cc_start: 0.8662 (tpp) cc_final: 0.8338 (tpp) REVERT: D1 81 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8322 (mp) REVERT: D1 100 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7988 (pt) REVERT: D1 192 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7722 (tm-30) REVERT: D1 233 MET cc_start: 0.8392 (tmm) cc_final: 0.7683 (tmm) REVERT: D1 234 MET cc_start: 0.8918 (mmt) cc_final: 0.8580 (mpp) REVERT: D1 239 THR cc_start: 0.8977 (m) cc_final: 0.8767 (p) REVERT: D1 266 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8451 (tt) REVERT: D1 271 LEU cc_start: 0.8204 (tm) cc_final: 0.7890 (tm) REVERT: D1 272 TRP cc_start: 0.7265 (t60) cc_final: 0.6482 (t-100) REVERT: D1 284 GLN cc_start: 0.6924 (mt0) cc_final: 0.6495 (pt0) REVERT: D6 17 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7771 (t80) REVERT: D6 98 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8658 (tm) REVERT: D6 100 GLU cc_start: 0.6884 (tp30) cc_final: 0.6622 (tp30) REVERT: D6 136 PHE cc_start: 0.8415 (p90) cc_final: 0.7925 (p90) REVERT: 4L 1 MET cc_start: 0.7400 (ttm) cc_final: 0.6240 (tmm) REVERT: 4L 36 MET cc_start: 0.8682 (ttm) cc_final: 0.8475 (ttm) REVERT: 4L 88 ASP cc_start: 0.8493 (p0) cc_final: 0.8059 (p0) REVERT: D5 53 MET cc_start: 0.7667 (tpt) cc_final: 0.7466 (tpt) REVERT: D5 60 GLU cc_start: 0.5694 (mt-10) cc_final: 0.4636 (mt-10) REVERT: D5 86 SER cc_start: 0.9021 (m) cc_final: 0.8717 (t) REVERT: D5 94 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9182 (mm) REVERT: D5 150 MET cc_start: 0.8302 (mmp) cc_final: 0.7707 (tpp) REVERT: D5 154 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8839 (mm) REVERT: D5 161 ARG cc_start: 0.8007 (tpt-90) cc_final: 0.7642 (tpt170) REVERT: D5 355 ASP cc_start: 0.8854 (t0) cc_final: 0.8653 (t0) REVERT: D5 393 ASP cc_start: 0.8542 (m-30) cc_final: 0.8152 (m-30) REVERT: D5 397 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7734 (mt-10) REVERT: D5 487 LYS cc_start: 0.7821 (ttmp) cc_final: 0.7176 (ttmt) REVERT: D5 511 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6716 (pp) REVERT: D5 544 MET cc_start: 0.7166 (ttt) cc_final: 0.6749 (ttt) REVERT: D4 1 MET cc_start: 0.7563 (tpp) cc_final: 0.7301 (tpp) REVERT: D4 9 MET cc_start: 0.7263 (ttt) cc_final: 0.6768 (tmm) REVERT: D4 23 ILE cc_start: 0.7684 (pp) cc_final: 0.7439 (pt) REVERT: D4 108 MET cc_start: 0.8267 (ttm) cc_final: 0.7922 (ttm) REVERT: D4 119 TYR cc_start: 0.8958 (t80) cc_final: 0.8476 (t80) REVERT: D4 152 TYR cc_start: 0.8474 (m-80) cc_final: 0.7950 (m-80) REVERT: D4 221 VAL cc_start: 0.9112 (m) cc_final: 0.8844 (p) REVERT: D4 257 MET cc_start: 0.7248 (mmm) cc_final: 0.6704 (mmm) REVERT: D4 263 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7508 (mmt) REVERT: D4 325 MET cc_start: 0.7713 (ttp) cc_final: 0.7173 (ttp) REVERT: D2 14 MET cc_start: 0.7331 (tmm) cc_final: 0.6927 (tmm) REVERT: D2 36 ASN cc_start: 0.8763 (t0) cc_final: 0.8323 (t0) REVERT: D2 86 VAL cc_start: 0.9501 (t) cc_final: 0.9284 (m) REVERT: D2 91 ASN cc_start: 0.8467 (t0) cc_final: 0.7904 (t0) REVERT: D2 100 MET cc_start: 0.8772 (mtt) cc_final: 0.8541 (mtp) REVERT: D2 104 MET cc_start: 0.8755 (mtt) cc_final: 0.8462 (mtt) REVERT: D2 105 LYS cc_start: 0.8958 (tptp) cc_final: 0.8495 (mmmt) REVERT: D2 129 ILE cc_start: 0.9031 (tt) cc_final: 0.8727 (mt) REVERT: D2 130 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7662 (pp) REVERT: D2 217 THR cc_start: 0.9214 (m) cc_final: 0.8905 (p) REVERT: D2 268 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8952 (tm-30) REVERT: D2 313 MET cc_start: 0.8276 (tmt) cc_final: 0.7867 (tmm) REVERT: AK 8 TYR cc_start: 0.9158 (t80) cc_final: 0.8876 (t80) REVERT: AK 11 ILE cc_start: 0.9018 (mm) cc_final: 0.8729 (mp) REVERT: AK 117 MET cc_start: 0.7770 (mmt) cc_final: 0.7071 (mpp) REVERT: B5 93 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8844 (mt) REVERT: B5 114 MET cc_start: 0.8975 (ttm) cc_final: 0.8759 (ttm) REVERT: AB 54 MET cc_start: 0.8959 (mmp) cc_final: 0.8648 (mmp) REVERT: AB 64 ASP cc_start: 0.8267 (m-30) cc_final: 0.7777 (t70) REVERT: AB 83 LYS cc_start: 0.8890 (ttmm) cc_final: 0.8524 (ttmm) REVERT: A8 76 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.6931 (t-90) REVERT: A8 95 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8427 (mt) REVERT: BJ 16 THR cc_start: 0.9036 (m) cc_final: 0.8543 (p) REVERT: BJ 48 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8485 (tpt-90) REVERT: BJ 60 TYR cc_start: 0.6333 (m-80) cc_final: 0.5834 (t80) REVERT: BJ 162 MET cc_start: 0.7921 (mtt) cc_final: 0.7605 (mtt) REVERT: AJ 18 MET cc_start: 0.8003 (mmm) cc_final: 0.7577 (mmm) REVERT: AJ 267 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8433 (mp) REVERT: AJ 271 ASN cc_start: 0.8124 (m110) cc_final: 0.7646 (m110) REVERT: AJ 308 TYR cc_start: 0.8053 (m-80) cc_final: 0.7687 (m-80) REVERT: AJ 315 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6441 (ttmm) REVERT: S5 69 GLN cc_start: 0.8001 (mm110) cc_final: 0.7688 (mt0) REVERT: S5 91 TYR cc_start: 0.6437 (OUTLIER) cc_final: 0.5836 (p90) REVERT: A3 45 ASN cc_start: 0.8973 (t0) cc_final: 0.8649 (t0) REVERT: C2 11 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6935 (pp) REVERT: C2 80 ASP cc_start: 0.8361 (t0) cc_final: 0.8115 (t0) REVERT: B4 27 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B4 40 SER cc_start: 0.9497 (p) cc_final: 0.9192 (t) REVERT: B4 43 LYS cc_start: 0.9059 (mtpm) cc_final: 0.8548 (ttmm) REVERT: B4 45 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8040 (tm-30) REVERT: B4 47 GLN cc_start: 0.8564 (mt0) cc_final: 0.8133 (mt0) REVERT: B4 74 ASN cc_start: 0.7915 (t0) cc_final: 0.7462 (t0) REVERT: B4 116 GLN cc_start: 0.8713 (tp40) cc_final: 0.8454 (tp-100) REVERT: B4 124 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.6292 (p90) REVERT: AM 49 MET cc_start: 0.7648 (tmm) cc_final: 0.7432 (tmm) REVERT: AM 50 MET cc_start: 0.8471 (tmm) cc_final: 0.8123 (tmm) REVERT: B6 3 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.6153 (m-10) REVERT: B6 14 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9018 (tp) REVERT: B6 31 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.5557 (pp20) REVERT: B6 107 ASP cc_start: 0.7799 (m-30) cc_final: 0.7457 (m-30) REVERT: B6 114 GLU cc_start: 0.7667 (pm20) cc_final: 0.7125 (pm20) REVERT: B7 8 TYR cc_start: 0.7252 (m-80) cc_final: 0.6965 (m-80) REVERT: B7 17 GLU cc_start: 0.7261 (pm20) cc_final: 0.6761 (pp20) REVERT: B7 49 GLN cc_start: 0.8169 (tp-100) cc_final: 0.7427 (tp-100) REVERT: B7 56 ASP cc_start: 0.8891 (p0) cc_final: 0.8490 (p0) REVERT: B7 65 PHE cc_start: 0.8375 (t80) cc_final: 0.7912 (t80) REVERT: B9 93 TYR cc_start: 0.8138 (m-80) cc_final: 0.7901 (m-80) REVERT: B2 26 GLU cc_start: 0.8332 (tp30) cc_final: 0.7916 (tp30) REVERT: B2 28 PHE cc_start: 0.8120 (t80) cc_final: 0.7910 (t80) REVERT: B8 52 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.7991 (t70) REVERT: B8 58 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7446 (mpp80) REVERT: B8 80 ASP cc_start: 0.8975 (m-30) cc_final: 0.8697 (m-30) REVERT: B8 103 LYS cc_start: 0.8098 (mttt) cc_final: 0.7847 (tttp) REVERT: B8 122 TYR cc_start: 0.8274 (m-10) cc_final: 0.7877 (m-10) REVERT: BK 39 GLU cc_start: 0.8526 (mp0) cc_final: 0.8228 (mp0) REVERT: BK 92 GLU cc_start: 0.8367 (tp30) cc_final: 0.8147 (tp30) REVERT: C1 5 GLN cc_start: 0.7513 (pp30) cc_final: 0.6988 (pp30) REVERT: C1 9 HIS cc_start: 0.6845 (p90) cc_final: 0.6392 (p-80) REVERT: C1 37 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7593 (tm-30) REVERT: B1 8 ARG cc_start: 0.5890 (mmp-170) cc_final: 0.4831 (ptp-170) REVERT: A1 4 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7097 (tt0) REVERT: A1 16 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8247 (mm) REVERT: A1 28 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7521 (ttp80) REVERT: A1 34 ARG cc_start: 0.8432 (mpt180) cc_final: 0.8161 (mmt90) outliers start: 239 outliers final: 165 residues processed: 1276 average time/residue: 0.2206 time to fit residues: 474.7812 Evaluate side-chains 1279 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 1089 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 1 MET Chi-restraints excluded: chain D3 residue 7 LEU Chi-restraints excluded: chain D3 residue 88 LEU Chi-restraints excluded: chain D3 residue 101 SER Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 81 LEU Chi-restraints excluded: chain D1 residue 97 ASN Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 113 VAL Chi-restraints excluded: chain D1 residue 129 LEU Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 235 ASN Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D6 residue 17 PHE Chi-restraints excluded: chain D6 residue 20 PHE Chi-restraints excluded: chain D6 residue 25 SER Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 56 VAL Chi-restraints excluded: chain D6 residue 76 THR Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 102 LEU Chi-restraints excluded: chain D6 residue 106 TYR Chi-restraints excluded: chain D6 residue 125 TRP Chi-restraints excluded: chain D6 residue 132 ASP Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain 4L residue 69 CYS Chi-restraints excluded: chain 4L residue 75 LEU Chi-restraints excluded: chain 4L residue 76 SER Chi-restraints excluded: chain 4L residue 77 LEU Chi-restraints excluded: chain 4L residue 79 VAL Chi-restraints excluded: chain D5 residue 7 LEU Chi-restraints excluded: chain D5 residue 9 LEU Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 69 LEU Chi-restraints excluded: chain D5 residue 78 LEU Chi-restraints excluded: chain D5 residue 94 LEU Chi-restraints excluded: chain D5 residue 100 ILE Chi-restraints excluded: chain D5 residue 125 LEU Chi-restraints excluded: chain D5 residue 137 LEU Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 217 ILE Chi-restraints excluded: chain D5 residue 233 LEU Chi-restraints excluded: chain D5 residue 254 VAL Chi-restraints excluded: chain D5 residue 276 ILE Chi-restraints excluded: chain D5 residue 312 LEU Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 380 LEU Chi-restraints excluded: chain D5 residue 381 THR Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 404 THR Chi-restraints excluded: chain D5 residue 441 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 500 LEU Chi-restraints excluded: chain D5 residue 508 THR Chi-restraints excluded: chain D5 residue 511 LEU Chi-restraints excluded: chain D5 residue 536 LEU Chi-restraints excluded: chain D5 residue 590 SER Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 6 ILE Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 78 MET Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 191 SER Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D4 residue 410 MET Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 18 ILE Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 130 LEU Chi-restraints excluded: chain D2 residue 145 ILE Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 205 LEU Chi-restraints excluded: chain D2 residue 241 THR Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 248 LEU Chi-restraints excluded: chain D2 residue 266 ILE Chi-restraints excluded: chain D2 residue 281 LEU Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 289 ASN Chi-restraints excluded: chain D2 residue 294 MET Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain D2 residue 343 LEU Chi-restraints excluded: chain AK residue 4 LEU Chi-restraints excluded: chain AK residue 42 LEU Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 51 ILE Chi-restraints excluded: chain AB residue 86 VAL Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 36 ASP Chi-restraints excluded: chain A8 residue 65 CYS Chi-restraints excluded: chain A8 residue 76 HIS Chi-restraints excluded: chain A8 residue 95 LEU Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 144 ARG Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 23 THR Chi-restraints excluded: chain BJ residue 48 ARG Chi-restraints excluded: chain BJ residue 51 ILE Chi-restraints excluded: chain BJ residue 81 VAL Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain BJ residue 150 SER Chi-restraints excluded: chain BJ residue 163 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 77 CYS Chi-restraints excluded: chain AJ residue 106 LEU Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 144 ILE Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 209 THR Chi-restraints excluded: chain AJ residue 259 LEU Chi-restraints excluded: chain AJ residue 267 LEU Chi-restraints excluded: chain AJ residue 279 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 14 ASP Chi-restraints excluded: chain S5 residue 36 GLU Chi-restraints excluded: chain S5 residue 91 TYR Chi-restraints excluded: chain S5 residue 92 THR Chi-restraints excluded: chain A3 residue 35 SER Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 43 LEU Chi-restraints excluded: chain C2 residue 65 ILE Chi-restraints excluded: chain C2 residue 68 PHE Chi-restraints excluded: chain C2 residue 69 VAL Chi-restraints excluded: chain C2 residue 76 LEU Chi-restraints excluded: chain C2 residue 119 VAL Chi-restraints excluded: chain B4 residue 64 LEU Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain B4 residue 87 LEU Chi-restraints excluded: chain B4 residue 124 PHE Chi-restraints excluded: chain AM residue 32 TYR Chi-restraints excluded: chain AM residue 65 GLU Chi-restraints excluded: chain AM residue 68 ILE Chi-restraints excluded: chain AM residue 86 LEU Chi-restraints excluded: chain AM residue 95 THR Chi-restraints excluded: chain AM residue 126 LEU Chi-restraints excluded: chain B6 residue 3 TYR Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 34 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 110 LEU Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B7 residue 30 PHE Chi-restraints excluded: chain B9 residue 50 HIS Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 39 ASP Chi-restraints excluded: chain B8 residue 52 ASP Chi-restraints excluded: chain B8 residue 53 ARG Chi-restraints excluded: chain B8 residue 58 ARG Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 71 LEU Chi-restraints excluded: chain B8 residue 109 VAL Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 131 LYS Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 71 VAL Chi-restraints excluded: chain C1 residue 39 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 16 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 96 optimal weight: 0.3980 chunk 296 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 393 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 82 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D3 108 GLN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 235 ASN D1 317 GLN 4L 83 ASN ** D4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 374 ASN ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 289 ASN ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 49 GLN ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 13 GLN BK 103 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.107771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096637 restraints weight = 86786.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.099277 restraints weight = 44219.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.101008 restraints weight = 26659.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102244 restraints weight = 17987.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103034 restraints weight = 13008.616| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39038 Z= 0.156 Angle : 0.821 13.742 52918 Z= 0.400 Chirality : 0.045 0.229 5820 Planarity : 0.005 0.061 6543 Dihedral : 8.190 82.259 5349 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.60 % Favored : 90.35 % Rotamer: Outliers : 5.59 % Allowed : 25.14 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 1.08 % Twisted General : 0.14 % 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: -0.42 (0.13), residues: 4561 helix: 1.28 (0.10), residues: 2866 sheet: -2.06 (1.03), residues: 22 loop : -3.22 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGBK 25 TYR 0.032 0.001 TYRD1 250 PHE 0.026 0.002 PHEB2 34 TRP 0.040 0.001 TRPAM 103 HIS 0.013 0.001 HISD5 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (39024) covalent geometry : angle 0.82075 / 0.40 (52894) SS BOND : bond 0.00398 / 0.19 ( 12) SS BOND : angle 1.41322 / 0.97 ( 24) hydrogen bonds : bond 0.04468 / 2.89 ( 2139) hydrogen bonds : angle 4.42410 / 3.09 ( 6366) Misc. bond : bond 0.00331 / 0.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1377 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 1148 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 29 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8300 (tmtt) REVERT: S2 34 ASN cc_start: 0.8456 (p0) cc_final: 0.8071 (p0) REVERT: D3 11 PHE cc_start: 0.8459 (t80) cc_final: 0.7851 (t80) REVERT: D1 23 VAL cc_start: 0.8425 (t) cc_final: 0.8199 (p) REVERT: D1 25 ARG cc_start: 0.8908 (ttm110) cc_final: 0.8399 (ttm-80) REVERT: D1 26 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8751 (mtpp) REVERT: D1 30 TYR cc_start: 0.7228 (m-80) cc_final: 0.6954 (m-80) REVERT: D1 70 MET cc_start: 0.8690 (tpp) cc_final: 0.8148 (tpp) REVERT: D1 81 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8112 (mp) REVERT: D1 85 MET cc_start: 0.8080 (mmm) cc_final: 0.7781 (mmm) REVERT: D1 100 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8074 (pt) REVERT: D1 192 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7590 (tm-30) REVERT: D1 195 ARG cc_start: 0.7296 (mtp180) cc_final: 0.7068 (mtm180) REVERT: D1 239 THR cc_start: 0.9032 (m) cc_final: 0.8770 (p) REVERT: D1 266 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8433 (tt) REVERT: D1 272 TRP cc_start: 0.7241 (t60) cc_final: 0.6459 (t-100) REVERT: D1 284 GLN cc_start: 0.6887 (mt0) cc_final: 0.6571 (pt0) REVERT: D6 2 MET cc_start: 0.5035 (tpp) cc_final: 0.4811 (mmt) REVERT: D6 17 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7751 (t80) REVERT: D6 98 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8626 (tm) REVERT: D6 122 MET cc_start: 0.5130 (OUTLIER) cc_final: 0.4845 (ptp) REVERT: D6 136 PHE cc_start: 0.8411 (p90) cc_final: 0.7973 (p90) REVERT: 4L 1 MET cc_start: 0.7597 (ttm) cc_final: 0.6807 (ttp) REVERT: 4L 47 MET cc_start: 0.7592 (tpp) cc_final: 0.7198 (tpp) REVERT: D5 86 SER cc_start: 0.9011 (m) cc_final: 0.8696 (t) REVERT: D5 94 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9161 (mm) REVERT: D5 149 ILE cc_start: 0.9317 (tp) cc_final: 0.8915 (tp) REVERT: D5 154 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8755 (mm) REVERT: D5 246 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8829 (tt) REVERT: D5 290 MET cc_start: 0.8091 (tpp) cc_final: 0.7878 (tpp) REVERT: D5 314 MET cc_start: 0.8487 (mmm) cc_final: 0.8166 (mtp) REVERT: D5 355 ASP cc_start: 0.8711 (t0) cc_final: 0.8155 (t0) REVERT: D5 393 ASP cc_start: 0.8455 (m-30) cc_final: 0.7911 (m-30) REVERT: D5 396 ILE cc_start: 0.8799 (pp) cc_final: 0.8555 (mt) REVERT: D5 397 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7612 (mt-10) REVERT: D5 480 MET cc_start: 0.7470 (tpt) cc_final: 0.7220 (tpt) REVERT: D5 487 LYS cc_start: 0.7767 (ttmp) cc_final: 0.7168 (ttmt) REVERT: D5 511 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6464 (pp) REVERT: D4 1 MET cc_start: 0.7481 (tpp) cc_final: 0.6935 (tpp) REVERT: D4 3 LYS cc_start: 0.8641 (pttp) cc_final: 0.8390 (pttp) REVERT: D4 9 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6769 (tmm) REVERT: D4 23 ILE cc_start: 0.7785 (pp) cc_final: 0.7476 (pt) REVERT: D4 108 MET cc_start: 0.8254 (ttm) cc_final: 0.7880 (ttm) REVERT: D4 119 TYR cc_start: 0.9024 (t80) cc_final: 0.8618 (t80) REVERT: D4 221 VAL cc_start: 0.9119 (m) cc_final: 0.8860 (p) REVERT: D4 257 MET cc_start: 0.7255 (mmm) cc_final: 0.6641 (mmm) REVERT: D4 259 TYR cc_start: 0.8387 (m-10) cc_final: 0.7859 (m-80) REVERT: D4 263 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7519 (mmt) REVERT: D2 14 MET cc_start: 0.7335 (tmm) cc_final: 0.6388 (tmm) REVERT: D2 18 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.7886 (mt) REVERT: D2 36 ASN cc_start: 0.8765 (t0) cc_final: 0.8301 (t0) REVERT: D2 91 ASN cc_start: 0.8428 (t0) cc_final: 0.7879 (t0) REVERT: D2 100 MET cc_start: 0.8742 (mtt) cc_final: 0.8464 (mtp) REVERT: D2 105 LYS cc_start: 0.8968 (tptp) cc_final: 0.8486 (mmmt) REVERT: D2 117 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8289 (mm-30) REVERT: D2 129 ILE cc_start: 0.9041 (tt) cc_final: 0.8716 (mt) REVERT: D2 130 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7665 (pp) REVERT: D2 217 THR cc_start: 0.9218 (m) cc_final: 0.8919 (p) REVERT: D2 266 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8907 (mt) REVERT: D2 270 MET cc_start: 0.8543 (ttm) cc_final: 0.8260 (ttp) REVERT: D2 313 MET cc_start: 0.8281 (tmt) cc_final: 0.7869 (tmm) REVERT: AK 8 TYR cc_start: 0.9275 (t80) cc_final: 0.8958 (t80) REVERT: AK 117 MET cc_start: 0.7662 (mmt) cc_final: 0.7124 (mmp) REVERT: B5 93 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8847 (mt) REVERT: B5 114 MET cc_start: 0.8960 (ttm) cc_final: 0.8729 (ttm) REVERT: AB 54 MET cc_start: 0.8847 (mmp) cc_final: 0.8580 (mmp) REVERT: AB 64 ASP cc_start: 0.8235 (m-30) cc_final: 0.7727 (t70) REVERT: AB 83 LYS cc_start: 0.8899 (ttmm) cc_final: 0.8511 (ttmm) REVERT: A8 76 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.6833 (t-90) REVERT: BJ 16 THR cc_start: 0.9025 (m) cc_final: 0.8581 (p) REVERT: BJ 48 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7813 (tpm-80) REVERT: BJ 52 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7452 (mm-30) REVERT: BJ 162 MET cc_start: 0.7894 (mtt) cc_final: 0.7537 (mtt) REVERT: AJ 18 MET cc_start: 0.7912 (mmm) cc_final: 0.7486 (mmm) REVERT: AJ 267 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8409 (mp) REVERT: AJ 271 ASN cc_start: 0.8220 (m110) cc_final: 0.7731 (m110) REVERT: AJ 315 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.6472 (ttmm) REVERT: S5 69 GLN cc_start: 0.7988 (mm110) cc_final: 0.7745 (mt0) REVERT: S5 91 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.6169 (p90) REVERT: A3 45 ASN cc_start: 0.9006 (t0) cc_final: 0.8678 (t0) REVERT: C2 11 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6879 (pp) REVERT: C2 80 ASP cc_start: 0.8362 (t0) cc_final: 0.8117 (t0) REVERT: B4 30 LYS cc_start: 0.8882 (ptmm) cc_final: 0.8570 (ptpp) REVERT: B4 40 SER cc_start: 0.9512 (p) cc_final: 0.9212 (t) REVERT: B4 43 LYS cc_start: 0.9091 (mtpm) cc_final: 0.8621 (ttmm) REVERT: B4 45 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8081 (tm-30) REVERT: B4 47 GLN cc_start: 0.8504 (mt0) cc_final: 0.8105 (mt0) REVERT: B4 74 ASN cc_start: 0.7548 (t0) cc_final: 0.7283 (t0) REVERT: B4 116 GLN cc_start: 0.8635 (tp40) cc_final: 0.8431 (tp-100) REVERT: B6 3 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.6074 (m-10) REVERT: B6 14 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9059 (tp) REVERT: B6 31 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.5492 (pp20) REVERT: B6 107 ASP cc_start: 0.7742 (m-30) cc_final: 0.7503 (m-30) REVERT: B6 114 GLU cc_start: 0.7686 (pm20) cc_final: 0.7265 (pm20) REVERT: B7 8 TYR cc_start: 0.7167 (m-80) cc_final: 0.6902 (m-80) REVERT: B7 17 GLU cc_start: 0.7277 (pm20) cc_final: 0.6773 (pp20) REVERT: B7 49 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7339 (tp-100) REVERT: B7 56 ASP cc_start: 0.8925 (p0) cc_final: 0.8541 (p0) REVERT: B7 65 PHE cc_start: 0.8344 (t80) cc_final: 0.7885 (t80) REVERT: B9 93 TYR cc_start: 0.8154 (m-80) cc_final: 0.7940 (m-80) REVERT: B9 96 TYR cc_start: 0.8206 (m-80) cc_final: 0.7896 (m-80) REVERT: B2 26 GLU cc_start: 0.8430 (tp30) cc_final: 0.8029 (tp30) REVERT: B8 52 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8095 (t70) REVERT: B8 58 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7389 (mpp80) REVERT: B8 80 ASP cc_start: 0.8903 (m-30) cc_final: 0.8408 (m-30) REVERT: B8 90 ASP cc_start: 0.7095 (p0) cc_final: 0.6759 (p0) REVERT: B8 103 LYS cc_start: 0.8100 (mttt) cc_final: 0.7812 (tttp) REVERT: B8 122 TYR cc_start: 0.8198 (m-10) cc_final: 0.7828 (m-10) REVERT: BK 39 GLU cc_start: 0.8577 (mp0) cc_final: 0.8125 (mp0) REVERT: BK 92 GLU cc_start: 0.8339 (tp30) cc_final: 0.7862 (tp30) REVERT: BK 94 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8300 (mt-10) REVERT: C1 5 GLN cc_start: 0.7505 (pp30) cc_final: 0.6965 (pp30) REVERT: C1 37 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7532 (tm-30) REVERT: B1 8 ARG cc_start: 0.5866 (mmp-170) cc_final: 0.4769 (ptp-170) REVERT: A1 16 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8164 (mm) REVERT: A1 28 ARG cc_start: 0.7837 (mtp180) cc_final: 0.7517 (ttp80) REVERT: A1 34 ARG cc_start: 0.8433 (mpt180) cc_final: 0.8158 (mmt90) outliers start: 229 outliers final: 157 residues processed: 1263 average time/residue: 0.2197 time to fit residues: 467.9290 Evaluate side-chains 1266 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 1081 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 1 MET Chi-restraints excluded: chain D3 residue 88 LEU Chi-restraints excluded: chain D3 residue 101 SER Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 81 LEU Chi-restraints excluded: chain D1 residue 97 ASN Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 103 LEU Chi-restraints excluded: chain D1 residue 129 LEU Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 235 ASN Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D6 residue 17 PHE Chi-restraints excluded: chain D6 residue 20 PHE Chi-restraints excluded: chain D6 residue 21 SER Chi-restraints excluded: chain D6 residue 25 SER Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 56 VAL Chi-restraints excluded: chain D6 residue 76 THR Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 102 LEU Chi-restraints excluded: chain D6 residue 106 TYR Chi-restraints excluded: chain D6 residue 122 MET Chi-restraints excluded: chain D6 residue 125 TRP Chi-restraints excluded: chain D6 residue 132 ASP Chi-restraints excluded: chain 4L residue 39 SER Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain 4L residue 48 ILE Chi-restraints excluded: chain 4L residue 69 CYS Chi-restraints excluded: chain 4L residue 77 LEU Chi-restraints excluded: chain 4L residue 79 VAL Chi-restraints excluded: chain D5 residue 7 LEU Chi-restraints excluded: chain D5 residue 9 LEU Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 69 LEU Chi-restraints excluded: chain D5 residue 78 LEU Chi-restraints excluded: chain D5 residue 94 LEU Chi-restraints excluded: chain D5 residue 100 ILE Chi-restraints excluded: chain D5 residue 125 LEU Chi-restraints excluded: chain D5 residue 137 LEU Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 217 ILE Chi-restraints excluded: chain D5 residue 246 LEU Chi-restraints excluded: chain D5 residue 254 VAL Chi-restraints excluded: chain D5 residue 276 ILE Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 380 LEU Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 404 THR Chi-restraints excluded: chain D5 residue 441 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 511 LEU Chi-restraints excluded: chain D5 residue 536 LEU Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 6 ILE Chi-restraints excluded: chain D4 residue 9 MET Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 183 VAL Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 256 PHE Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D4 residue 403 THR Chi-restraints excluded: chain D4 residue 410 MET Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 15 LEU Chi-restraints excluded: chain D2 residue 18 ILE Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 130 LEU Chi-restraints excluded: chain D2 residue 145 ILE Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 205 LEU Chi-restraints excluded: chain D2 residue 241 THR Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 248 LEU Chi-restraints excluded: chain D2 residue 258 SER Chi-restraints excluded: chain D2 residue 266 ILE Chi-restraints excluded: chain D2 residue 281 LEU Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 289 ASN Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 328 THR Chi-restraints excluded: chain D2 residue 332 LEU Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain D2 residue 343 LEU Chi-restraints excluded: chain AK residue 4 LEU Chi-restraints excluded: chain AK residue 42 LEU Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain B5 residue 110 VAL Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 51 ILE Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 36 ASP Chi-restraints excluded: chain A8 residue 65 CYS Chi-restraints excluded: chain A8 residue 76 HIS Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 144 ARG Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 48 ARG Chi-restraints excluded: chain BJ residue 51 ILE Chi-restraints excluded: chain BJ residue 81 VAL Chi-restraints excluded: chain BJ residue 83 CYS Chi-restraints excluded: chain BJ residue 98 ASP Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain BJ residue 150 SER Chi-restraints excluded: chain BJ residue 163 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 77 CYS Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 144 ILE Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 209 THR Chi-restraints excluded: chain AJ residue 259 LEU Chi-restraints excluded: chain AJ residue 267 LEU Chi-restraints excluded: chain AJ residue 279 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 5 VAL Chi-restraints excluded: chain S5 residue 91 TYR Chi-restraints excluded: chain S5 residue 92 THR Chi-restraints excluded: chain A3 residue 35 SER Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 48 ILE Chi-restraints excluded: chain C2 residue 65 ILE Chi-restraints excluded: chain C2 residue 68 PHE Chi-restraints excluded: chain C2 residue 69 VAL Chi-restraints excluded: chain C2 residue 119 VAL Chi-restraints excluded: chain B4 residue 64 LEU Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain B4 residue 87 LEU Chi-restraints excluded: chain AM residue 32 TYR Chi-restraints excluded: chain AM residue 68 ILE Chi-restraints excluded: chain AM residue 86 LEU Chi-restraints excluded: chain AM residue 95 THR Chi-restraints excluded: chain AM residue 126 LEU Chi-restraints excluded: chain B6 residue 3 TYR Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 34 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 110 LEU Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B7 residue 30 PHE Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 39 ASP Chi-restraints excluded: chain B8 residue 52 ASP Chi-restraints excluded: chain B8 residue 53 ARG Chi-restraints excluded: chain B8 residue 58 ARG Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 71 LEU Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 131 LYS Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 71 VAL Chi-restraints excluded: chain C1 residue 39 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 16 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 0 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 276 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 325 optimal weight: 0.4980 chunk 307 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D3 108 GLN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 317 GLN 4L 7 ASN 4L 83 ASN ** D5 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 270 ASN ** D4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 51 ASN ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 374 ASN ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 289 ASN A8 34 GLN ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 49 GLN ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 13 GLN B2 58 GLN B8 3 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.095774 restraints weight = 86837.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.098369 restraints weight = 44216.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100135 restraints weight = 26662.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101227 restraints weight = 17908.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.102051 restraints weight = 13307.369| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 39038 Z= 0.166 Angle : 0.855 15.212 52918 Z= 0.416 Chirality : 0.046 0.344 5820 Planarity : 0.005 0.061 6543 Dihedral : 8.194 101.111 5349 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.78 % Favored : 90.18 % Rotamer: Outliers : 5.45 % Allowed : 26.02 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 0.72 % Twisted General : 0.12 % 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: -0.42 (0.13), residues: 4561 helix: 1.28 (0.10), residues: 2862 sheet: -1.78 (1.14), residues: 22 loop : -3.22 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARGB6 15 TYR 0.034 0.001 TYRD1 250 PHE 0.041 0.002 PHED5 591 TRP 0.040 0.002 TRPAM 141 HIS 0.036 0.001 HISB9 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (39024) covalent geometry : angle 0.85516 / 0.42 (52894) SS BOND : bond 0.00407 / 0.18 ( 12) SS BOND : angle 1.34207 / 0.90 ( 24) hydrogen bonds : bond 0.04551 / 2.94 ( 2139) hydrogen bonds : angle 4.43864 / 3.10 ( 6366) Misc. bond : bond 0.00671 / 0.32 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 1123 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 9 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7421 (mm-30) REVERT: S2 34 ASN cc_start: 0.8423 (p0) cc_final: 0.8047 (p0) REVERT: D3 11 PHE cc_start: 0.8457 (t80) cc_final: 0.8089 (t80) REVERT: D1 1 MET cc_start: 0.7837 (mmt) cc_final: 0.7379 (mmt) REVERT: D1 25 ARG cc_start: 0.8901 (ttm110) cc_final: 0.8416 (ttm-80) REVERT: D1 26 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8764 (mtpp) REVERT: D1 30 TYR cc_start: 0.7042 (m-80) cc_final: 0.6726 (m-80) REVERT: D1 81 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8149 (mp) REVERT: D1 85 MET cc_start: 0.8110 (mmm) cc_final: 0.7830 (mmm) REVERT: D1 100 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8017 (pt) REVERT: D1 156 MET cc_start: 0.8614 (mmt) cc_final: 0.8306 (mmt) REVERT: D1 192 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7633 (tm-30) REVERT: D1 195 ARG cc_start: 0.7249 (mtp180) cc_final: 0.6944 (mtm180) REVERT: D1 235 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8321 (t0) REVERT: D1 239 THR cc_start: 0.9119 (m) cc_final: 0.8854 (p) REVERT: D1 266 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8657 (tt) REVERT: D1 272 TRP cc_start: 0.7239 (t60) cc_final: 0.6225 (t60) REVERT: D1 284 GLN cc_start: 0.6930 (mt0) cc_final: 0.6594 (pt0) REVERT: D1 317 GLN cc_start: 0.8109 (tm130) cc_final: 0.7782 (tm-30) REVERT: D6 17 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7711 (t80) REVERT: D6 68 PHE cc_start: 0.8119 (m-80) cc_final: 0.7738 (m-80) REVERT: D6 98 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8675 (tm) REVERT: D6 114 GLU cc_start: 0.7780 (tt0) cc_final: 0.7383 (pm20) REVERT: D6 136 PHE cc_start: 0.8428 (p90) cc_final: 0.8025 (p90) REVERT: D6 162 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8371 (mm) REVERT: 4L 1 MET cc_start: 0.7721 (ttm) cc_final: 0.7314 (tmm) REVERT: 4L 47 MET cc_start: 0.7666 (tpp) cc_final: 0.7236 (tpp) REVERT: D5 86 SER cc_start: 0.9064 (m) cc_final: 0.8685 (t) REVERT: D5 94 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9158 (mm) REVERT: D5 149 ILE cc_start: 0.9343 (tp) cc_final: 0.8883 (tp) REVERT: D5 150 MET cc_start: 0.8259 (mmp) cc_final: 0.7717 (tpp) REVERT: D5 154 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8730 (mm) REVERT: D5 246 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8848 (tt) REVERT: D5 314 MET cc_start: 0.8461 (mmm) cc_final: 0.8217 (mtp) REVERT: D5 393 ASP cc_start: 0.8342 (m-30) cc_final: 0.7838 (m-30) REVERT: D5 397 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7616 (mt-10) REVERT: D5 480 MET cc_start: 0.7527 (tpt) cc_final: 0.7131 (tpt) REVERT: D5 487 LYS cc_start: 0.7725 (ttmp) cc_final: 0.7159 (ttmt) REVERT: D5 511 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6521 (pp) REVERT: D4 1 MET cc_start: 0.8036 (tpp) cc_final: 0.7645 (tpp) REVERT: D4 3 LYS cc_start: 0.8655 (pttp) cc_final: 0.8387 (pttp) REVERT: D4 9 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6583 (tmm) REVERT: D4 23 ILE cc_start: 0.7796 (pp) cc_final: 0.7569 (pt) REVERT: D4 108 MET cc_start: 0.8304 (ttm) cc_final: 0.7468 (ttm) REVERT: D4 119 TYR cc_start: 0.9033 (t80) cc_final: 0.8655 (t80) REVERT: D4 121 MET cc_start: 0.7725 (tpp) cc_final: 0.7076 (tpp) REVERT: D4 141 GLU cc_start: 0.7645 (pm20) cc_final: 0.7034 (pm20) REVERT: D4 169 ASN cc_start: 0.8108 (m-40) cc_final: 0.7481 (m-40) REVERT: D4 221 VAL cc_start: 0.9129 (m) cc_final: 0.8866 (p) REVERT: D4 257 MET cc_start: 0.7165 (mmm) cc_final: 0.6662 (mmm) REVERT: D4 259 TYR cc_start: 0.8421 (m-10) cc_final: 0.7866 (m-80) REVERT: D4 263 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7378 (mmt) REVERT: D4 359 TRP cc_start: 0.8893 (m100) cc_final: 0.7570 (m100) REVERT: D4 441 MET cc_start: 0.7678 (mmp) cc_final: 0.7457 (mmp) REVERT: D2 14 MET cc_start: 0.7304 (tmm) cc_final: 0.6795 (tmm) REVERT: D2 36 ASN cc_start: 0.8829 (t0) cc_final: 0.8359 (t0) REVERT: D2 91 ASN cc_start: 0.8463 (t0) cc_final: 0.7920 (t0) REVERT: D2 100 MET cc_start: 0.8814 (mtt) cc_final: 0.8594 (mtp) REVERT: D2 104 MET cc_start: 0.9046 (ttm) cc_final: 0.8733 (ttm) REVERT: D2 105 LYS cc_start: 0.8864 (tptp) cc_final: 0.8402 (mmmt) REVERT: D2 117 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8357 (mm-30) REVERT: D2 129 ILE cc_start: 0.9063 (tt) cc_final: 0.8724 (mt) REVERT: D2 130 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7677 (pp) REVERT: D2 215 MET cc_start: 0.8662 (tpp) cc_final: 0.8205 (tpp) REVERT: D2 217 THR cc_start: 0.9235 (m) cc_final: 0.8945 (p) REVERT: D2 266 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8882 (mt) REVERT: D2 313 MET cc_start: 0.8318 (tmt) cc_final: 0.7919 (tmm) REVERT: AK 8 TYR cc_start: 0.9207 (t80) cc_final: 0.8912 (t80) REVERT: AK 60 PHE cc_start: 0.8807 (t80) cc_final: 0.8337 (t80) REVERT: AK 117 MET cc_start: 0.7631 (mmt) cc_final: 0.7122 (mmp) REVERT: B5 93 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8942 (mt) REVERT: AB 28 GLU cc_start: 0.8595 (pm20) cc_final: 0.8177 (pm20) REVERT: AB 54 MET cc_start: 0.8859 (mmp) cc_final: 0.8613 (mmp) REVERT: AB 64 ASP cc_start: 0.8228 (m-30) cc_final: 0.7777 (t70) REVERT: AB 83 LYS cc_start: 0.8895 (ttmm) cc_final: 0.8510 (ttmm) REVERT: A8 76 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.6925 (t-90) REVERT: BJ 16 THR cc_start: 0.9015 (m) cc_final: 0.8535 (p) REVERT: BJ 48 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.7717 (tpm-80) REVERT: BJ 52 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7417 (mm-30) REVERT: BJ 162 MET cc_start: 0.7848 (mtt) cc_final: 0.7488 (mtt) REVERT: AJ 18 MET cc_start: 0.7940 (mmm) cc_final: 0.7469 (mmm) REVERT: AJ 267 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8370 (mp) REVERT: AJ 271 ASN cc_start: 0.8234 (m110) cc_final: 0.7751 (m110) REVERT: AJ 315 LYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6416 (ttmm) REVERT: S5 69 GLN cc_start: 0.7936 (mm110) cc_final: 0.7529 (mm-40) REVERT: S5 91 TYR cc_start: 0.6671 (OUTLIER) cc_final: 0.6105 (p90) REVERT: A3 45 ASN cc_start: 0.9017 (t0) cc_final: 0.8717 (t0) REVERT: C2 11 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6880 (pp) REVERT: C2 80 ASP cc_start: 0.8406 (t0) cc_final: 0.8187 (t0) REVERT: B4 27 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7176 (tm-30) REVERT: B4 30 LYS cc_start: 0.8869 (ptmm) cc_final: 0.8548 (ptpp) REVERT: B4 40 SER cc_start: 0.9552 (p) cc_final: 0.9215 (t) REVERT: B4 43 LYS cc_start: 0.9037 (mtpm) cc_final: 0.8470 (ttmm) REVERT: B4 45 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8086 (tm-30) REVERT: B4 47 GLN cc_start: 0.8491 (mt0) cc_final: 0.8117 (mt0) REVERT: B4 74 ASN cc_start: 0.7629 (t0) cc_final: 0.7408 (t0) REVERT: B4 101 TYR cc_start: 0.8832 (t80) cc_final: 0.8523 (t80) REVERT: B4 116 GLN cc_start: 0.8665 (tp40) cc_final: 0.8410 (tp-100) REVERT: B4 117 GLU cc_start: 0.7824 (tm-30) cc_final: 0.6598 (tm-30) REVERT: B4 119 LYS cc_start: 0.8688 (ptmm) cc_final: 0.8270 (ptpp) REVERT: B4 124 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.6310 (p90) REVERT: AM 70 LEU cc_start: 0.8721 (tp) cc_final: 0.8475 (tp) REVERT: AM 85 MET cc_start: 0.8005 (mmt) cc_final: 0.7614 (mmt) REVERT: AM 90 LEU cc_start: 0.8511 (mp) cc_final: 0.8122 (tt) REVERT: B6 3 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6278 (m-10) REVERT: B6 14 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9033 (tp) REVERT: B6 31 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.5582 (pp20) REVERT: B6 107 ASP cc_start: 0.7719 (m-30) cc_final: 0.7485 (m-30) REVERT: B6 114 GLU cc_start: 0.7781 (pm20) cc_final: 0.7351 (pm20) REVERT: B7 8 TYR cc_start: 0.7164 (m-80) cc_final: 0.6894 (m-80) REVERT: B7 15 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7065 (tp30) REVERT: B7 17 GLU cc_start: 0.7355 (pm20) cc_final: 0.6794 (pp20) REVERT: B7 49 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7328 (tp-100) REVERT: B7 56 ASP cc_start: 0.8942 (p0) cc_final: 0.8564 (p0) REVERT: B7 65 PHE cc_start: 0.8357 (t80) cc_final: 0.7919 (t80) REVERT: B7 102 GLU cc_start: 0.8302 (tp30) cc_final: 0.7945 (tp30) REVERT: B9 27 GLU cc_start: 0.8197 (tp30) cc_final: 0.7979 (mm-30) REVERT: B9 93 TYR cc_start: 0.8213 (m-80) cc_final: 0.8002 (m-80) REVERT: B9 96 TYR cc_start: 0.8249 (m-80) cc_final: 0.7956 (m-80) REVERT: B2 26 GLU cc_start: 0.8402 (tp30) cc_final: 0.8046 (tp30) REVERT: B8 52 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8107 (t70) REVERT: B8 90 ASP cc_start: 0.7094 (p0) cc_final: 0.6777 (p0) REVERT: B8 103 LYS cc_start: 0.8114 (mttt) cc_final: 0.7793 (tttp) REVERT: B8 122 TYR cc_start: 0.8217 (m-10) cc_final: 0.7876 (m-10) REVERT: BK 92 GLU cc_start: 0.8365 (tp30) cc_final: 0.7830 (tp30) REVERT: BK 94 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8307 (mt-10) REVERT: C1 5 GLN cc_start: 0.7492 (pp30) cc_final: 0.6952 (pp30) REVERT: C1 37 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7406 (tm-30) REVERT: B1 8 ARG cc_start: 0.5892 (mmp-170) cc_final: 0.4773 (ptp-170) REVERT: A1 16 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8147 (mm) REVERT: A1 28 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7534 (ttp80) REVERT: A1 34 ARG cc_start: 0.8491 (mpt180) cc_final: 0.8198 (mmt90) outliers start: 223 outliers final: 156 residues processed: 1236 average time/residue: 0.2177 time to fit residues: 453.7330 Evaluate side-chains 1262 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 1078 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 1 MET Chi-restraints excluded: chain D3 residue 7 LEU Chi-restraints excluded: chain D3 residue 88 LEU Chi-restraints excluded: chain D3 residue 101 SER Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 81 LEU Chi-restraints excluded: chain D1 residue 97 ASN Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 103 LEU Chi-restraints excluded: chain D1 residue 129 LEU Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 183 MET Chi-restraints excluded: chain D1 residue 235 ASN Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D6 residue 17 PHE Chi-restraints excluded: chain D6 residue 20 PHE Chi-restraints excluded: chain D6 residue 21 SER Chi-restraints excluded: chain D6 residue 25 SER Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 56 VAL Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 106 TYR Chi-restraints excluded: chain D6 residue 125 TRP Chi-restraints excluded: chain D6 residue 132 ASP Chi-restraints excluded: chain D6 residue 162 LEU Chi-restraints excluded: chain 4L residue 39 SER Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain 4L residue 69 CYS Chi-restraints excluded: chain 4L residue 75 LEU Chi-restraints excluded: chain 4L residue 76 SER Chi-restraints excluded: chain 4L residue 77 LEU Chi-restraints excluded: chain 4L residue 79 VAL Chi-restraints excluded: chain D5 residue 7 LEU Chi-restraints excluded: chain D5 residue 9 LEU Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 69 LEU Chi-restraints excluded: chain D5 residue 94 LEU Chi-restraints excluded: chain D5 residue 100 ILE Chi-restraints excluded: chain D5 residue 125 LEU Chi-restraints excluded: chain D5 residue 130 ILE Chi-restraints excluded: chain D5 residue 137 LEU Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 217 ILE Chi-restraints excluded: chain D5 residue 233 LEU Chi-restraints excluded: chain D5 residue 246 LEU Chi-restraints excluded: chain D5 residue 254 VAL Chi-restraints excluded: chain D5 residue 276 ILE Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 380 LEU Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 404 THR Chi-restraints excluded: chain D5 residue 441 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 500 LEU Chi-restraints excluded: chain D5 residue 508 THR Chi-restraints excluded: chain D5 residue 511 LEU Chi-restraints excluded: chain D5 residue 536 LEU Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 9 MET Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 183 VAL Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 256 PHE Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D4 residue 406 TYR Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 130 LEU Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 202 LEU Chi-restraints excluded: chain D2 residue 205 LEU Chi-restraints excluded: chain D2 residue 241 THR Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 248 LEU Chi-restraints excluded: chain D2 residue 258 SER Chi-restraints excluded: chain D2 residue 266 ILE Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 328 THR Chi-restraints excluded: chain D2 residue 332 LEU Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain D2 residue 343 LEU Chi-restraints excluded: chain AK residue 4 LEU Chi-restraints excluded: chain AK residue 42 LEU Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain B5 residue 110 VAL Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 51 ILE Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 36 ASP Chi-restraints excluded: chain A8 residue 65 CYS Chi-restraints excluded: chain A8 residue 76 HIS Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 144 ARG Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 23 THR Chi-restraints excluded: chain BJ residue 48 ARG Chi-restraints excluded: chain BJ residue 51 ILE Chi-restraints excluded: chain BJ residue 70 VAL Chi-restraints excluded: chain BJ residue 81 VAL Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 77 CYS Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 144 ILE Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 195 THR Chi-restraints excluded: chain AJ residue 209 THR Chi-restraints excluded: chain AJ residue 259 LEU Chi-restraints excluded: chain AJ residue 267 LEU Chi-restraints excluded: chain AJ residue 279 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 5 VAL Chi-restraints excluded: chain S5 residue 14 ASP Chi-restraints excluded: chain S5 residue 54 GLU Chi-restraints excluded: chain S5 residue 91 TYR Chi-restraints excluded: chain S5 residue 92 THR Chi-restraints excluded: chain A3 residue 35 SER Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 43 LEU Chi-restraints excluded: chain C2 residue 48 ILE Chi-restraints excluded: chain C2 residue 65 ILE Chi-restraints excluded: chain C2 residue 68 PHE Chi-restraints excluded: chain C2 residue 69 VAL Chi-restraints excluded: chain C2 residue 76 LEU Chi-restraints excluded: chain C2 residue 119 VAL Chi-restraints excluded: chain B4 residue 64 LEU Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain B4 residue 87 LEU Chi-restraints excluded: chain B4 residue 124 PHE Chi-restraints excluded: chain AM residue 32 TYR Chi-restraints excluded: chain AM residue 68 ILE Chi-restraints excluded: chain AM residue 126 LEU Chi-restraints excluded: chain B6 residue 3 TYR Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 34 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 110 LEU Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B7 residue 30 PHE Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 39 ASP Chi-restraints excluded: chain B8 residue 52 ASP Chi-restraints excluded: chain B8 residue 53 ARG Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 71 LEU Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 131 LYS Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 71 VAL Chi-restraints excluded: chain C1 residue 39 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 16 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 262 optimal weight: 5.9990 chunk 361 optimal weight: 2.9990 chunk 299 optimal weight: 0.2980 chunk 293 optimal weight: 0.7980 chunk 206 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 400 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D3 108 GLN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 374 ASN ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 289 ASN ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.107550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.096388 restraints weight = 87980.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.099018 restraints weight = 45147.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.100774 restraints weight = 27300.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.101872 restraints weight = 18425.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.102708 restraints weight = 13737.840| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39038 Z= 0.162 Angle : 0.862 14.748 52918 Z= 0.417 Chirality : 0.046 0.295 5820 Planarity : 0.006 0.124 6543 Dihedral : 8.134 101.092 5349 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.54 % Favored : 90.44 % Rotamer: Outliers : 5.06 % Allowed : 26.63 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 0.72 % Twisted General : 0.09 % 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: -0.39 (0.13), residues: 4561 helix: 1.28 (0.10), residues: 2869 sheet: -1.77 (1.13), residues: 22 loop : -3.18 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARGBJ 53 TYR 0.037 0.002 TYRB9 90 PHE 0.039 0.002 PHED5 591 TRP 0.037 0.002 TRPAM 141 HIS 0.022 0.001 HISB9 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (39024) covalent geometry : angle 0.86174 / 0.42 (52894) SS BOND : bond 0.00445 / 0.21 ( 12) SS BOND : angle 1.42039 / 0.94 ( 24) hydrogen bonds : bond 0.04505 / 2.91 ( 2139) hydrogen bonds : angle 4.43416 / 3.10 ( 6366) Misc. bond : bond 0.00412 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 1137 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 34 ASN cc_start: 0.8358 (p0) cc_final: 0.7941 (p0) REVERT: D3 11 PHE cc_start: 0.8489 (t80) cc_final: 0.8117 (t80) REVERT: D1 1 MET cc_start: 0.7577 (mmt) cc_final: 0.7174 (mmt) REVERT: D1 25 ARG cc_start: 0.8992 (ttm110) cc_final: 0.8326 (ttm-80) REVERT: D1 26 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8742 (mtpp) REVERT: D1 81 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8205 (mp) REVERT: D1 85 MET cc_start: 0.8162 (mmm) cc_final: 0.7892 (mmm) REVERT: D1 100 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8002 (pt) REVERT: D1 192 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7495 (tm-30) REVERT: D1 195 ARG cc_start: 0.7311 (mtp180) cc_final: 0.7056 (mtm180) REVERT: D1 233 MET cc_start: 0.8186 (tmm) cc_final: 0.7420 (tmm) REVERT: D1 234 MET cc_start: 0.8940 (mmt) cc_final: 0.8525 (mpp) REVERT: D1 239 THR cc_start: 0.9129 (m) cc_final: 0.8789 (p) REVERT: D1 266 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8540 (tt) REVERT: D1 272 TRP cc_start: 0.7119 (t60) cc_final: 0.6175 (t60) REVERT: D1 284 GLN cc_start: 0.6932 (mt0) cc_final: 0.6540 (pt0) REVERT: D1 317 GLN cc_start: 0.8022 (tm130) cc_final: 0.7793 (tm-30) REVERT: D6 17 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7702 (t80) REVERT: D6 98 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8688 (tm) REVERT: D6 109 LYS cc_start: 0.7284 (mmtt) cc_final: 0.6996 (mmtt) REVERT: D6 114 GLU cc_start: 0.7693 (tt0) cc_final: 0.7345 (pm20) REVERT: D6 162 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8262 (mm) REVERT: 4L 1 MET cc_start: 0.7432 (ttm) cc_final: 0.7226 (tmm) REVERT: 4L 47 MET cc_start: 0.8093 (tpp) cc_final: 0.7614 (mmm) REVERT: D5 66 TRP cc_start: 0.8267 (t60) cc_final: 0.8014 (t60) REVERT: D5 76 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8951 (pp) REVERT: D5 86 SER cc_start: 0.9115 (m) cc_final: 0.8693 (t) REVERT: D5 87 MET cc_start: 0.8063 (tpp) cc_final: 0.7542 (tpp) REVERT: D5 94 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9140 (mm) REVERT: D5 149 ILE cc_start: 0.9347 (tp) cc_final: 0.8957 (tp) REVERT: D5 154 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8726 (mm) REVERT: D5 246 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8803 (tt) REVERT: D5 393 ASP cc_start: 0.8285 (m-30) cc_final: 0.7886 (m-30) REVERT: D5 487 LYS cc_start: 0.7740 (ttmp) cc_final: 0.7305 (ttmt) REVERT: D5 511 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6510 (pp) REVERT: D4 1 MET cc_start: 0.8016 (tpp) cc_final: 0.7530 (tpp) REVERT: D4 3 LYS cc_start: 0.8629 (pttp) cc_final: 0.8327 (pttp) REVERT: D4 9 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6647 (tmm) REVERT: D4 108 MET cc_start: 0.8301 (ttm) cc_final: 0.7169 (ttm) REVERT: D4 119 TYR cc_start: 0.9029 (t80) cc_final: 0.8728 (t80) REVERT: D4 121 MET cc_start: 0.7680 (tpp) cc_final: 0.6892 (tpp) REVERT: D4 169 ASN cc_start: 0.8315 (m-40) cc_final: 0.7889 (m-40) REVERT: D4 221 VAL cc_start: 0.9113 (m) cc_final: 0.8848 (p) REVERT: D4 257 MET cc_start: 0.7241 (mmm) cc_final: 0.6816 (mmm) REVERT: D4 259 TYR cc_start: 0.8444 (m-10) cc_final: 0.7876 (m-80) REVERT: D4 263 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7365 (mmt) REVERT: D2 14 MET cc_start: 0.7192 (tmm) cc_final: 0.6723 (tmm) REVERT: D2 91 ASN cc_start: 0.8488 (t0) cc_final: 0.7934 (t0) REVERT: D2 93 MET cc_start: 0.9129 (tpp) cc_final: 0.8831 (tpp) REVERT: D2 96 MET cc_start: 0.7969 (tmm) cc_final: 0.7290 (tmm) REVERT: D2 100 MET cc_start: 0.8864 (mtt) cc_final: 0.8453 (mtp) REVERT: D2 105 LYS cc_start: 0.8792 (tptp) cc_final: 0.8456 (mmmt) REVERT: D2 117 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8321 (mm-30) REVERT: D2 129 ILE cc_start: 0.9075 (tt) cc_final: 0.8736 (mt) REVERT: D2 130 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7698 (pp) REVERT: D2 139 MET cc_start: 0.7894 (mmm) cc_final: 0.6965 (mtt) REVERT: D2 217 THR cc_start: 0.9246 (m) cc_final: 0.8962 (p) REVERT: D2 266 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.8959 (mt) REVERT: D2 270 MET cc_start: 0.8442 (ttm) cc_final: 0.8176 (ttp) REVERT: D2 313 MET cc_start: 0.8289 (tmt) cc_final: 0.7890 (tmm) REVERT: AK 8 TYR cc_start: 0.9271 (t80) cc_final: 0.8954 (t80) REVERT: AK 60 PHE cc_start: 0.8804 (t80) cc_final: 0.8288 (t80) REVERT: AK 117 MET cc_start: 0.7592 (mmt) cc_final: 0.7053 (mmp) REVERT: B5 93 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8928 (mt) REVERT: AB 64 ASP cc_start: 0.8274 (m-30) cc_final: 0.7781 (t70) REVERT: AB 83 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8512 (ttmm) REVERT: A8 76 HIS cc_start: 0.7523 (OUTLIER) cc_final: 0.6929 (t-90) REVERT: BJ 16 THR cc_start: 0.9017 (m) cc_final: 0.8528 (p) REVERT: BJ 48 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7676 (tpm-80) REVERT: BJ 52 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7319 (mm-30) REVERT: BJ 60 TYR cc_start: 0.6465 (OUTLIER) cc_final: 0.6211 (t80) REVERT: BJ 162 MET cc_start: 0.7859 (mtt) cc_final: 0.7442 (mtt) REVERT: AJ 18 MET cc_start: 0.7988 (mmm) cc_final: 0.7499 (mmm) REVERT: AJ 267 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8357 (mp) REVERT: AJ 271 ASN cc_start: 0.8220 (m110) cc_final: 0.7753 (m110) REVERT: AJ 315 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6461 (ttmm) REVERT: S5 69 GLN cc_start: 0.7909 (mm110) cc_final: 0.7503 (mm-40) REVERT: S5 78 ILE cc_start: 0.9322 (mm) cc_final: 0.8752 (tt) REVERT: S5 91 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6423 (p90) REVERT: A3 45 ASN cc_start: 0.9039 (t0) cc_final: 0.8743 (t0) REVERT: B3 29 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7979 (mt-10) REVERT: C2 11 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6930 (pp) REVERT: C2 80 ASP cc_start: 0.8413 (t0) cc_final: 0.8212 (t0) REVERT: C2 82 MET cc_start: 0.8844 (tpt) cc_final: 0.8343 (tpt) REVERT: B4 27 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7178 (tm-30) REVERT: B4 34 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6933 (tm-30) REVERT: B4 40 SER cc_start: 0.9513 (p) cc_final: 0.9303 (t) REVERT: B4 43 LYS cc_start: 0.9061 (mtpm) cc_final: 0.8466 (ttmm) REVERT: B4 45 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8126 (tm-30) REVERT: B4 47 GLN cc_start: 0.8461 (mt0) cc_final: 0.8077 (mt0) REVERT: B4 74 ASN cc_start: 0.7598 (t0) cc_final: 0.7386 (t0) REVERT: B4 101 TYR cc_start: 0.8812 (t80) cc_final: 0.8523 (t80) REVERT: B4 116 GLN cc_start: 0.8668 (tp40) cc_final: 0.8407 (tp-100) REVERT: B4 117 GLU cc_start: 0.7770 (tm-30) cc_final: 0.6476 (tm-30) REVERT: B4 119 LYS cc_start: 0.8716 (ptmm) cc_final: 0.8336 (ptpp) REVERT: AM 65 GLU cc_start: 0.7580 (tt0) cc_final: 0.7120 (tt0) REVERT: AM 70 LEU cc_start: 0.8713 (tp) cc_final: 0.8461 (tp) REVERT: B6 3 TYR cc_start: 0.7577 (OUTLIER) cc_final: 0.6277 (m-10) REVERT: B6 14 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9063 (tp) REVERT: B6 31 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.5674 (pp20) REVERT: B6 107 ASP cc_start: 0.7686 (m-30) cc_final: 0.7463 (m-30) REVERT: B6 114 GLU cc_start: 0.7797 (pm20) cc_final: 0.7375 (pm20) REVERT: B7 8 TYR cc_start: 0.7048 (m-80) cc_final: 0.6801 (m-80) REVERT: B7 49 GLN cc_start: 0.8047 (tp-100) cc_final: 0.7320 (tp-100) REVERT: B7 56 ASP cc_start: 0.8940 (p0) cc_final: 0.8575 (p0) REVERT: B7 65 PHE cc_start: 0.8362 (t80) cc_final: 0.7910 (t80) REVERT: B7 102 GLU cc_start: 0.8264 (tp30) cc_final: 0.7088 (tp30) REVERT: B9 96 TYR cc_start: 0.8255 (m-80) cc_final: 0.7946 (m-80) REVERT: B2 26 GLU cc_start: 0.8383 (tp30) cc_final: 0.8057 (tp30) REVERT: B8 52 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8091 (t70) REVERT: B8 103 LYS cc_start: 0.8114 (mttt) cc_final: 0.7787 (tttp) REVERT: B8 112 MET cc_start: 0.8316 (mmm) cc_final: 0.7759 (mmm) REVERT: B8 122 TYR cc_start: 0.8008 (m-10) cc_final: 0.7631 (m-10) REVERT: BK 39 GLU cc_start: 0.8514 (mp0) cc_final: 0.8185 (mp0) REVERT: BK 92 GLU cc_start: 0.8335 (tp30) cc_final: 0.7834 (tp30) REVERT: C1 5 GLN cc_start: 0.7493 (pp30) cc_final: 0.6929 (pp30) REVERT: C1 37 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7402 (tm-30) REVERT: B1 8 ARG cc_start: 0.5903 (mmp-170) cc_final: 0.4774 (ptp-170) REVERT: A1 16 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8042 (mm) REVERT: A1 28 ARG cc_start: 0.7888 (mtp180) cc_final: 0.7551 (ttp80) REVERT: A1 34 ARG cc_start: 0.8496 (mpt180) cc_final: 0.8210 (mmt90) outliers start: 207 outliers final: 157 residues processed: 1236 average time/residue: 0.2211 time to fit residues: 460.9559 Evaluate side-chains 1271 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 1086 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 1 MET Chi-restraints excluded: chain D3 residue 7 LEU Chi-restraints excluded: chain D3 residue 101 SER Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 81 LEU Chi-restraints excluded: chain D1 residue 97 ASN Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 129 LEU Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 228 TYR Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 273 ILE Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D6 residue 17 PHE Chi-restraints excluded: chain D6 residue 20 PHE Chi-restraints excluded: chain D6 residue 21 SER Chi-restraints excluded: chain D6 residue 25 SER Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 106 TYR Chi-restraints excluded: chain D6 residue 122 MET Chi-restraints excluded: chain D6 residue 125 TRP Chi-restraints excluded: chain D6 residue 132 ASP Chi-restraints excluded: chain D6 residue 162 LEU Chi-restraints excluded: chain D6 residue 165 VAL Chi-restraints excluded: chain 4L residue 39 SER Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain 4L residue 69 CYS Chi-restraints excluded: chain 4L residue 75 LEU Chi-restraints excluded: chain 4L residue 76 SER Chi-restraints excluded: chain 4L residue 77 LEU Chi-restraints excluded: chain 4L residue 79 VAL Chi-restraints excluded: chain D5 residue 7 LEU Chi-restraints excluded: chain D5 residue 9 LEU Chi-restraints excluded: chain D5 residue 61 MET Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 69 LEU Chi-restraints excluded: chain D5 residue 76 LEU Chi-restraints excluded: chain D5 residue 94 LEU Chi-restraints excluded: chain D5 residue 125 LEU Chi-restraints excluded: chain D5 residue 130 ILE Chi-restraints excluded: chain D5 residue 137 LEU Chi-restraints excluded: chain D5 residue 142 ILE Chi-restraints excluded: chain D5 residue 150 MET Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 217 ILE Chi-restraints excluded: chain D5 residue 233 LEU Chi-restraints excluded: chain D5 residue 246 LEU Chi-restraints excluded: chain D5 residue 276 ILE Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 380 LEU Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 404 THR Chi-restraints excluded: chain D5 residue 441 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 500 LEU Chi-restraints excluded: chain D5 residue 511 LEU Chi-restraints excluded: chain D5 residue 536 LEU Chi-restraints excluded: chain D5 residue 562 LEU Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 6 ILE Chi-restraints excluded: chain D4 residue 9 MET Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 183 VAL Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 256 PHE Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D4 residue 406 TYR Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 130 LEU Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 202 LEU Chi-restraints excluded: chain D2 residue 241 THR Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 248 LEU Chi-restraints excluded: chain D2 residue 258 SER Chi-restraints excluded: chain D2 residue 266 ILE Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 328 THR Chi-restraints excluded: chain D2 residue 332 LEU Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain D2 residue 343 LEU Chi-restraints excluded: chain AK residue 4 LEU Chi-restraints excluded: chain AK residue 42 LEU Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain B5 residue 110 VAL Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 51 ILE Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 36 ASP Chi-restraints excluded: chain A8 residue 65 CYS Chi-restraints excluded: chain A8 residue 76 HIS Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 144 ARG Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 23 THR Chi-restraints excluded: chain BJ residue 48 ARG Chi-restraints excluded: chain BJ residue 51 ILE Chi-restraints excluded: chain BJ residue 60 TYR Chi-restraints excluded: chain BJ residue 70 VAL Chi-restraints excluded: chain BJ residue 81 VAL Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 77 CYS Chi-restraints excluded: chain AJ residue 106 LEU Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 144 ILE Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 195 THR Chi-restraints excluded: chain AJ residue 209 THR Chi-restraints excluded: chain AJ residue 259 LEU Chi-restraints excluded: chain AJ residue 267 LEU Chi-restraints excluded: chain AJ residue 279 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 5 VAL Chi-restraints excluded: chain S5 residue 14 ASP Chi-restraints excluded: chain S5 residue 54 GLU Chi-restraints excluded: chain S5 residue 91 TYR Chi-restraints excluded: chain S5 residue 92 THR Chi-restraints excluded: chain A3 residue 29 VAL Chi-restraints excluded: chain A3 residue 35 SER Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 43 LEU Chi-restraints excluded: chain C2 residue 48 ILE Chi-restraints excluded: chain C2 residue 65 ILE Chi-restraints excluded: chain C2 residue 68 PHE Chi-restraints excluded: chain C2 residue 69 VAL Chi-restraints excluded: chain C2 residue 76 LEU Chi-restraints excluded: chain C2 residue 119 VAL Chi-restraints excluded: chain B4 residue 64 LEU Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain B4 residue 87 LEU Chi-restraints excluded: chain AM residue 32 TYR Chi-restraints excluded: chain AM residue 68 ILE Chi-restraints excluded: chain AM residue 126 LEU Chi-restraints excluded: chain B6 residue 3 TYR Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 34 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 110 LEU Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B7 residue 30 PHE Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 52 ASP Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 71 LEU Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 131 LYS Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 71 VAL Chi-restraints excluded: chain C1 residue 39 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 122 optimal weight: 1.9990 chunk 256 optimal weight: 0.7980 chunk 353 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 292 optimal weight: 0.0000 chunk 385 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 286 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 301 optimal weight: 3.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D3 108 GLN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 83 ASN ** D4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 289 ASN ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4 49 GLN AM 53 ASN ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.097019 restraints weight = 86892.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.099648 restraints weight = 44547.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.101390 restraints weight = 26974.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.102589 restraints weight = 18111.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103326 restraints weight = 13262.258| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39038 Z= 0.161 Angle : 0.881 15.263 52918 Z= 0.426 Chirality : 0.046 0.256 5820 Planarity : 0.006 0.098 6543 Dihedral : 8.081 102.521 5349 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.87 % Favored : 90.11 % Rotamer: Outliers : 4.74 % Allowed : 27.66 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 0.72 % Twisted General : 0.07 % 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: -0.36 (0.13), residues: 4561 helix: 1.28 (0.10), residues: 2873 sheet: -1.76 (1.13), residues: 22 loop : -3.12 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGBJ 53 TYR 0.043 0.001 TYRD6 60 PHE 0.049 0.002 PHED5 591 TRP 0.039 0.002 TRPAM 141 HIS 0.015 0.001 HISB9 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (39024) covalent geometry : angle 0.88093 / 0.43 (52894) SS BOND : bond 0.00389 / 0.18 ( 12) SS BOND : angle 1.36048 / 0.90 ( 24) hydrogen bonds : bond 0.04456 / 2.87 ( 2139) hydrogen bonds : angle 4.44604 / 3.11 ( 6366) Misc. bond : bond 0.00267 / 0.13 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 1112 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 34 ASN cc_start: 0.8421 (p0) cc_final: 0.7966 (p0) REVERT: D3 11 PHE cc_start: 0.8498 (t80) cc_final: 0.8117 (t80) REVERT: D1 1 MET cc_start: 0.7578 (mmt) cc_final: 0.7196 (mmt) REVERT: D1 25 ARG cc_start: 0.9018 (ttm110) cc_final: 0.8317 (ttm-80) REVERT: D1 26 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8770 (mtpp) REVERT: D1 81 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8065 (mp) REVERT: D1 85 MET cc_start: 0.8124 (mmm) cc_final: 0.7871 (mmm) REVERT: D1 100 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7938 (pt) REVERT: D1 192 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7562 (tm-30) REVERT: D1 195 ARG cc_start: 0.7315 (mtp180) cc_final: 0.6898 (mtm180) REVERT: D1 234 MET cc_start: 0.8839 (mmt) cc_final: 0.8614 (mmt) REVERT: D1 239 THR cc_start: 0.9111 (m) cc_final: 0.8803 (p) REVERT: D1 266 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8574 (tt) REVERT: D1 272 TRP cc_start: 0.7046 (t60) cc_final: 0.6210 (t60) REVERT: D1 284 GLN cc_start: 0.6918 (mt0) cc_final: 0.6533 (pt0) REVERT: D6 17 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7675 (t80) REVERT: D6 98 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8693 (tm) REVERT: D6 109 LYS cc_start: 0.7397 (mmtt) cc_final: 0.7083 (mmtt) REVERT: D6 114 GLU cc_start: 0.7626 (tt0) cc_final: 0.7326 (pm20) REVERT: D6 136 PHE cc_start: 0.8391 (p90) cc_final: 0.8160 (p90) REVERT: D6 162 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8557 (mm) REVERT: 4L 34 GLU cc_start: 0.8059 (tp30) cc_final: 0.6925 (tp30) REVERT: 4L 38 LEU cc_start: 0.9026 (tp) cc_final: 0.8681 (mp) REVERT: D5 53 MET cc_start: 0.7992 (tmm) cc_final: 0.7525 (tmm) REVERT: D5 78 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6810 (pp) REVERT: D5 86 SER cc_start: 0.9108 (m) cc_final: 0.8747 (t) REVERT: D5 149 ILE cc_start: 0.9358 (tp) cc_final: 0.8970 (tp) REVERT: D5 154 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8662 (mm) REVERT: D5 246 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8843 (tt) REVERT: D5 314 MET cc_start: 0.8501 (mmm) cc_final: 0.8224 (mtp) REVERT: D5 393 ASP cc_start: 0.8208 (m-30) cc_final: 0.7909 (m-30) REVERT: D5 397 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7567 (mt-10) REVERT: D5 480 MET cc_start: 0.7278 (tpt) cc_final: 0.6971 (tpt) REVERT: D5 487 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7272 (ttmt) REVERT: D5 511 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6688 (pp) REVERT: D4 1 MET cc_start: 0.8402 (tpp) cc_final: 0.7921 (tpp) REVERT: D4 3 LYS cc_start: 0.8739 (pttp) cc_final: 0.8464 (pttp) REVERT: D4 9 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.6820 (tmm) REVERT: D4 108 MET cc_start: 0.8313 (ttm) cc_final: 0.7126 (ttm) REVERT: D4 119 TYR cc_start: 0.8991 (t80) cc_final: 0.8722 (t80) REVERT: D4 121 MET cc_start: 0.7650 (tpp) cc_final: 0.6874 (tpp) REVERT: D4 141 GLU cc_start: 0.7645 (pm20) cc_final: 0.7077 (pm20) REVERT: D4 221 VAL cc_start: 0.9122 (m) cc_final: 0.8861 (p) REVERT: D4 243 MET cc_start: 0.9320 (ttp) cc_final: 0.9053 (ttp) REVERT: D4 257 MET cc_start: 0.7215 (mmm) cc_final: 0.6841 (mmm) REVERT: D4 259 TYR cc_start: 0.8444 (m-10) cc_final: 0.7802 (m-10) REVERT: D4 263 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7294 (mmt) REVERT: D4 294 MET cc_start: 0.8757 (mmm) cc_final: 0.8401 (mmp) REVERT: D4 325 MET cc_start: 0.7246 (ttp) cc_final: 0.6861 (ttp) REVERT: D2 14 MET cc_start: 0.7196 (tmm) cc_final: 0.6702 (tmm) REVERT: D2 91 ASN cc_start: 0.8469 (t0) cc_final: 0.7944 (t0) REVERT: D2 96 MET cc_start: 0.7967 (tmm) cc_final: 0.7287 (tmm) REVERT: D2 100 MET cc_start: 0.8668 (mtt) cc_final: 0.8364 (mtp) REVERT: D2 105 LYS cc_start: 0.8698 (tptp) cc_final: 0.8230 (mmmt) REVERT: D2 117 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8315 (mm-30) REVERT: D2 129 ILE cc_start: 0.9070 (tt) cc_final: 0.8692 (mt) REVERT: D2 130 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7639 (pp) REVERT: D2 139 MET cc_start: 0.7301 (mmm) cc_final: 0.6085 (mmm) REVERT: D2 179 MET cc_start: 0.8574 (tpp) cc_final: 0.8136 (mpp) REVERT: D2 213 SER cc_start: 0.8675 (m) cc_final: 0.8249 (t) REVERT: D2 217 THR cc_start: 0.9285 (m) cc_final: 0.8996 (p) REVERT: D2 270 MET cc_start: 0.8398 (ttm) cc_final: 0.8122 (ttp) REVERT: AK 8 TYR cc_start: 0.9266 (t80) cc_final: 0.8958 (t80) REVERT: AK 60 PHE cc_start: 0.8791 (t80) cc_final: 0.8283 (t80) REVERT: AK 117 MET cc_start: 0.7587 (mmt) cc_final: 0.7102 (mmp) REVERT: B5 93 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8918 (mt) REVERT: AB 52 MET cc_start: 0.8355 (tmm) cc_final: 0.8106 (tpt) REVERT: AB 64 ASP cc_start: 0.8137 (m-30) cc_final: 0.7790 (t70) REVERT: AB 83 LYS cc_start: 0.9036 (ttmm) cc_final: 0.8670 (ttmm) REVERT: A8 76 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.6783 (t-90) REVERT: BJ 16 THR cc_start: 0.9128 (m) cc_final: 0.8635 (p) REVERT: BJ 48 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7671 (tpm-80) REVERT: BJ 52 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7297 (mm-30) REVERT: BJ 60 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.6599 (t80) REVERT: BJ 162 MET cc_start: 0.7850 (mtt) cc_final: 0.7455 (mtt) REVERT: AJ 18 MET cc_start: 0.7935 (mmm) cc_final: 0.7422 (mmm) REVERT: AJ 271 ASN cc_start: 0.8256 (m110) cc_final: 0.7770 (m110) REVERT: AJ 315 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6459 (ttmm) REVERT: S5 69 GLN cc_start: 0.7899 (mm110) cc_final: 0.7481 (mm-40) REVERT: S5 91 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.6275 (p90) REVERT: A3 45 ASN cc_start: 0.9044 (t0) cc_final: 0.8776 (t0) REVERT: C2 11 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6938 (pp) REVERT: C2 80 ASP cc_start: 0.8423 (t0) cc_final: 0.8204 (t0) REVERT: C2 82 MET cc_start: 0.8775 (tpt) cc_final: 0.8364 (tpt) REVERT: B4 27 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7211 (tm-30) REVERT: B4 34 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6899 (tm-30) REVERT: B4 40 SER cc_start: 0.9534 (p) cc_final: 0.9253 (t) REVERT: B4 43 LYS cc_start: 0.9053 (mtpm) cc_final: 0.8460 (ttmm) REVERT: B4 45 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8131 (tm-30) REVERT: B4 47 GLN cc_start: 0.8446 (mt0) cc_final: 0.8052 (mt0) REVERT: B4 101 TYR cc_start: 0.8799 (t80) cc_final: 0.8525 (t80) REVERT: B4 116 GLN cc_start: 0.8675 (tp40) cc_final: 0.8420 (tp-100) REVERT: AM 65 GLU cc_start: 0.7591 (tt0) cc_final: 0.7100 (tt0) REVERT: AM 70 LEU cc_start: 0.8712 (tp) cc_final: 0.8470 (tp) REVERT: AM 85 MET cc_start: 0.8009 (mmt) cc_final: 0.7698 (mmt) REVERT: B6 3 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6249 (m-10) REVERT: B6 14 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9082 (tp) REVERT: B6 31 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.5685 (pp20) REVERT: B6 75 LEU cc_start: 0.7558 (mm) cc_final: 0.7114 (tp) REVERT: B6 107 ASP cc_start: 0.7682 (m-30) cc_final: 0.7470 (m-30) REVERT: B6 114 GLU cc_start: 0.7942 (pm20) cc_final: 0.7567 (pm20) REVERT: B7 8 TYR cc_start: 0.6989 (m-80) cc_final: 0.6751 (m-80) REVERT: B7 49 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7340 (tp-100) REVERT: B7 56 ASP cc_start: 0.8988 (p0) cc_final: 0.8608 (p0) REVERT: B7 102 GLU cc_start: 0.8439 (tp30) cc_final: 0.8158 (tp30) REVERT: B9 93 TYR cc_start: 0.8219 (m-80) cc_final: 0.7943 (m-80) REVERT: B9 96 TYR cc_start: 0.8278 (m-80) cc_final: 0.7972 (m-80) REVERT: B2 26 GLU cc_start: 0.8387 (tp30) cc_final: 0.8094 (tp30) REVERT: B2 48 LEU cc_start: 0.8422 (mt) cc_final: 0.7453 (mp) REVERT: B8 30 ARG cc_start: 0.8429 (ttm-80) cc_final: 0.8209 (ttm-80) REVERT: B8 52 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8020 (t70) REVERT: B8 90 ASP cc_start: 0.7156 (p0) cc_final: 0.6856 (p0) REVERT: B8 103 LYS cc_start: 0.8106 (mttt) cc_final: 0.7769 (tttp) REVERT: B8 112 MET cc_start: 0.8306 (mmm) cc_final: 0.7764 (mmm) REVERT: B8 122 TYR cc_start: 0.7975 (m-10) cc_final: 0.7588 (m-10) REVERT: BK 92 GLU cc_start: 0.8343 (tp30) cc_final: 0.7834 (tp30) REVERT: C1 5 GLN cc_start: 0.7513 (pp30) cc_final: 0.6909 (pp30) REVERT: C1 37 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B1 8 ARG cc_start: 0.5891 (mmp-170) cc_final: 0.4779 (ptp-170) REVERT: A1 16 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8117 (mm) REVERT: A1 28 ARG cc_start: 0.7921 (mtp180) cc_final: 0.7557 (ttp80) REVERT: A1 34 ARG cc_start: 0.8508 (mpt180) cc_final: 0.7978 (mmt90) outliers start: 194 outliers final: 154 residues processed: 1212 average time/residue: 0.2243 time to fit residues: 459.5792 Evaluate side-chains 1250 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 1071 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 1 MET Chi-restraints excluded: chain D3 residue 7 LEU Chi-restraints excluded: chain D3 residue 101 SER Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 68 ILE Chi-restraints excluded: chain D1 residue 81 LEU Chi-restraints excluded: chain D1 residue 97 ASN Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 129 LEU Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D6 residue 17 PHE Chi-restraints excluded: chain D6 residue 20 PHE Chi-restraints excluded: chain D6 residue 21 SER Chi-restraints excluded: chain D6 residue 25 SER Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 106 TYR Chi-restraints excluded: chain D6 residue 122 MET Chi-restraints excluded: chain D6 residue 125 TRP Chi-restraints excluded: chain D6 residue 132 ASP Chi-restraints excluded: chain D6 residue 162 LEU Chi-restraints excluded: chain 4L residue 39 SER Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain 4L residue 69 CYS Chi-restraints excluded: chain 4L residue 75 LEU Chi-restraints excluded: chain 4L residue 76 SER Chi-restraints excluded: chain 4L residue 77 LEU Chi-restraints excluded: chain 4L residue 79 VAL Chi-restraints excluded: chain D5 residue 7 LEU Chi-restraints excluded: chain D5 residue 9 LEU Chi-restraints excluded: chain D5 residue 61 MET Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 69 LEU Chi-restraints excluded: chain D5 residue 78 LEU Chi-restraints excluded: chain D5 residue 125 LEU Chi-restraints excluded: chain D5 residue 130 ILE Chi-restraints excluded: chain D5 residue 137 LEU Chi-restraints excluded: chain D5 residue 142 ILE Chi-restraints excluded: chain D5 residue 150 MET Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 217 ILE Chi-restraints excluded: chain D5 residue 233 LEU Chi-restraints excluded: chain D5 residue 246 LEU Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 380 LEU Chi-restraints excluded: chain D5 residue 383 MET Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 404 THR Chi-restraints excluded: chain D5 residue 441 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 500 LEU Chi-restraints excluded: chain D5 residue 511 LEU Chi-restraints excluded: chain D5 residue 536 LEU Chi-restraints excluded: chain D5 residue 562 LEU Chi-restraints excluded: chain D5 residue 591 PHE Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 9 MET Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 183 VAL Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 256 PHE Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D4 residue 369 LEU Chi-restraints excluded: chain D4 residue 406 TYR Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 130 LEU Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 241 THR Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 248 LEU Chi-restraints excluded: chain D2 residue 258 SER Chi-restraints excluded: chain D2 residue 266 ILE Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 328 THR Chi-restraints excluded: chain D2 residue 332 LEU Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain D2 residue 343 LEU Chi-restraints excluded: chain AK residue 4 LEU Chi-restraints excluded: chain AK residue 123 LEU Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain B5 residue 110 VAL Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 51 ILE Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 36 ASP Chi-restraints excluded: chain A8 residue 65 CYS Chi-restraints excluded: chain A8 residue 76 HIS Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 144 ARG Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 23 THR Chi-restraints excluded: chain BJ residue 48 ARG Chi-restraints excluded: chain BJ residue 51 ILE Chi-restraints excluded: chain BJ residue 60 TYR Chi-restraints excluded: chain BJ residue 70 VAL Chi-restraints excluded: chain BJ residue 81 VAL Chi-restraints excluded: chain BJ residue 135 VAL Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 77 CYS Chi-restraints excluded: chain AJ residue 106 LEU Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 144 ILE Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 195 THR Chi-restraints excluded: chain AJ residue 209 THR Chi-restraints excluded: chain AJ residue 259 LEU Chi-restraints excluded: chain AJ residue 279 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 5 VAL Chi-restraints excluded: chain S5 residue 78 ILE Chi-restraints excluded: chain S5 residue 91 TYR Chi-restraints excluded: chain S5 residue 92 THR Chi-restraints excluded: chain A3 residue 35 SER Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 43 LEU Chi-restraints excluded: chain C2 residue 48 ILE Chi-restraints excluded: chain C2 residue 65 ILE Chi-restraints excluded: chain C2 residue 68 PHE Chi-restraints excluded: chain C2 residue 69 VAL Chi-restraints excluded: chain C2 residue 119 VAL Chi-restraints excluded: chain B4 residue 64 LEU Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain B4 residue 87 LEU Chi-restraints excluded: chain B4 residue 124 PHE Chi-restraints excluded: chain AM residue 32 TYR Chi-restraints excluded: chain AM residue 68 ILE Chi-restraints excluded: chain AM residue 126 LEU Chi-restraints excluded: chain B6 residue 3 TYR Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 34 LEU Chi-restraints excluded: chain B6 residue 110 LEU Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B7 residue 30 PHE Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 52 ASP Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 71 LEU Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 131 LYS Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 71 VAL Chi-restraints excluded: chain C1 residue 39 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 9 ILE Chi-restraints excluded: chain A1 residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 304 optimal weight: 5.9990 chunk 384 optimal weight: 2.9990 chunk 355 optimal weight: 2.9990 chunk 280 optimal weight: 0.0000 chunk 334 optimal weight: 4.9990 chunk 354 optimal weight: 0.8980 chunk 250 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 342 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 314 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 108 GLN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 51 ASN ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 289 ASN ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 107 HIS B2 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.107214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096120 restraints weight = 87720.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098745 restraints weight = 45048.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100495 restraints weight = 27204.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.101663 restraints weight = 18372.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.102389 restraints weight = 13482.331| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 39038 Z= 0.169 Angle : 0.893 16.262 52918 Z= 0.432 Chirality : 0.047 0.237 5820 Planarity : 0.006 0.081 6543 Dihedral : 8.098 103.561 5349 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.80 % Favored : 90.18 % Rotamer: Outliers : 4.81 % Allowed : 27.68 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 0.72 % Twisted General : 0.09 % 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: -0.37 (0.13), residues: 4561 helix: 1.26 (0.10), residues: 2880 sheet: -1.72 (1.13), residues: 22 loop : -3.11 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGBJ 53 TYR 0.042 0.002 TYRD1 250 PHE 0.044 0.002 PHED5 591 TRP 0.055 0.002 TRPD1 118 HIS 0.014 0.001 HISB9 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (39024) covalent geometry : angle 0.89247 / 0.43 (52894) SS BOND : bond 0.00422 / 0.20 ( 12) SS BOND : angle 1.45504 / 0.95 ( 24) hydrogen bonds : bond 0.04567 / 2.94 ( 2139) hydrogen bonds : angle 4.46189 / 3.11 ( 6366) Misc. bond : bond 0.00242 / 0.12 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8982.79 seconds wall clock time: 155 minutes 11.78 seconds (9311.78 seconds total)