Starting phenix.real_space_refine on Mon Jun 23 16:47:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyh_29578/06_2025/8fyh_29578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyh_29578/06_2025/8fyh_29578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fyh_29578/06_2025/8fyh_29578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyh_29578/06_2025/8fyh_29578.map" model { file = "/net/cci-nas-00/data/ceres_data/8fyh_29578/06_2025/8fyh_29578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyh_29578/06_2025/8fyh_29578.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1862 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 14 6.06 5 P 16 5.49 5 S 118 5.16 5 C 16116 2.51 5 N 4722 2.21 5 O 4652 1.98 5 H 195 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25833 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 2931 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 17, 'TRANS': 415} Chain breaks: 10 Unresolved non-hydrogen bonds: 684 Unresolved non-hydrogen angles: 852 Unresolved non-hydrogen dihedrals: 546 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 12, 'TYR:plan': 2, 'ASN:plan1': 11, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 24, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 362 Chain: "C" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2654 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 12, 'TRANS': 354} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 7, 'ASN:plan1': 5, 'HIS:plan': 2, 'GLU:plan': 12, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 162 Chain: "D" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2722 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 22, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 398 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 15, 'ASN:plan1': 10, 'HIS:plan': 1, 'GLU:plan': 20, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 199 Chain: "A" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3425 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 207} Link IDs: {'PTRANS': 25, 'TRANS': 488} Chain breaks: 6 Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 934 Unresolved non-hydrogen dihedrals: 605 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 17, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 460 Chain: "E" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 187 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 27} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 696 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 94 Chain: "H" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 2931 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 17, 'TRANS': 415} Chain breaks: 10 Unresolved non-hydrogen bonds: 684 Unresolved non-hydrogen angles: 852 Unresolved non-hydrogen dihedrals: 546 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 12, 'TYR:plan': 2, 'ASN:plan1': 11, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 24, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 362 Chain: "I" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2654 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 12, 'TRANS': 354} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 7, 'ASN:plan1': 5, 'HIS:plan': 2, 'GLU:plan': 12, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 162 Chain: "J" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2722 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 22, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 398 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 15, 'ASN:plan1': 10, 'HIS:plan': 1, 'GLU:plan': 20, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 199 Chain: "G" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3425 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 207} Link IDs: {'PTRANS': 25, 'TRANS': 488} Chain breaks: 6 Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 934 Unresolved non-hydrogen dihedrals: 605 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 17, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 460 Chain: "K" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 187 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 27} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "L" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 696 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 94 Chain: "M" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 589 Inner-chain residues flagged as termini: ['pdbres=" G M 13 "'] Classifications: {'RNA': 18} Modifications used: {'5*END': 2, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10238 SG CYS A 528 90.339 116.747 101.330 1.00 60.88 S ATOM 10283 SG CYS A 535 90.228 113.510 103.412 1.00 64.47 S ATOM 10306 SG CYS A 539 87.780 116.324 104.167 1.00 62.99 S ATOM 10238 SG CYS A 528 90.339 116.747 101.330 1.00 60.88 S ATOM 10319 SG CYS A 541 86.635 117.692 101.125 1.00 58.37 S ATOM 10371 SG CYS A 548 87.792 114.126 100.436 1.00 52.02 S ATOM 10406 SG CYS A 552 88.656 116.974 97.981 1.00 54.69 S ATOM 10283 SG CYS A 535 90.228 113.510 103.412 1.00 64.47 S ATOM 10371 SG CYS A 548 87.792 114.126 100.436 1.00 52.02 S ATOM 10417 SG CYS A 554 91.461 113.258 99.843 1.00 63.09 S ATOM 10440 SG CYS A 558 89.164 110.638 101.245 1.00 60.11 S ATOM 10483 SG CYS A 565 80.615 107.180 84.657 1.00 41.18 S ATOM 10500 SG CYS A 567 77.901 104.647 83.793 1.00 42.37 S ATOM 10529 SG CYS A 571 78.377 107.825 81.753 1.00 43.37 S ATOM 10568 SG CYS A 576 76.870 107.831 85.365 1.00 41.61 S ATOM 10529 SG CYS A 571 78.377 107.825 81.753 1.00 43.37 S ATOM 10635 SG CYS A 585 79.879 110.752 83.790 1.00 40.34 S ATOM 10687 SG CYS A 593 81.762 109.337 80.816 1.00 45.19 S ATOM 10752 SG CYS A 606 78.593 111.403 80.386 1.00 45.47 S ATOM 10483 SG CYS A 565 80.615 107.180 84.657 1.00 41.18 S ATOM 10581 SG CYS A 578 80.133 109.766 87.445 1.00 39.24 S ATOM 10635 SG CYS A 585 79.879 110.752 83.790 1.00 40.34 S ATOM 10666 SG CYS A 590 83.240 109.917 85.431 1.00 40.89 S ATOM 9400 SG CYS A 286 90.777 127.789 90.691 1.00 47.70 S ATOM 9422 SG CYS A 289 89.985 128.993 87.154 1.00 48.85 S ATOM 9464 SG CYS A 294 88.805 131.009 90.118 1.00 52.79 S ATOM 22853 SG CYS G 528 59.702 94.795 98.482 1.00 66.92 S ATOM 22898 SG CYS G 535 59.018 98.554 98.482 1.00 75.43 S ATOM 22921 SG CYS G 539 60.623 96.897 101.551 1.00 72.84 S ATOM 22853 SG CYS G 528 59.702 94.795 98.482 1.00 66.92 S ATOM 22934 SG CYS G 541 62.975 94.420 100.451 1.00 66.08 S ATOM 22986 SG CYS G 548 62.570 97.127 97.799 1.00 59.26 S ATOM 23021 SG CYS G 552 62.658 93.378 96.783 1.00 62.91 S ATOM 22898 SG CYS G 535 59.018 98.554 98.482 1.00 75.43 S ATOM 22986 SG CYS G 548 62.570 97.127 97.799 1.00 59.26 S ATOM 23032 SG CYS G 554 59.866 97.024 95.106 1.00 68.11 S ATOM 23055 SG CYS G 558 61.321 100.342 96.145 1.00 60.99 S ATOM 23098 SG CYS G 565 77.208 97.039 86.046 1.00 51.59 S ATOM 23115 SG CYS G 567 80.326 99.205 85.523 1.00 52.76 S ATOM 23144 SG CYS G 571 80.441 95.423 85.244 1.00 50.12 S ATOM 23183 SG CYS G 576 79.995 97.323 88.679 1.00 48.33 S ATOM 23144 SG CYS G 571 80.441 95.423 85.244 1.00 50.12 S ATOM 23250 SG CYS G 585 77.790 93.647 87.384 1.00 47.91 S ATOM 23302 SG CYS G 593 77.778 93.291 83.553 1.00 52.35 S ATOM 23367 SG CYS G 606 80.365 91.604 85.781 1.00 52.79 S ATOM 23098 SG CYS G 565 77.208 97.039 86.046 1.00 51.59 S ATOM 23196 SG CYS G 578 75.887 96.170 89.555 1.00 47.84 S ATOM 23250 SG CYS G 585 77.790 93.647 87.384 1.00 47.91 S ATOM 23281 SG CYS G 590 74.200 94.646 86.600 1.00 49.28 S ATOM 22015 SG CYS G 286 63.244 80.196 95.522 1.00 53.44 S ATOM 22037 SG CYS G 289 65.666 77.827 93.732 1.00 52.91 S ATOM 22079 SG CYS G 294 64.902 77.319 97.365 1.00 57.60 S Residues with excluded nonbonded symmetry interactions: 14 residue: pdb="ZN ZN A 801 " occ=0.47 residue: pdb="ZN ZN A 802 " occ=0.40 residue: pdb="ZN ZN A 803 " occ=0.67 residue: pdb="ZN ZN A 804 " occ=0.49 residue: pdb="ZN ZN A 805 " occ=0.62 residue: pdb="ZN ZN A 806 " occ=0.00 residue: pdb="ZN ZN A 807 " occ=0.51 residue: pdb="ZN ZN G 801 " occ=0.47 residue: pdb="ZN ZN G 802 " occ=0.29 residue: pdb="ZN ZN G 803 " occ=0.68 residue: pdb="ZN ZN G 804 " occ=0.37 residue: pdb="ZN ZN G 805 " occ=0.57 ... (remaining 2 not shown) Time building chain proxies: 14.62, per 1000 atoms: 0.57 Number of scatterers: 25833 At special positions: 0 Unit cell: (171.214, 203.117, 146.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 14 29.99 S 118 16.00 P 16 15.00 O 4652 8.00 N 4722 7.00 C 16116 6.00 H 195 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 457 " distance=1.79 Simple disulfide: pdb=" SG CYS G 325 " - pdb=" SG CYS G 457 " distance=1.82 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.27 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 530 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 535 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 539 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 528 " pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 528 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 552 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 541 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 548 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 554 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 558 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 535 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 548 " pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 567 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 571 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 565 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 576 " pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 606 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 585 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 593 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 571 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 578 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 585 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 590 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 565 " pdb=" ZN A 807 " pdb="ZN ZN A 807 " - pdb=" ND1 HIS A 297 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 294 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 286 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 289 " pdb=" ZN G 801 " pdb="ZN ZN G 801 " - pdb=" NE2 HIS G 530 " pdb="ZN ZN G 801 " - pdb=" SG CYS G 528 " pdb="ZN ZN G 801 " - pdb=" SG CYS G 539 " pdb="ZN ZN G 801 " - pdb=" SG CYS G 535 " pdb=" ZN G 802 " pdb="ZN ZN G 802 " - pdb=" SG CYS G 528 " pdb="ZN ZN G 802 " - pdb=" SG CYS G 552 " pdb="ZN ZN G 802 " - pdb=" SG CYS G 541 " pdb="ZN ZN G 802 " - pdb=" SG CYS G 548 " pdb=" ZN G 803 " pdb="ZN ZN G 803 " - pdb=" SG CYS G 558 " pdb="ZN ZN G 803 " - pdb=" SG CYS G 554 " pdb="ZN ZN G 803 " - pdb=" SG CYS G 535 " pdb="ZN ZN G 803 " - pdb=" SG CYS G 548 " pdb=" ZN G 804 " pdb="ZN ZN G 804 " - pdb=" SG CYS G 567 " pdb="ZN ZN G 804 " - pdb=" SG CYS G 565 " pdb="ZN ZN G 804 " - pdb=" SG CYS G 571 " pdb="ZN ZN G 804 " - pdb=" SG CYS G 576 " pdb=" ZN G 805 " pdb="ZN ZN G 805 " - pdb=" SG CYS G 585 " pdb="ZN ZN G 805 " - pdb=" SG CYS G 606 " pdb="ZN ZN G 805 " - pdb=" SG CYS G 593 " pdb="ZN ZN G 805 " - pdb=" SG CYS G 571 " pdb=" ZN G 806 " pdb="ZN ZN G 806 " - pdb=" SG CYS G 585 " pdb="ZN ZN G 806 " - pdb=" SG CYS G 578 " pdb="ZN ZN G 806 " - pdb=" SG CYS G 590 " pdb="ZN ZN G 806 " - pdb=" SG CYS G 565 " pdb=" ZN G 807 " pdb="ZN ZN G 807 " - pdb=" ND1 HIS G 297 " pdb="ZN ZN G 807 " - pdb=" SG CYS G 294 " pdb="ZN ZN G 807 " - pdb=" SG CYS G 289 " pdb="ZN ZN G 807 " - pdb=" SG CYS G 286 " Number of angles added : 72 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7092 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 46 sheets defined 24.6% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'B' and resid 80 through 105 removed outlier: 3.546A pdb=" N GLU B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Proline residue: B 93 - end of helix removed outlier: 3.535A pdb=" N LEU B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 5.599A pdb=" N THR B 116 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR B 117 " --> pdb=" O THR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 459 through 470 Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.587A pdb=" N GLU B 542 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 544 " --> pdb=" O SER B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 579 Processing helix chain 'B' and resid 589 through 602 Processing helix chain 'B' and resid 607 through 625 Processing helix chain 'B' and resid 628 through 643 removed outlier: 3.679A pdb=" N ASN B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS B 634 " --> pdb=" O ASN B 630 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET B 637 " --> pdb=" O ASN B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 651 Processing helix chain 'B' and resid 652 through 666 Processing helix chain 'B' and resid 670 through 689 Processing helix chain 'C' and resid 127 through 131 removed outlier: 3.587A pdb=" N GLY C 130 " --> pdb=" O HIS C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'D' and resid 4 through 27 Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.210A pdb=" N TYR D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 61 Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 239 through 250 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 278 through 284 Processing helix chain 'A' and resid 335 through 345 Processing helix chain 'A' and resid 438 through 453 Processing helix chain 'A' and resid 455 through 463 Processing helix chain 'A' and resid 467 through 479 Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 653 through 664 Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 730 through 734 removed outlier: 4.258A pdb=" N TYR A 733 " --> pdb=" O ASP A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.806A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 149 Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.555A pdb=" N ARG E 164 " --> pdb=" O PHE E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 210 Processing helix chain 'F' and resid 255 through 262 Processing helix chain 'F' and resid 270 through 272 No H-bonds generated for 'chain 'F' and resid 270 through 272' Processing helix chain 'F' and resid 276 through 281 Processing helix chain 'H' and resid 81 through 105 Proline residue: H 93 - end of helix removed outlier: 3.614A pdb=" N LEU H 105 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 removed outlier: 5.878A pdb=" N THR H 116 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR H 117 " --> pdb=" O THR H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 459 through 470 Processing helix chain 'H' and resid 502 through 508 removed outlier: 3.555A pdb=" N ARG H 508 " --> pdb=" O ASP H 505 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 544 removed outlier: 3.538A pdb=" N GLU H 542 " --> pdb=" O SER H 539 " (cutoff:3.500A) Processing helix chain 'H' and resid 589 through 602 Processing helix chain 'H' and resid 607 through 625 Processing helix chain 'H' and resid 628 through 643 removed outlier: 3.813A pdb=" N ASN H 633 " --> pdb=" O ASP H 629 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS H 634 " --> pdb=" O ASN H 630 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET H 637 " --> pdb=" O ASN H 633 " (cutoff:3.500A) Processing helix chain 'H' and resid 643 through 651 Processing helix chain 'H' and resid 652 through 666 Processing helix chain 'H' and resid 670 through 689 Processing helix chain 'I' and resid 127 through 131 removed outlier: 3.611A pdb=" N GLY I 130 " --> pdb=" O HIS I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 279 Processing helix chain 'J' and resid 4 through 27 Processing helix chain 'J' and resid 348 through 350 No H-bonds generated for 'chain 'J' and resid 348 through 350' Processing helix chain 'J' and resid 355 through 362 Processing helix chain 'J' and resid 406 through 409 Processing helix chain 'G' and resid 23 through 61 Processing helix chain 'G' and resid 168 through 178 Processing helix chain 'G' and resid 223 through 231 Processing helix chain 'G' and resid 239 through 250 Processing helix chain 'G' and resid 273 through 278 Processing helix chain 'G' and resid 278 through 284 Processing helix chain 'G' and resid 335 through 345 Processing helix chain 'G' and resid 438 through 453 Processing helix chain 'G' and resid 455 through 463 Processing helix chain 'G' and resid 467 through 479 Processing helix chain 'G' and resid 539 through 544 Processing helix chain 'G' and resid 576 through 581 Processing helix chain 'G' and resid 609 through 614 Processing helix chain 'G' and resid 652 through 664 Processing helix chain 'G' and resid 688 through 691 Processing helix chain 'G' and resid 730 through 734 removed outlier: 4.120A pdb=" N TYR G 733 " --> pdb=" O ASP G 730 " (cutoff:3.500A) Processing helix chain 'G' and resid 737 through 742 removed outlier: 4.006A pdb=" N TYR G 741 " --> pdb=" O ASP G 737 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 151 Processing helix chain 'K' and resid 159 through 164 Processing helix chain 'L' and resid 192 through 209 Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 270 through 272 No H-bonds generated for 'chain 'L' and resid 270 through 272' Processing helix chain 'L' and resid 276 through 281 Processing sheet with id=AA1, first strand: chain 'B' and resid 163 through 164 removed outlier: 3.502A pdb=" N GLU B 316 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS F 229 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE F 227 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL F 226 " --> pdb=" O HIS F 242 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N HIS F 242 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL F 252 " --> pdb=" O LEU F 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 233 removed outlier: 3.647A pdb=" N THR B 358 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 316 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS F 229 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE F 227 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 203 through 206 removed outlier: 3.545A pdb=" N SER B 247 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 438 through 441 removed outlier: 6.302A pdb=" N PHE B 429 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL B 489 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN B 431 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE B 491 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N LEU B 433 " --> pdb=" O ILE B 491 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 557 through 560 removed outlier: 3.832A pdb=" N TYR B 557 " --> pdb=" O ILE B 528 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL D 35 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 34 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 82 through 87 removed outlier: 6.953A pdb=" N ARG C 436 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER C 87 " --> pdb=" O ILE C 434 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE C 434 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 415 " --> pdb=" O VAL C 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 96 through 101 removed outlier: 4.129A pdb=" N LEU C 111 " --> pdb=" O CYS C 126 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 121 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N SER C 137 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU C 123 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N LYS A 99 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER C 137 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.537A pdb=" N ALA C 166 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS C 184 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN C 176 " --> pdb=" O CYS C 182 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N CYS C 182 " --> pdb=" O ASN C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 193 through 198 removed outlier: 6.412A pdb=" N LEU C 215 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE C 228 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 217 " --> pdb=" O VAL C 226 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 241 through 244 Processing sheet with id=AB2, first strand: chain 'C' and resid 309 through 315 removed outlier: 3.976A pdb=" N CYS C 311 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER C 323 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS C 332 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE C 352 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 369 through 370 Processing sheet with id=AB4, first strand: chain 'D' and resid 47 through 54 removed outlier: 3.618A pdb=" N GLN D 48 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG D 65 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASP D 52 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE D 63 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 77 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 121 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N SER D 83 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE D 117 " --> pdb=" O SER D 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 139 through 143 Processing sheet with id=AB6, first strand: chain 'D' and resid 184 through 185 Processing sheet with id=AB7, first strand: chain 'D' and resid 230 through 235 Processing sheet with id=AB8, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AB9, first strand: chain 'D' and resid 320 through 325 removed outlier: 5.779A pdb=" N ASP D 346 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU D 366 " --> pdb=" O ASP D 346 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 82 through 85 Processing sheet with id=AC2, first strand: chain 'A' and resid 114 through 115 removed outlier: 5.545A pdb=" N SER A 114 " --> pdb=" O GLY A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 120 through 121 removed outlier: 6.252A pdb=" N PHE A 120 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N SER A 652 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 619 through 623 Processing sheet with id=AC5, first strand: chain 'A' and resid 642 through 645 removed outlier: 6.901A pdb=" N ILE A 715 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU A 645 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A 713 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 163 through 164 removed outlier: 3.742A pdb=" N GLU H 316 " --> pdb=" O LYS L 229 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS L 229 " --> pdb=" O GLU H 316 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE L 227 " --> pdb=" O ALA H 318 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU L 240 " --> pdb=" O ILE L 227 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 232 through 233 removed outlier: 3.742A pdb=" N GLU H 316 " --> pdb=" O LYS L 229 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS L 229 " --> pdb=" O GLU H 316 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE L 227 " --> pdb=" O ALA H 318 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 203 through 206 removed outlier: 3.625A pdb=" N SER H 247 " --> pdb=" O VAL H 191 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 438 through 443 removed outlier: 6.266A pdb=" N PHE H 429 " --> pdb=" O ILE H 487 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL H 489 " --> pdb=" O PHE H 429 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N GLN H 431 " --> pdb=" O VAL H 489 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ILE H 491 " --> pdb=" O GLN H 431 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N LEU H 433 " --> pdb=" O ILE H 491 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 557 through 560 removed outlier: 3.723A pdb=" N TYR H 557 " --> pdb=" O ILE H 528 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL J 35 " --> pdb=" O LEU H 529 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU J 34 " --> pdb=" O GLN J 403 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE J 398 " --> pdb=" O SER J 394 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 82 through 87 removed outlier: 7.015A pdb=" N ARG I 436 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER I 87 " --> pdb=" O ILE I 434 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE I 434 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN I 415 " --> pdb=" O VAL I 428 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 96 through 101 removed outlier: 6.727A pdb=" N VAL I 116 " --> pdb=" O PHE I 97 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL I 99 " --> pdb=" O ALA I 114 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA I 114 " --> pdb=" O VAL I 99 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N PHE I 101 " --> pdb=" O VAL I 112 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL I 112 " --> pdb=" O PHE I 101 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU I 111 " --> pdb=" O CYS I 126 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN I 136 " --> pdb=" O LEU I 123 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU I 125 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU I 134 " --> pdb=" O GLU I 125 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 149 through 154 removed outlier: 3.507A pdb=" N LYS I 184 " --> pdb=" O ILE I 174 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN I 176 " --> pdb=" O CYS I 182 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N CYS I 182 " --> pdb=" O ASN I 176 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 193 through 198 removed outlier: 6.420A pdb=" N LEU I 215 " --> pdb=" O ILE I 228 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE I 228 " --> pdb=" O LEU I 215 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU I 217 " --> pdb=" O VAL I 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 241 through 244 Processing sheet with id=AD7, first strand: chain 'I' and resid 309 through 315 removed outlier: 3.894A pdb=" N CYS I 311 " --> pdb=" O LYS I 322 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER I 323 " --> pdb=" O ALA I 327 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA I 327 " --> pdb=" O SER I 323 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS I 332 " --> pdb=" O ILE I 352 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE I 352 " --> pdb=" O LYS I 332 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 369 through 370 Processing sheet with id=AD9, first strand: chain 'J' and resid 49 through 54 removed outlier: 4.763A pdb=" N ARG J 65 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP J 52 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE J 63 " --> pdb=" O ASP J 52 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASN J 77 " --> pdb=" O ASN J 122 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASN J 122 " --> pdb=" O ASN J 77 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU J 79 " --> pdb=" O LYS J 120 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS J 120 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE J 81 " --> pdb=" O GLU J 118 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 139 through 143 Processing sheet with id=AE2, first strand: chain 'J' and resid 184 through 185 Processing sheet with id=AE3, first strand: chain 'J' and resid 232 through 235 Processing sheet with id=AE4, first strand: chain 'J' and resid 280 through 281 Processing sheet with id=AE5, first strand: chain 'J' and resid 322 through 325 removed outlier: 5.625A pdb=" N ASP J 346 " --> pdb=" O LEU J 366 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU J 366 " --> pdb=" O ASP J 346 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 82 through 85 Processing sheet with id=AE7, first strand: chain 'G' and resid 114 through 115 removed outlier: 5.617A pdb=" N SER G 114 " --> pdb=" O GLY G 686 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 114 through 115 removed outlier: 5.617A pdb=" N SER G 114 " --> pdb=" O GLY G 686 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 619 through 623 Processing sheet with id=AF1, first strand: chain 'G' and resid 642 through 645 removed outlier: 6.803A pdb=" N ILE G 715 " --> pdb=" O ILE G 643 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU G 645 " --> pdb=" O ILE G 713 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE G 713 " --> pdb=" O GLU G 645 " (cutoff:3.500A) 1050 hydrogen bonds defined for protein. 2841 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: 11.63 Time building geometry restraints manager: 8.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 195 1.13 - 1.30: 4197 1.30 - 1.47: 11351 1.47 - 1.64: 10590 1.64 - 1.81: 152 Bond restraints: 26485 Sorted by residual: bond pdb=" C8 G M 14 " pdb=" H8 G M 14 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C6 U M 22 " pdb=" H6 U M 22 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" C6 U M 16 " pdb=" H6 U M 16 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" C6 U M 4 " pdb=" H6 U M 4 " ideal model delta sigma weight residual 0.930 1.090 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" C8 G M 15 " pdb=" H8 G M 15 " ideal model delta sigma weight residual 0.930 1.090 -0.160 2.00e-02 2.50e+03 6.37e+01 ... (remaining 26480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 36259 2.57 - 5.14: 271 5.14 - 7.71: 7 7.71 - 10.28: 1 10.28 - 12.84: 1 Bond angle restraints: 36539 Sorted by residual: angle pdb=" C THR A 310 " pdb=" CA THR A 310 " pdb=" CB THR A 310 " ideal model delta sigma weight residual 116.54 110.18 6.36 1.15e+00 7.56e-01 3.06e+01 angle pdb=" C5' G M 1 " pdb=" O5' G M 1 " pdb="HO5' G M 1 " ideal model delta sigma weight residual 120.00 107.16 12.84 3.00e+00 1.11e-01 1.83e+01 angle pdb=" N ILE I 265 " pdb=" CA ILE I 265 " pdb=" C ILE I 265 " ideal model delta sigma weight residual 112.29 108.34 3.95 9.40e-01 1.13e+00 1.77e+01 angle pdb=" O4' G M 21 " pdb=" C4' G M 21 " pdb=" C3' G M 21 " ideal model delta sigma weight residual 104.00 107.99 -3.99 1.00e+00 1.00e+00 1.59e+01 angle pdb=" CA ASN A 434 " pdb=" CB ASN A 434 " pdb=" CG ASN A 434 " ideal model delta sigma weight residual 112.60 116.59 -3.99 1.00e+00 1.00e+00 1.59e+01 ... (remaining 36534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.99: 14846 29.99 - 59.98: 542 59.98 - 89.97: 49 89.97 - 119.96: 1 119.96 - 149.95: 2 Dihedral angle restraints: 15440 sinusoidal: 4614 harmonic: 10826 Sorted by residual: dihedral pdb=" C5' G M 7 " pdb=" C4' G M 7 " pdb=" C3' G M 7 " pdb=" O3' G M 7 " ideal model delta sinusoidal sigma weight residual 147.00 100.36 46.64 1 8.00e+00 1.56e-02 4.70e+01 dihedral pdb=" O4' G M 7 " pdb=" C4' G M 7 " pdb=" C3' G M 7 " pdb=" C2' G M 7 " ideal model delta sinusoidal sigma weight residual 24.00 -19.31 43.31 1 8.00e+00 1.56e-02 4.08e+01 dihedral pdb=" C3' G M 7 " pdb=" C4' G M 7 " pdb=" O4' G M 7 " pdb=" C1' G M 7 " ideal model delta sinusoidal sigma weight residual -2.00 35.87 -37.87 1 8.00e+00 1.56e-02 3.16e+01 ... (remaining 15437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3476 0.057 - 0.114: 578 0.114 - 0.170: 43 0.170 - 0.227: 5 0.227 - 0.284: 12 Chirality restraints: 4114 Sorted by residual: chirality pdb=" C3' G M 3 " pdb=" C4' G M 3 " pdb=" O3' G M 3 " pdb=" C2' G M 3 " both_signs ideal model delta sigma weight residual False -2.48 -2.76 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C3' G M 15 " pdb=" C4' G M 15 " pdb=" O3' G M 15 " pdb=" C2' G M 15 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ASN A 434 " pdb=" N ASN A 434 " pdb=" C ASN A 434 " pdb=" CB ASN A 434 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 4111 not shown) Planarity restraints: 4720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A M 18 " 0.076 2.00e-02 2.50e+03 3.77e-02 4.62e+01 pdb=" N9 A M 18 " 0.002 2.00e-02 2.50e+03 pdb=" C8 A M 18 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A M 18 " 0.007 2.00e-02 2.50e+03 pdb=" C5 A M 18 " 0.016 2.00e-02 2.50e+03 pdb=" C6 A M 18 " 0.016 2.00e-02 2.50e+03 pdb=" N6 A M 18 " 0.026 2.00e-02 2.50e+03 pdb=" N1 A M 18 " 0.009 2.00e-02 2.50e+03 pdb=" C2 A M 18 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A M 18 " -0.000 2.00e-02 2.50e+03 pdb=" C4 A M 18 " 0.008 2.00e-02 2.50e+03 pdb=" H8 A M 18 " -0.085 2.00e-02 2.50e+03 pdb=" H2 A M 18 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G M 1 " 0.081 2.00e-02 2.50e+03 2.98e-02 3.10e+01 pdb=" N9 G M 1 " -0.007 2.00e-02 2.50e+03 pdb=" C8 G M 1 " -0.011 2.00e-02 2.50e+03 pdb=" N7 G M 1 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G M 1 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G M 1 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G M 1 " 0.037 2.00e-02 2.50e+03 pdb=" N1 G M 1 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G M 1 " -0.013 2.00e-02 2.50e+03 pdb=" N2 G M 1 " -0.029 2.00e-02 2.50e+03 pdb=" N3 G M 1 " -0.014 2.00e-02 2.50e+03 pdb=" C4 G M 1 " -0.009 2.00e-02 2.50e+03 pdb=" H8 G M 1 " -0.052 2.00e-02 2.50e+03 pdb=" H1 G M 1 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A M 6 " 0.059 2.00e-02 2.50e+03 2.98e-02 2.90e+01 pdb=" N9 A M 6 " 0.002 2.00e-02 2.50e+03 pdb=" C8 A M 6 " -0.007 2.00e-02 2.50e+03 pdb=" N7 A M 6 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A M 6 " 0.013 2.00e-02 2.50e+03 pdb=" C6 A M 6 " 0.013 2.00e-02 2.50e+03 pdb=" N6 A M 6 " 0.020 2.00e-02 2.50e+03 pdb=" N1 A M 6 " 0.008 2.00e-02 2.50e+03 pdb=" C2 A M 6 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A M 6 " 0.001 2.00e-02 2.50e+03 pdb=" C4 A M 6 " 0.008 2.00e-02 2.50e+03 pdb=" H8 A M 6 " -0.067 2.00e-02 2.50e+03 pdb=" H2 A M 6 " -0.052 2.00e-02 2.50e+03 ... (remaining 4717 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 76 2.08 - 2.71: 1485 2.71 - 3.34: 31650 3.34 - 3.97: 50973 3.97 - 4.60: 72674 Nonbonded interactions: 156858 Sorted by model distance: nonbonded pdb="HO2' G M 20 " pdb=" O5' G M 21 " model vdw 1.454 2.450 nonbonded pdb="HO2' G M 8 " pdb=" O5' G M 9 " model vdw 1.486 2.450 nonbonded pdb=" O ASP C 303 " pdb=" OD1 ASP C 303 " model vdw 1.508 2.800 nonbonded pdb="HO2' G M 14 " pdb=" O4' G M 15 " model vdw 1.537 2.450 nonbonded pdb=" SD MET I 366 " pdb=" O ILE I 413 " model vdw 1.582 3.200 ... (remaining 156853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'L' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.810 Extract box with map and model: 0.940 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 67.400 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 : 0.003 0.246 26348 Z= 0.183 Angle : 0.583 33.161 36168 Z= 0.321 Chirality : 0.044 0.284 4114 Planarity : 0.003 0.036 4706 Dihedral : 15.124 149.954 8306 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.62 % Favored : 93.16 % Rotamer: Outliers : 0.05 % Allowed : 24.56 % Favored : 75.39 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3596 helix: 1.92 (0.19), residues: 802 sheet: -0.63 (0.18), residues: 866 loop : -0.84 (0.15), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP I 331 HIS 0.005 0.001 HIS D 316 PHE 0.014 0.001 PHE B 86 TYR 0.011 0.001 TYR I 308 ARG 0.006 0.000 ARG F 199 Details of bonding type rmsd hydrogen bonds : bond 0.18019 ( 1032) hydrogen bonds : angle 7.72543 ( 2841) metal coordination : bond 0.00523 ( 56) metal coordination : angle 2.45207 ( 72) SS BOND : bond 0.22944 ( 2) SS BOND : angle 24.01724 ( 4) covalent geometry : bond 0.00274 (26290) covalent geometry : angle 0.51474 (36092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.3591 time to fit residues: 69.5247 Evaluate side-chains 101 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 443 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 308 optimal weight: 7.9990 chunk 276 optimal weight: 20.0000 chunk 153 optimal weight: 8.9990 chunk 94 optimal weight: 50.0000 chunk 186 optimal weight: 5.9990 chunk 147 optimal weight: 0.0270 chunk 286 optimal weight: 40.0000 chunk 110 optimal weight: 40.0000 chunk 173 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 331 optimal weight: 7.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 449 HIS C 281 ASN ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN D 311 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS H 504 GLN H 507 HIS H 667 ASN J 176 HIS J 311 HIS J 329 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.045122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.034352 restraints weight = 259094.568| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 4.57 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26348 Z= 0.195 Angle : 0.548 11.641 36168 Z= 0.278 Chirality : 0.041 0.137 4114 Planarity : 0.004 0.039 4706 Dihedral : 9.097 158.254 4143 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.73 % Favored : 92.07 % Rotamer: Outliers : 2.93 % Allowed : 22.88 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3596 helix: 2.17 (0.19), residues: 808 sheet: -0.57 (0.18), residues: 850 loop : -1.04 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 437 HIS 0.007 0.001 HIS D 157 PHE 0.018 0.001 PHE I 289 TYR 0.015 0.001 TYR H 495 ARG 0.005 0.000 ARG I 414 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 1032) hydrogen bonds : angle 5.51901 ( 2841) metal coordination : bond 0.01698 ( 56) metal coordination : angle 4.03846 ( 72) SS BOND : bond 0.00364 ( 2) SS BOND : angle 1.89115 ( 4) covalent geometry : bond 0.00392 (26290) covalent geometry : angle 0.51776 (36092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 99 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 SER cc_start: 0.8847 (t) cc_final: 0.8519 (p) REVERT: D 279 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7348 (pt) REVERT: D 404 MET cc_start: 0.6823 (ttp) cc_final: 0.6614 (ttp) REVERT: A 444 MET cc_start: 0.8111 (tmm) cc_final: 0.7647 (tmm) REVERT: J 377 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8713 (mp) REVERT: G 576 CYS cc_start: 0.8714 (OUTLIER) cc_final: 0.7799 (t) REVERT: K 150 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7539 (mmm160) REVERT: L 190 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.6511 (m-80) outliers start: 56 outliers final: 32 residues processed: 147 average time/residue: 0.4578 time to fit residues: 123.0768 Evaluate side-chains 136 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 3.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain H residue 661 VAL Chi-restraints excluded: chain H residue 663 MET Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain J residue 355 SER Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain J residue 398 ILE Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 297 HIS Chi-restraints excluded: chain G residue 576 CYS Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain K residue 150 ARG Chi-restraints excluded: chain L residue 190 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 288 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 272 optimal weight: 30.0000 chunk 119 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 chunk 324 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 211 optimal weight: 10.0000 chunk 305 optimal weight: 30.0000 chunk 123 optimal weight: 50.0000 chunk 161 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN H 449 HIS ** I 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.044356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.033676 restraints weight = 259914.176| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 4.49 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 26348 Z= 0.180 Angle : 0.508 10.778 36168 Z= 0.255 Chirality : 0.041 0.157 4114 Planarity : 0.003 0.039 4706 Dihedral : 9.076 159.514 4140 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.31 % Favored : 92.49 % Rotamer: Outliers : 3.66 % Allowed : 22.62 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3596 helix: 2.24 (0.19), residues: 806 sheet: -0.75 (0.18), residues: 868 loop : -1.09 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 205 HIS 0.005 0.001 HIS H 624 PHE 0.016 0.001 PHE I 289 TYR 0.027 0.001 TYR H 117 ARG 0.005 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 1032) hydrogen bonds : angle 4.99717 ( 2841) metal coordination : bond 0.01684 ( 56) metal coordination : angle 4.26836 ( 72) SS BOND : bond 0.00074 ( 2) SS BOND : angle 1.17148 ( 4) covalent geometry : bond 0.00366 (26290) covalent geometry : angle 0.47180 (36092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 96 time to evaluate : 2.770 Fit side-chains revert: symmetry clash REVERT: C 415 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: D 279 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7211 (pt) REVERT: A 444 MET cc_start: 0.8333 (tmm) cc_final: 0.7947 (tmm) REVERT: A 539 CYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8046 (t) REVERT: A 576 CYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7407 (t) REVERT: A 676 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7189 (m-40) REVERT: G 444 MET cc_start: 0.8075 (tmm) cc_final: 0.7839 (tmm) REVERT: G 576 CYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7841 (t) REVERT: L 190 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.6516 (m-80) outliers start: 70 outliers final: 44 residues processed: 159 average time/residue: 0.3024 time to fit residues: 84.1540 Evaluate side-chains 146 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 95 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 314 TRP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 415 GLN Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain H residue 86 PHE Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 514 PHE Chi-restraints excluded: chain H residue 605 ASP Chi-restraints excluded: chain H residue 663 MET Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 398 ILE Chi-restraints excluded: chain J residue 409 TYR Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 297 HIS Chi-restraints excluded: chain G residue 566 ARG Chi-restraints excluded: chain G residue 576 CYS Chi-restraints excluded: chain G residue 616 LYS Chi-restraints excluded: chain K residue 150 ARG Chi-restraints excluded: chain L residue 190 PHE Chi-restraints excluded: chain L residue 267 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 68 optimal weight: 6.9990 chunk 321 optimal weight: 0.0030 chunk 135 optimal weight: 8.9990 chunk 341 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 305 optimal weight: 2.9990 chunk 308 optimal weight: 6.9990 overall best weight: 4.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN D 78 HIS ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 382 GLN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.044195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.033492 restraints weight = 264650.360| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 4.50 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26348 Z= 0.177 Angle : 0.504 10.979 36168 Z= 0.250 Chirality : 0.040 0.134 4114 Planarity : 0.003 0.041 4706 Dihedral : 9.045 161.670 4140 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.09 % Favored : 91.74 % Rotamer: Outliers : 3.81 % Allowed : 23.35 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3596 helix: 2.18 (0.19), residues: 814 sheet: -0.71 (0.18), residues: 848 loop : -1.19 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 205 HIS 0.005 0.001 HIS H 624 PHE 0.014 0.001 PHE I 289 TYR 0.013 0.001 TYR H 495 ARG 0.006 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 1032) hydrogen bonds : angle 4.84005 ( 2841) metal coordination : bond 0.01508 ( 56) metal coordination : angle 4.41004 ( 72) SS BOND : bond 0.00350 ( 2) SS BOND : angle 0.53301 ( 4) covalent geometry : bond 0.00357 (26290) covalent geometry : angle 0.46409 (36092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 96 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 279 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7248 (pt) REVERT: D 398 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8812 (tt) REVERT: A 444 MET cc_start: 0.8194 (tmm) cc_final: 0.7801 (tmm) REVERT: A 539 CYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8236 (t) REVERT: A 576 CYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7329 (t) REVERT: G 444 MET cc_start: 0.7952 (tmm) cc_final: 0.7743 (tmm) REVERT: G 566 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8354 (mtp-110) REVERT: G 576 CYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7659 (t) REVERT: K 150 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8382 (mmp80) REVERT: L 190 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.6556 (m-80) outliers start: 73 outliers final: 56 residues processed: 161 average time/residue: 0.2926 time to fit residues: 84.0518 Evaluate side-chains 160 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 96 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 314 TRP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain H residue 86 PHE Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 514 PHE Chi-restraints excluded: chain H residue 572 LEU Chi-restraints excluded: chain H residue 600 ILE Chi-restraints excluded: chain H residue 605 ASP Chi-restraints excluded: chain H residue 661 VAL Chi-restraints excluded: chain H residue 663 MET Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 213 HIS Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain J residue 398 ILE Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 69 HIS Chi-restraints excluded: chain G residue 297 HIS Chi-restraints excluded: chain G residue 459 ILE Chi-restraints excluded: chain G residue 566 ARG Chi-restraints excluded: chain G residue 573 THR Chi-restraints excluded: chain G residue 576 CYS Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain K residue 150 ARG Chi-restraints excluded: chain L residue 190 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 296 optimal weight: 10.0000 chunk 194 optimal weight: 50.0000 chunk 210 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 273 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 HIS ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.043992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.033357 restraints weight = 263637.380| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 4.45 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26348 Z= 0.168 Angle : 0.493 10.874 36168 Z= 0.245 Chirality : 0.040 0.130 4114 Planarity : 0.003 0.039 4706 Dihedral : 8.986 162.379 4140 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 29.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.95 % Favored : 91.88 % Rotamer: Outliers : 4.96 % Allowed : 23.09 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3596 helix: 2.19 (0.19), residues: 816 sheet: -0.76 (0.18), residues: 852 loop : -1.19 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 205 HIS 0.006 0.001 HIS G 530 PHE 0.012 0.001 PHE B 90 TYR 0.011 0.001 TYR H 643 ARG 0.005 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.03122 ( 1032) hydrogen bonds : angle 4.69035 ( 2841) metal coordination : bond 0.01542 ( 56) metal coordination : angle 4.41074 ( 72) SS BOND : bond 0.00359 ( 2) SS BOND : angle 0.34379 ( 4) covalent geometry : bond 0.00337 (26290) covalent geometry : angle 0.45285 (36092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 95 time to evaluate : 3.312 Fit side-chains revert: symmetry clash REVERT: C 252 MET cc_start: 0.8520 (tpt) cc_final: 0.8314 (tpt) REVERT: D 279 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7142 (pt) REVERT: D 398 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8782 (tt) REVERT: A 444 MET cc_start: 0.8162 (tmm) cc_final: 0.7768 (tmm) REVERT: A 539 CYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8365 (t) REVERT: A 576 CYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7233 (t) REVERT: G 444 MET cc_start: 0.8049 (tmm) cc_final: 0.7847 (tmm) REVERT: G 566 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8347 (mtp-110) REVERT: G 576 CYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7621 (t) outliers start: 95 outliers final: 69 residues processed: 182 average time/residue: 0.3208 time to fit residues: 101.8548 Evaluate side-chains 170 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 95 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 314 TRP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain H residue 86 PHE Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 514 PHE Chi-restraints excluded: chain H residue 572 LEU Chi-restraints excluded: chain H residue 600 ILE Chi-restraints excluded: chain H residue 605 ASP Chi-restraints excluded: chain H residue 663 MET Chi-restraints excluded: chain I residue 213 HIS Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain J residue 398 ILE Chi-restraints excluded: chain J residue 409 TYR Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 69 HIS Chi-restraints excluded: chain G residue 286 CYS Chi-restraints excluded: chain G residue 297 HIS Chi-restraints excluded: chain G residue 566 ARG Chi-restraints excluded: chain G residue 573 THR Chi-restraints excluded: chain G residue 576 CYS Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain G residue 616 LYS Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 150 ARG Chi-restraints excluded: chain L residue 190 PHE Chi-restraints excluded: chain L residue 267 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 225 optimal weight: 0.4980 chunk 217 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 chunk 338 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 327 optimal weight: 10.0000 chunk 310 optimal weight: 0.8980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 HIS ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** H 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.044064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.033461 restraints weight = 263210.205| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 4.46 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26348 Z= 0.143 Angle : 0.467 10.235 36168 Z= 0.230 Chirality : 0.040 0.130 4114 Planarity : 0.003 0.038 4706 Dihedral : 8.933 163.005 4140 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 29.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.04 % Favored : 91.80 % Rotamer: Outliers : 4.44 % Allowed : 23.88 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 3596 helix: 2.33 (0.19), residues: 818 sheet: -0.71 (0.18), residues: 850 loop : -1.15 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 205 HIS 0.004 0.001 HIS G 530 PHE 0.009 0.001 PHE I 289 TYR 0.012 0.001 TYR C 244 ARG 0.006 0.000 ARG J 172 Details of bonding type rmsd hydrogen bonds : bond 0.02910 ( 1032) hydrogen bonds : angle 4.56999 ( 2841) metal coordination : bond 0.01305 ( 56) metal coordination : angle 4.20197 ( 72) SS BOND : bond 0.00346 ( 2) SS BOND : angle 0.33516 ( 4) covalent geometry : bond 0.00289 (26290) covalent geometry : angle 0.42788 (36092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 94 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.8516 (tpt) cc_final: 0.8313 (tpt) REVERT: D 279 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7130 (pt) REVERT: D 398 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8741 (tt) REVERT: A 444 MET cc_start: 0.8222 (tmm) cc_final: 0.7827 (tmm) REVERT: A 539 CYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8473 (t) REVERT: A 576 CYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7154 (t) REVERT: I 376 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7730 (ptp) REVERT: G 444 MET cc_start: 0.8061 (tmm) cc_final: 0.7860 (tmm) REVERT: G 566 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8327 (mtp-110) outliers start: 85 outliers final: 76 residues processed: 171 average time/residue: 0.3036 time to fit residues: 92.1429 Evaluate side-chains 176 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 94 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 314 TRP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain H residue 86 PHE Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 514 PHE Chi-restraints excluded: chain H residue 600 ILE Chi-restraints excluded: chain H residue 605 ASP Chi-restraints excluded: chain H residue 661 VAL Chi-restraints excluded: chain H residue 663 MET Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 213 HIS Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 352 ILE Chi-restraints excluded: chain I residue 376 MET Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain J residue 108 PHE Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain J residue 398 ILE Chi-restraints excluded: chain J residue 409 TYR Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 286 CYS Chi-restraints excluded: chain G residue 297 HIS Chi-restraints excluded: chain G residue 459 ILE Chi-restraints excluded: chain G residue 566 ARG Chi-restraints excluded: chain G residue 573 THR Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain K residue 150 ARG Chi-restraints excluded: chain L residue 190 PHE Chi-restraints excluded: chain L residue 267 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 134 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 344 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 chunk 352 optimal weight: 2.9990 chunk 131 optimal weight: 40.0000 chunk 189 optimal weight: 50.0000 chunk 311 optimal weight: 50.0000 chunk 184 optimal weight: 0.3980 chunk 289 optimal weight: 20.0000 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** H 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.043627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.033058 restraints weight = 266169.394| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 4.47 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26348 Z= 0.207 Angle : 0.530 10.375 36168 Z= 0.263 Chirality : 0.041 0.132 4114 Planarity : 0.003 0.040 4706 Dihedral : 9.015 163.913 4140 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 33.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.51 % Favored : 90.29 % Rotamer: Outliers : 5.17 % Allowed : 23.62 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3596 helix: 2.00 (0.19), residues: 818 sheet: -0.74 (0.18), residues: 834 loop : -1.29 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 205 HIS 0.007 0.001 HIS B 624 PHE 0.013 0.001 PHE A 456 TYR 0.015 0.001 TYR C 244 ARG 0.003 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 1032) hydrogen bonds : angle 4.78284 ( 2841) metal coordination : bond 0.01860 ( 56) metal coordination : angle 4.48152 ( 72) SS BOND : bond 0.00414 ( 2) SS BOND : angle 0.23918 ( 4) covalent geometry : bond 0.00417 (26290) covalent geometry : angle 0.49081 (36092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 95 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.8532 (tpt) cc_final: 0.8313 (tpt) REVERT: D 279 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7037 (pt) REVERT: D 398 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8726 (tt) REVERT: A 444 MET cc_start: 0.8317 (tmm) cc_final: 0.7913 (tmm) REVERT: A 539 CYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8590 (t) REVERT: A 576 CYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7257 (t) REVERT: I 376 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7776 (ptp) REVERT: G 566 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8274 (mtp-110) REVERT: G 576 CYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7718 (t) outliers start: 99 outliers final: 81 residues processed: 185 average time/residue: 0.3227 time to fit residues: 105.9556 Evaluate side-chains 182 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 94 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 314 TRP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain H residue 86 PHE Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 514 PHE Chi-restraints excluded: chain H residue 600 ILE Chi-restraints excluded: chain H residue 605 ASP Chi-restraints excluded: chain H residue 663 MET Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 213 HIS Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 237 ASP Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 376 MET Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain J residue 108 PHE Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain J residue 398 ILE Chi-restraints excluded: chain J residue 409 TYR Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 286 CYS Chi-restraints excluded: chain G residue 297 HIS Chi-restraints excluded: chain G residue 459 ILE Chi-restraints excluded: chain G residue 566 ARG Chi-restraints excluded: chain G residue 573 THR Chi-restraints excluded: chain G residue 576 CYS Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain G residue 616 LYS Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 150 ARG Chi-restraints excluded: chain L residue 190 PHE Chi-restraints excluded: chain L residue 267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 320 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 352 optimal weight: 0.9980 chunk 138 optimal weight: 50.0000 chunk 295 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 98 optimal weight: 50.0000 chunk 56 optimal weight: 9.9990 chunk 121 optimal weight: 0.3980 chunk 241 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 HIS ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** H 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.044009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.033425 restraints weight = 261789.936| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 4.47 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26348 Z= 0.120 Angle : 0.450 8.720 36168 Z= 0.223 Chirality : 0.040 0.130 4114 Planarity : 0.003 0.038 4706 Dihedral : 8.913 163.740 4140 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 30.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.76 % Favored : 92.07 % Rotamer: Outliers : 3.87 % Allowed : 24.97 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3596 helix: 2.39 (0.19), residues: 816 sheet: -0.65 (0.18), residues: 850 loop : -1.16 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 243 HIS 0.004 0.001 HIS G 297 PHE 0.008 0.001 PHE H 86 TYR 0.010 0.001 TYR H 495 ARG 0.003 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.02814 ( 1032) hydrogen bonds : angle 4.48936 ( 2841) metal coordination : bond 0.01156 ( 56) metal coordination : angle 3.96420 ( 72) SS BOND : bond 0.00312 ( 2) SS BOND : angle 0.32312 ( 4) covalent geometry : bond 0.00244 (26290) covalent geometry : angle 0.41449 (36092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 96 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8955 (p) REVERT: D 279 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7085 (pt) REVERT: D 398 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8671 (tt) REVERT: A 444 MET cc_start: 0.8301 (tmm) cc_final: 0.7946 (tmm) REVERT: A 539 CYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8510 (t) REVERT: A 576 CYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7104 (t) REVERT: I 376 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7801 (ptp) REVERT: G 566 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8320 (mtp-110) outliers start: 74 outliers final: 58 residues processed: 164 average time/residue: 0.3040 time to fit residues: 88.7263 Evaluate side-chains 161 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 96 time to evaluate : 3.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain H residue 86 PHE Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 514 PHE Chi-restraints excluded: chain H residue 600 ILE Chi-restraints excluded: chain H residue 605 ASP Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 213 HIS Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 376 MET Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain J residue 108 PHE Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 69 HIS Chi-restraints excluded: chain G residue 286 CYS Chi-restraints excluded: chain G residue 297 HIS Chi-restraints excluded: chain G residue 459 ILE Chi-restraints excluded: chain G residue 566 ARG Chi-restraints excluded: chain G residue 573 THR Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 150 ARG Chi-restraints excluded: chain L residue 190 PHE Chi-restraints excluded: chain L residue 267 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 179 optimal weight: 30.0000 chunk 167 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 287 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 309 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 168 optimal weight: 4.9990 chunk 233 optimal weight: 7.9990 chunk 257 optimal weight: 0.0570 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 HIS ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.043633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.033108 restraints weight = 264921.581| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.44 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26348 Z= 0.184 Angle : 0.500 9.838 36168 Z= 0.249 Chirality : 0.040 0.132 4114 Planarity : 0.003 0.039 4706 Dihedral : 8.972 164.269 4140 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 34.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.65 % Favored : 90.18 % Rotamer: Outliers : 3.97 % Allowed : 24.87 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3596 helix: 2.17 (0.19), residues: 816 sheet: -0.73 (0.19), residues: 822 loop : -1.27 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 205 HIS 0.005 0.001 HIS G 297 PHE 0.011 0.001 PHE A 456 TYR 0.014 0.001 TYR C 244 ARG 0.003 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 1032) hydrogen bonds : angle 4.64527 ( 2841) metal coordination : bond 0.01681 ( 56) metal coordination : angle 4.17289 ( 72) SS BOND : bond 0.00427 ( 2) SS BOND : angle 0.26667 ( 4) covalent geometry : bond 0.00371 (26290) covalent geometry : angle 0.46437 (36092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 95 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 279 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7017 (pt) REVERT: D 398 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8675 (tt) REVERT: A 444 MET cc_start: 0.8338 (tmm) cc_final: 0.7936 (tmm) REVERT: A 539 CYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8601 (t) REVERT: A 576 CYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7222 (t) REVERT: I 376 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7784 (ptp) REVERT: G 566 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8383 (mtp-110) outliers start: 76 outliers final: 66 residues processed: 166 average time/residue: 0.3049 time to fit residues: 89.2810 Evaluate side-chains 167 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 95 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 314 TRP Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain H residue 86 PHE Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 514 PHE Chi-restraints excluded: chain H residue 600 ILE Chi-restraints excluded: chain H residue 605 ASP Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 213 HIS Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 237 ASP Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 376 MET Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain J residue 108 PHE Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain J residue 398 ILE Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 286 CYS Chi-restraints excluded: chain G residue 297 HIS Chi-restraints excluded: chain G residue 459 ILE Chi-restraints excluded: chain G residue 566 ARG Chi-restraints excluded: chain G residue 573 THR Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 150 ARG Chi-restraints excluded: chain L residue 190 PHE Chi-restraints excluded: chain L residue 267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 209 optimal weight: 0.0670 chunk 356 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 113 optimal weight: 0.0980 chunk 112 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 169 optimal weight: 0.8980 chunk 207 optimal weight: 0.0970 chunk 144 optimal weight: 10.0000 chunk 277 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 overall best weight: 1.2318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 HIS ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 667 ASN ** J 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.044245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.033713 restraints weight = 260176.506| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 4.44 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26348 Z= 0.079 Angle : 0.419 7.671 36168 Z= 0.208 Chirality : 0.039 0.133 4114 Planarity : 0.003 0.037 4706 Dihedral : 8.838 163.845 4140 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 30.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.12 % Favored : 92.71 % Rotamer: Outliers : 2.04 % Allowed : 26.91 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3596 helix: 2.61 (0.19), residues: 818 sheet: -0.58 (0.18), residues: 846 loop : -1.05 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 255 HIS 0.004 0.000 HIS C 189 PHE 0.008 0.001 PHE H 86 TYR 0.009 0.001 TYR H 495 ARG 0.002 0.000 ARG I 439 Details of bonding type rmsd hydrogen bonds : bond 0.02585 ( 1032) hydrogen bonds : angle 4.27630 ( 2841) metal coordination : bond 0.00784 ( 56) metal coordination : angle 3.47559 ( 72) SS BOND : bond 0.00254 ( 2) SS BOND : angle 0.40885 ( 4) covalent geometry : bond 0.00164 (26290) covalent geometry : angle 0.38940 (36092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 279 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7099 (pt) REVERT: A 444 MET cc_start: 0.8279 (tmm) cc_final: 0.7926 (tmm) REVERT: A 539 CYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8510 (t) REVERT: G 566 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8255 (mtp-110) outliers start: 39 outliers final: 33 residues processed: 133 average time/residue: 0.3131 time to fit residues: 72.9698 Evaluate side-chains 132 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain H residue 86 PHE Chi-restraints excluded: chain H residue 514 PHE Chi-restraints excluded: chain H residue 600 ILE Chi-restraints excluded: chain H residue 663 MET Chi-restraints excluded: chain I residue 213 HIS Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 286 CYS Chi-restraints excluded: chain G residue 297 HIS Chi-restraints excluded: chain G residue 566 ARG Chi-restraints excluded: chain G residue 573 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 150 ARG Chi-restraints excluded: chain L residue 190 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 327 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 263 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 195 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 323 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 HIS ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.043752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.033242 restraints weight = 264871.046| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 4.46 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26348 Z= 0.159 Angle : 0.473 8.974 36168 Z= 0.236 Chirality : 0.040 0.132 4114 Planarity : 0.003 0.038 4706 Dihedral : 8.887 164.302 4140 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 33.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.93 % Favored : 90.91 % Rotamer: Outliers : 2.51 % Allowed : 26.44 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3596 helix: 2.43 (0.19), residues: 818 sheet: -0.63 (0.19), residues: 832 loop : -1.14 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 205 HIS 0.005 0.001 HIS G 297 PHE 0.010 0.001 PHE A 120 TYR 0.012 0.001 TYR H 495 ARG 0.003 0.000 ARG K 150 Details of bonding type rmsd hydrogen bonds : bond 0.02880 ( 1032) hydrogen bonds : angle 4.42871 ( 2841) metal coordination : bond 0.01490 ( 56) metal coordination : angle 3.76749 ( 72) SS BOND : bond 0.00342 ( 2) SS BOND : angle 0.20777 ( 4) covalent geometry : bond 0.00321 (26290) covalent geometry : angle 0.44264 (36092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16478.46 seconds wall clock time: 285 minutes 49.53 seconds (17149.53 seconds total)