Starting phenix.real_space_refine on Mon Aug 25 10:40:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyh_29578/08_2025/8fyh_29578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyh_29578/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fyh_29578/08_2025/8fyh_29578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyh_29578/08_2025/8fyh_29578.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fyh_29578/08_2025/8fyh_29578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyh_29578/08_2025/8fyh_29578.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'GLU:plan': 24, 'ARG:plan': 9, 'HIS:plan': 6, 'ASN:plan1': 11, 'PHE:plan': 6, 'TYR:plan': 2} 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: {'ASN:plan1': 5, 'GLU:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 7, 'ASP:plan': 14, 'HIS:plan': 2} 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: {'ASP:plan': 15, 'GLU:plan': 20, 'GLN:plan1': 6, 'ASN:plan1': 10, 'ARG:plan': 3, 'HIS:plan': 1} 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: {'GLU:plan': 27, 'TYR:plan': 8, 'ARG:plan': 17, 'GLN:plan1': 13, 'PHE:plan': 6, 'ASN:plan1': 17, 'ASP:plan': 16, 'HIS:plan': 3, 'TRP:plan': 1} 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, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG: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: {'ARG:plan': 6, 'ASP:plan': 5, 'ASN:plan1': 3, 'GLU:plan': 5, 'PHE:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 1} 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, 'GLU:plan': 24, 'ARG:plan': 9, 'HIS:plan': 6, 'ASN:plan1': 11, 'PHE:plan': 6, 'TYR:plan': 2} 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: {'ASN:plan1': 5, 'GLU:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 7, 'ASP:plan': 14, 'HIS:plan': 2} 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: {'ASP:plan': 15, 'GLU:plan': 20, 'GLN:plan1': 6, 'ASN:plan1': 10, 'ARG:plan': 3, 'HIS:plan': 1} 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: {'GLU:plan': 27, 'TYR:plan': 8, 'ARG:plan': 17, 'GLN:plan1': 13, 'PHE:plan': 6, 'ASN:plan1': 17, 'ASP:plan': 16, 'HIS:plan': 3, 'TRP:plan': 1} 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, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG: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: {'ARG:plan': 6, 'ASP:plan': 5, 'ASN:plan1': 3, 'GLU:plan': 5, 'PHE:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 1} 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: 6.43, per 1000 atoms: 0.25 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: 2.31 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.17 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: 5.77 Time building geometry restraints manager: 3.02 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.280 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 29.200 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 : 10.62 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG F 199 TYR 0.011 0.001 TYR I 308 PHE 0.014 0.001 PHE B 86 TRP 0.035 0.001 TRP I 331 HIS 0.005 0.001 HIS D 316 Details of bonding type rmsd covalent geometry : bond 0.00274 (26290) covalent geometry : angle 0.51474 (36092) SS BOND : bond 0.22944 ( 2) SS BOND : angle 24.01724 ( 4) hydrogen bonds : bond 0.18019 ( 1032) hydrogen bonds : angle 7.72543 ( 2841) metal coordination : bond 0.00523 ( 56) metal coordination : angle 2.45207 ( 72) *********************** 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 : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.1358 time to fit residues: 25.6204 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 : 0.933 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.0470 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 5.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN D 311 HIS D 329 ASN ** 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 = 0.3655 r_free = 0.3655 target = 0.045170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.034396 restraints weight = 258943.928| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.59 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 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 = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26348 Z= 0.185 Angle : 0.540 11.510 36168 Z= 0.274 Chirality : 0.041 0.136 4114 Planarity : 0.004 0.038 4706 Dihedral : 9.102 159.135 4143 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.70 % Favored : 92.10 % Rotamer: Outliers : 2.72 % Allowed : 23.20 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.14), residues: 3596 helix: 2.20 (0.19), residues: 808 sheet: -0.57 (0.18), residues: 850 loop : -1.02 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 414 TYR 0.015 0.001 TYR H 495 PHE 0.018 0.001 PHE I 289 TRP 0.015 0.001 TRP I 437 HIS 0.006 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00370 (26290) covalent geometry : angle 0.50949 (36092) SS BOND : bond 0.01279 ( 2) SS BOND : angle 1.43925 ( 4) hydrogen bonds : bond 0.03841 ( 1032) hydrogen bonds : angle 5.49153 ( 2841) metal coordination : bond 0.01589 ( 56) metal coordination : angle 4.05888 ( 72) *********************** 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 151 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 99 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 SER cc_start: 0.8822 (t) cc_final: 0.8501 (p) REVERT: D 279 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7353 (pt) REVERT: A 444 MET cc_start: 0.8111 (tmm) cc_final: 0.7658 (tmm) REVERT: J 377 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8710 (mp) REVERT: G 576 CYS cc_start: 0.8802 (OUTLIER) cc_final: 0.7920 (t) REVERT: K 150 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7538 (mmm160) REVERT: L 190 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.6499 (m-80) outliers start: 52 outliers final: 29 residues processed: 144 average time/residue: 0.1355 time to fit residues: 34.5217 Evaluate side-chains 133 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 355 SER Chi-restraints excluded: chain J residue 377 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 296 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 chunk 262 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 281 optimal weight: 40.0000 chunk 131 optimal weight: 50.0000 chunk 245 optimal weight: 4.9990 chunk 348 optimal weight: 10.0000 chunk 323 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN D 78 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.044011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.033299 restraints weight = 265244.920| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 4.49 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: 0.8157 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26348 Z= 0.226 Angle : 0.579 12.220 36168 Z= 0.289 Chirality : 0.042 0.142 4114 Planarity : 0.004 0.041 4706 Dihedral : 9.192 160.049 4140 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.23 % Favored : 91.57 % Rotamer: Outliers : 4.44 % Allowed : 22.88 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.14), residues: 3596 helix: 1.88 (0.19), residues: 806 sheet: -0.77 (0.18), residues: 840 loop : -1.26 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 566 TYR 0.025 0.002 TYR H 117 PHE 0.022 0.002 PHE I 289 TRP 0.015 0.002 TRP I 263 HIS 0.006 0.001 HIS H 624 Details of bonding type rmsd covalent geometry : bond 0.00458 (26290) covalent geometry : angle 0.53832 (36092) SS BOND : bond 0.00550 ( 2) SS BOND : angle 0.80726 ( 4) hydrogen bonds : bond 0.04048 ( 1032) hydrogen bonds : angle 5.20128 ( 2841) metal coordination : bond 0.02021 ( 56) metal coordination : angle 4.81644 ( 72) *********************** 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 179 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 94 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 465 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8414 (ttmm) REVERT: D 279 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7163 (pt) REVERT: D 347 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8340 (mp) REVERT: D 398 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8840 (tt) REVERT: A 444 MET cc_start: 0.8384 (tmm) cc_final: 0.8017 (tmm) REVERT: A 539 CYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8245 (t) REVERT: A 576 CYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7521 (t) REVERT: G 444 MET cc_start: 0.8350 (tmm) cc_final: 0.8139 (tmm) REVERT: G 576 CYS cc_start: 0.8695 (OUTLIER) cc_final: 0.7945 (t) REVERT: L 190 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.6464 (m-80) outliers start: 85 outliers final: 54 residues processed: 172 average time/residue: 0.1498 time to fit residues: 44.6086 Evaluate side-chains 156 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 94 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 465 LYS 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 210 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 D residue 117 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 347 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 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 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 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 226 VAL Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 291 SER 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 140 ILE Chi-restraints excluded: chain J residue 200 HIS 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 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 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 59 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 40.0000 chunk 120 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 271 optimal weight: 30.0000 chunk 183 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 620 HIS ** 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** ** H 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 382 GLN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.043791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.033136 restraints weight = 262855.027| |-----------------------------------------------------------------------------| 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: 0.8170 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 26348 Z= 0.223 Angle : 0.555 12.537 36168 Z= 0.276 Chirality : 0.041 0.139 4114 Planarity : 0.004 0.043 4706 Dihedral : 9.155 162.165 4140 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 30.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.84 % Favored : 90.96 % Rotamer: Outliers : 4.75 % Allowed : 23.98 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.14), residues: 3596 helix: 1.71 (0.19), residues: 808 sheet: -0.80 (0.18), residues: 838 loop : -1.32 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 566 TYR 0.018 0.001 TYR H 117 PHE 0.016 0.001 PHE I 289 TRP 0.014 0.001 TRP D 205 HIS 0.006 0.001 HIS G 530 Details of bonding type rmsd covalent geometry : bond 0.00449 (26290) covalent geometry : angle 0.51010 (36092) SS BOND : bond 0.00366 ( 2) SS BOND : angle 0.43716 ( 4) hydrogen bonds : bond 0.03466 ( 1032) hydrogen bonds : angle 5.10758 ( 2841) metal coordination : bond 0.01939 ( 56) metal coordination : angle 4.92674 ( 72) *********************** 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 186 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 95 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 279 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7173 (pt) REVERT: D 347 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8376 (mp) REVERT: A 444 MET cc_start: 0.8220 (tmm) cc_final: 0.7873 (tmm) REVERT: A 539 CYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8434 (t) REVERT: A 576 CYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7386 (t) REVERT: A 676 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7939 (m110) REVERT: I 376 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7829 (ptp) REVERT: G 566 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8347 (mtp-110) REVERT: G 576 CYS cc_start: 0.8542 (OUTLIER) cc_final: 0.7787 (t) outliers start: 91 outliers final: 64 residues processed: 176 average time/residue: 0.1322 time to fit residues: 41.1750 Evaluate side-chains 166 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 94 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 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 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 403 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 347 LEU 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 300 CYS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 467 THR 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 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 661 VAL 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 271 MET 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 403 THR Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 200 HIS 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 576 CYS Chi-restraints excluded: chain G residue 582 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 341 optimal weight: 0.0270 chunk 121 optimal weight: 10.0000 chunk 171 optimal weight: 0.0170 chunk 310 optimal weight: 9.9990 chunk 319 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 182 optimal weight: 40.0000 chunk 188 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 314 optimal weight: 0.0010 chunk 129 optimal weight: 4.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- 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 204 ASN ** 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 ** 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 = 0.3632 r_free = 0.3632 target = 0.044444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.033799 restraints weight = 261589.319| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 4.48 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 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 = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26348 Z= 0.088 Angle : 0.440 10.084 36168 Z= 0.216 Chirality : 0.040 0.132 4114 Planarity : 0.003 0.035 4706 Dihedral : 8.949 161.636 4140 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.84 % Favored : 92.99 % Rotamer: Outliers : 2.35 % Allowed : 25.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.15), residues: 3596 helix: 2.31 (0.19), residues: 816 sheet: -0.73 (0.18), residues: 846 loop : -1.09 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 172 TYR 0.009 0.001 TYR H 495 PHE 0.008 0.001 PHE H 86 TRP 0.010 0.001 TRP J 382 HIS 0.004 0.001 HIS G 530 Details of bonding type rmsd covalent geometry : bond 0.00182 (26290) covalent geometry : angle 0.40070 (36092) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.62259 ( 4) hydrogen bonds : bond 0.02819 ( 1032) hydrogen bonds : angle 4.59262 ( 2841) metal coordination : bond 0.00897 ( 56) metal coordination : angle 4.10843 ( 72) *********************** 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 143 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 98 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 279 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7164 (pt) REVERT: D 347 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8443 (mp) REVERT: A 444 MET cc_start: 0.8129 (tmm) cc_final: 0.7745 (tmm) REVERT: A 539 CYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8340 (t) REVERT: A 576 CYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7406 (t) REVERT: G 566 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8219 (mtp-110) REVERT: K 150 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8240 (mmp80) outliers start: 45 outliers final: 30 residues processed: 135 average time/residue: 0.1582 time to fit residues: 36.8652 Evaluate side-chains 134 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 CYS 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 196 LEU Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 347 LEU 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 576 CYS 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 269 LEU 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 605 ASP Chi-restraints excluded: chain H residue 661 VAL Chi-restraints excluded: chain I residue 213 HIS Chi-restraints excluded: chain J residue 398 ILE Chi-restraints excluded: chain J residue 404 MET Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 69 HIS Chi-restraints excluded: chain G residue 297 HIS Chi-restraints excluded: chain G residue 566 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 87 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 223 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 297 optimal weight: 4.9990 chunk 339 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** ** 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** ** G 676 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 = 0.3597 r_free = 0.3597 target = 0.043595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.033026 restraints weight = 266021.336| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 4.44 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 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 = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26348 Z= 0.238 Angle : 0.566 10.997 36168 Z= 0.280 Chirality : 0.041 0.134 4114 Planarity : 0.004 0.040 4706 Dihedral : 9.082 163.198 4140 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 34.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.93 % Favored : 89.88 % Rotamer: Outliers : 4.23 % Allowed : 24.97 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.14), residues: 3596 helix: 1.82 (0.19), residues: 816 sheet: -0.82 (0.18), residues: 830 loop : -1.33 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 150 TYR 0.017 0.001 TYR J 409 PHE 0.016 0.001 PHE A 456 TRP 0.016 0.002 TRP I 263 HIS 0.007 0.001 HIS B 624 Details of bonding type rmsd covalent geometry : bond 0.00481 (26290) covalent geometry : angle 0.52486 (36092) SS BOND : bond 0.00491 ( 2) SS BOND : angle 0.32390 ( 4) hydrogen bonds : bond 0.03422 ( 1032) hydrogen bonds : angle 4.96875 ( 2841) metal coordination : bond 0.02092 ( 56) metal coordination : angle 4.75424 ( 72) *********************** 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 176 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 95 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 465 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8394 (ttmm) REVERT: D 279 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7142 (pt) REVERT: D 398 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8745 (tt) REVERT: A 444 MET cc_start: 0.8278 (tmm) cc_final: 0.7898 (tmm) REVERT: A 539 CYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8577 (t) REVERT: A 576 CYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7250 (t) REVERT: K 150 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8483 (mmp80) outliers start: 81 outliers final: 61 residues processed: 168 average time/residue: 0.1593 time to fit residues: 46.0490 Evaluate side-chains 162 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 95 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 465 LYS 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 C residue 85 VAL Chi-restraints excluded: chain C residue 213 HIS 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 108 PHE Chi-restraints excluded: chain D residue 117 ILE 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 41 MET 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 325 CYS Chi-restraints excluded: chain A residue 467 THR 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 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 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 I residue 220 ILE Chi-restraints excluded: chain I residue 226 VAL 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 J residue 108 PHE Chi-restraints excluded: chain J residue 200 HIS 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 566 ARG Chi-restraints excluded: chain G residue 573 THR Chi-restraints excluded: chain G residue 616 LYS 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 18 optimal weight: 30.0000 chunk 294 optimal weight: 0.0040 chunk 23 optimal weight: 0.9980 chunk 327 optimal weight: 20.0000 chunk 186 optimal weight: 40.0000 chunk 225 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 164 optimal weight: 10.0000 chunk 196 optimal weight: 40.0000 chunk 187 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.8194 ------------------------------------------------------------------------------- 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 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 = 0.3626 r_free = 0.3626 target = 0.044300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.033696 restraints weight = 262123.763| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 4.47 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 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 = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3079 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= 0.092 Angle : 0.439 8.048 36168 Z= 0.216 Chirality : 0.040 0.134 4114 Planarity : 0.003 0.036 4706 Dihedral : 8.915 162.857 4140 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 28.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.65 % Favored : 93.19 % Rotamer: Outliers : 2.72 % Allowed : 26.54 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.15), residues: 3596 helix: 2.36 (0.19), residues: 818 sheet: -0.60 (0.19), residues: 818 loop : -1.12 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 566 TYR 0.008 0.001 TYR C 244 PHE 0.008 0.001 PHE H 86 TRP 0.010 0.001 TRP J 382 HIS 0.003 0.000 HIS G 297 Details of bonding type rmsd covalent geometry : bond 0.00190 (26290) covalent geometry : angle 0.40253 (36092) SS BOND : bond 0.00256 ( 2) SS BOND : angle 0.52435 ( 4) hydrogen bonds : bond 0.02754 ( 1032) hydrogen bonds : angle 4.50362 ( 2841) metal coordination : bond 0.00897 ( 56) metal coordination : angle 3.93042 ( 72) *********************** 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 150 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 98 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 279 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7119 (pt) REVERT: D 347 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8473 (mp) REVERT: A 444 MET cc_start: 0.8226 (tmm) cc_final: 0.7857 (tmm) REVERT: A 539 CYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8431 (t) REVERT: A 576 CYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7388 (t) REVERT: G 566 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8268 (mtp-110) outliers start: 52 outliers final: 40 residues processed: 146 average time/residue: 0.1517 time to fit residues: 38.4971 Evaluate side-chains 141 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 96 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 419 SER Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 347 LEU 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 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 652 SER Chi-restraints excluded: chain A residue 705 MET 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 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 I residue 213 HIS Chi-restraints excluded: chain I residue 237 ASP Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain J residue 108 PHE 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 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 264 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 249 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 359 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 305 optimal weight: 50.0000 chunk 66 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 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** ** G 676 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 = 0.3613 r_free = 0.3613 target = 0.043940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.033349 restraints weight = 265029.431| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 4.46 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 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 = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26348 Z= 0.146 Angle : 0.466 8.737 36168 Z= 0.231 Chirality : 0.040 0.129 4114 Planarity : 0.003 0.037 4706 Dihedral : 8.907 163.436 4140 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 31.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.73 % Favored : 91.10 % Rotamer: Outliers : 3.03 % Allowed : 26.18 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.15), residues: 3596 helix: 2.35 (0.19), residues: 818 sheet: -0.72 (0.18), residues: 840 loop : -1.17 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 150 TYR 0.012 0.001 TYR H 495 PHE 0.009 0.001 PHE A 120 TRP 0.012 0.001 TRP D 205 HIS 0.004 0.001 HIS G 297 Details of bonding type rmsd covalent geometry : bond 0.00295 (26290) covalent geometry : angle 0.43207 (36092) SS BOND : bond 0.00353 ( 2) SS BOND : angle 0.21972 ( 4) hydrogen bonds : bond 0.02884 ( 1032) hydrogen bonds : angle 4.51838 ( 2841) metal coordination : bond 0.01374 ( 56) metal coordination : angle 3.91951 ( 72) *********************** 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 154 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 96 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 279 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7122 (pt) REVERT: D 347 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8524 (mp) REVERT: A 444 MET cc_start: 0.8280 (tmm) cc_final: 0.7909 (tmm) REVERT: A 539 CYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8480 (t) REVERT: A 576 CYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7107 (t) REVERT: I 376 MET cc_start: 0.8246 (pmm) cc_final: 0.7998 (pmm) REVERT: G 566 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8349 (mtp-110) outliers start: 58 outliers final: 50 residues processed: 148 average time/residue: 0.1477 time to fit residues: 38.6114 Evaluate side-chains 151 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 96 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 663 MET 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 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 347 LEU 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 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 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 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 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 301 THR Chi-restraints excluded: chain I residue 377 LEU 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 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 G residue 582 VAL Chi-restraints excluded: chain K residue 150 ARG Chi-restraints excluded: chain L residue 190 PHE Chi-restraints excluded: chain L residue 264 THR 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 125 optimal weight: 30.0000 chunk 275 optimal weight: 30.0000 chunk 212 optimal weight: 7.9990 chunk 152 optimal weight: 0.7980 chunk 200 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 272 optimal weight: 4.9990 chunk 19 optimal weight: 40.0000 chunk 179 optimal weight: 7.9990 chunk 351 optimal weight: 20.0000 overall best weight: 4.5186 ------------------------------------------------------------------------------- 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** ** 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 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.043734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.033202 restraints weight = 264959.357| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 4.43 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 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 = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26348 Z= 0.173 Angle : 0.492 9.686 36168 Z= 0.245 Chirality : 0.040 0.129 4114 Planarity : 0.003 0.037 4706 Dihedral : 8.961 164.081 4140 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 34.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.82 % Favored : 91.02 % Rotamer: Outliers : 3.50 % Allowed : 25.91 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.15), residues: 3596 helix: 2.18 (0.19), residues: 816 sheet: -0.71 (0.19), residues: 818 loop : -1.24 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 566 TYR 0.013 0.001 TYR C 244 PHE 0.010 0.001 PHE A 120 TRP 0.015 0.001 TRP D 205 HIS 0.007 0.001 HIS B 624 Details of bonding type rmsd covalent geometry : bond 0.00349 (26290) covalent geometry : angle 0.45774 (36092) SS BOND : bond 0.00425 ( 2) SS BOND : angle 0.20139 ( 4) hydrogen bonds : bond 0.03035 ( 1032) hydrogen bonds : angle 4.63452 ( 2841) metal coordination : bond 0.01615 ( 56) metal coordination : angle 4.06291 ( 72) *********************** 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 163 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 96 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8992 (p) REVERT: D 279 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7072 (pt) REVERT: D 398 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8728 (tt) REVERT: A 444 MET cc_start: 0.8327 (tmm) cc_final: 0.7941 (tmm) REVERT: A 539 CYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8567 (t) REVERT: A 576 CYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7184 (t) REVERT: A 676 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.6854 (m110) REVERT: I 376 MET cc_start: 0.8277 (pmm) cc_final: 0.7988 (pmm) REVERT: G 566 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8244 (mtp-110) outliers start: 67 outliers final: 57 residues processed: 157 average time/residue: 0.1372 time to fit residues: 37.6912 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 : 0.885 ------------------------------------------------------------------------------- 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 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 149 THR 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 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 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 325 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 676 ASN 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 269 LEU Chi-restraints excluded: chain H residue 86 PHE Chi-restraints excluded: chain H residue 191 VAL 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 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 291 SER Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 377 LEU 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 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 582 VAL Chi-restraints excluded: chain K residue 150 ARG Chi-restraints excluded: chain L residue 190 PHE Chi-restraints excluded: chain L residue 264 THR 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 179 optimal weight: 30.0000 chunk 242 optimal weight: 0.9980 chunk 259 optimal weight: 5.9990 chunk 304 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 15 optimal weight: 50.0000 chunk 353 optimal weight: 10.0000 chunk 63 optimal weight: 0.0670 chunk 26 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 333 optimal weight: 7.9990 overall best weight: 3.8124 ------------------------------------------------------------------------------- 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 123 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.043816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.033286 restraints weight = 263583.476| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 4.44 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 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 = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26348 Z= 0.151 Angle : 0.467 9.351 36168 Z= 0.233 Chirality : 0.040 0.127 4114 Planarity : 0.003 0.037 4706 Dihedral : 8.922 164.211 4140 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 33.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.87 % Favored : 90.96 % Rotamer: Outliers : 3.24 % Allowed : 26.23 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.15), residues: 3596 helix: 2.30 (0.19), residues: 814 sheet: -0.65 (0.18), residues: 824 loop : -1.22 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 150 TYR 0.011 0.001 TYR H 495 PHE 0.009 0.001 PHE I 229 TRP 0.011 0.001 TRP D 205 HIS 0.005 0.001 HIS G 297 Details of bonding type rmsd covalent geometry : bond 0.00305 (26290) covalent geometry : angle 0.43330 (36092) SS BOND : bond 0.00352 ( 2) SS BOND : angle 0.23439 ( 4) hydrogen bonds : bond 0.02900 ( 1032) hydrogen bonds : angle 4.52949 ( 2841) metal coordination : bond 0.01425 ( 56) metal coordination : angle 3.91751 ( 72) ********************** 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 158 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 96 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8979 (p) REVERT: D 279 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7054 (pt) REVERT: D 398 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8712 (tt) REVERT: A 444 MET cc_start: 0.8337 (tmm) cc_final: 0.7965 (tmm) REVERT: A 539 CYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8524 (t) REVERT: A 576 CYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7146 (t) REVERT: G 566 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8335 (mtp-110) outliers start: 62 outliers final: 54 residues processed: 154 average time/residue: 0.1416 time to fit residues: 38.3679 Evaluate side-chains 156 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 96 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 598 THR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 605 ASP 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 149 THR 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 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 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 573 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 611 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 269 LEU 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 605 ASP 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 301 THR Chi-restraints excluded: chain I residue 377 LEU 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 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 G residue 582 VAL Chi-restraints excluded: chain K residue 150 ARG Chi-restraints excluded: chain L residue 190 PHE Chi-restraints excluded: chain L residue 264 THR 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 145 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 358 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 100 optimal weight: 50.0000 chunk 15 optimal weight: 50.0000 chunk 292 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 318 optimal weight: 0.0040 overall best weight: 2.7396 ------------------------------------------------------------------------------- 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 123 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 = 0.3615 r_free = 0.3615 target = 0.043995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.033483 restraints weight = 262002.339| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.45 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 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 = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26348 Z= 0.119 Angle : 0.439 8.575 36168 Z= 0.219 Chirality : 0.040 0.130 4114 Planarity : 0.003 0.036 4706 Dihedral : 8.869 164.164 4140 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 32.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.98 % Favored : 91.85 % Rotamer: Outliers : 3.34 % Allowed : 26.02 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.15), residues: 3596 helix: 2.44 (0.19), residues: 816 sheet: -0.60 (0.18), residues: 832 loop : -1.15 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 269 TYR 0.010 0.001 TYR H 495 PHE 0.008 0.001 PHE H 86 TRP 0.009 0.001 TRP D 301 HIS 0.004 0.001 HIS G 297 Details of bonding type rmsd covalent geometry : bond 0.00244 (26290) covalent geometry : angle 0.40969 (36092) SS BOND : bond 0.00335 ( 2) SS BOND : angle 0.20780 ( 4) hydrogen bonds : bond 0.02728 ( 1032) hydrogen bonds : angle 4.38004 ( 2841) metal coordination : bond 0.01154 ( 56) metal coordination : angle 3.57229 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7700.95 seconds wall clock time: 132 minutes 26.28 seconds (7946.28 seconds total)