Starting phenix.real_space_refine on Thu Jun 26 04:07:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk1_34841/06_2025/8hk1_34841.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk1_34841/06_2025/8hk1_34841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hk1_34841/06_2025/8hk1_34841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk1_34841/06_2025/8hk1_34841.map" model { file = "/net/cci-nas-00/data/ceres_data/8hk1_34841/06_2025/8hk1_34841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk1_34841/06_2025/8hk1_34841.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.116 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 146 5.49 5 S 116 5.16 5 C 17829 2.51 5 N 5676 2.21 5 O 6465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 201 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30236 Number of models: 1 Model: "" Number of chains: 24 Chain: "H" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3142 Inner-chain residues flagged as termini: ['pdbres=" U H 69 "', 'pdbres=" G H 81 "'] Classifications: {'RNA': 148} Modifications used: {'5*END': 2, 'rna2p_pur': 6, 'rna2p_pyr': 9, 'rna3p_pur': 68, 'rna3p_pyr': 65} Link IDs: {'rna2p': 15, 'rna3p': 132} Chain breaks: 2 Chain: "1" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6487 Classifications: {'peptide': 815} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 780} Chain: "2" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1210 Classifications: {'peptide': 182} Incomplete info: {'backbone_only': 61} Link IDs: {'PTRANS': 22, 'TRANS': 159} Chain breaks: 4 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 138 Chain: "3" Number of atoms: 9247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9247 Classifications: {'peptide': 1180} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1119} Chain breaks: 5 Chain: "4" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 664 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 140} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 620 Unresolved non-hydrogen angles: 895 Unresolved non-hydrogen dihedrals: 400 Unresolved non-hydrogen chiralities: 181 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 10, 'GLU:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 324 Chain: "5" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 623 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "6" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 645 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "A" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 504 Classifications: {'peptide': 123} Incomplete info: {'backbone_only': 117} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 815 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 146 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 10, 'GLU:plan': 14, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 327 Chain: "B" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 421 Classifications: {'peptide': 100} Incomplete info: {'backbone_only': 89} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain breaks: 1 Unresolved non-hydrogen bonds: 459 Unresolved non-hydrogen angles: 647 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 264 Chain: "C" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 2103 Classifications: {'peptide': 422} Incomplete info: {'backbone_only': 293, 'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 409} Chain breaks: 2 Unresolved non-hydrogen bonds: 1490 Unresolved non-hydrogen angles: 2092 Unresolved non-hydrogen dihedrals: 996 Unresolved non-hydrogen chiralities: 366 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 22, 'TYR:plan': 18, 'ASN:plan1': 17, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 13, 'GLU:plan': 51, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 844 Chain: "D" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 579 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain breaks: 1 Chain: "F" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 666 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 150} Link IDs: {'PTRANS': 6, 'TRANS': 155} Unresolved non-hydrogen bonds: 660 Unresolved non-hydrogen angles: 948 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 207 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 305 Chain: "G" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 685 Classifications: {'peptide': 166} Incomplete info: {'backbone_only': 149} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain breaks: 2 Unresolved non-hydrogen bonds: 678 Unresolved non-hydrogen angles: 960 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 189 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 11, 'ASP:plan': 7, 'PHE:plan': 13, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 337 Chain: "a" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 372 Classifications: {'peptide': 90} Incomplete info: {'backbone_only': 83} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 522 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 168 Chain: "b" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 308 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 61} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "c" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 319 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 168 Chain: "d" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 305 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 391 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 117 Chain: "e" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 341 Classifications: {'peptide': 83} Incomplete info: {'backbone_only': 74} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 79} Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 101 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 140 Chain: "f" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 293 Classifications: {'peptide': 71} Incomplete info: {'backbone_only': 62} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 130 Chain: "g" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 337 Classifications: {'peptide': 82} Incomplete info: {'backbone_only': 75} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'9B0': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21501 SG CYS 6 23 130.582 88.141 156.767 1.00 30.04 S ATOM 21525 SG CYS 6 26 128.343 88.092 153.706 1.00 30.51 S ATOM 21772 SG CYS 6 58 126.649 88.085 157.128 1.00 30.08 S ATOM 21793 SG CYS 6 61 128.566 84.675 156.773 1.00 32.29 S ATOM 21414 SG CYS 6 11 112.719 83.213 160.570 1.00 25.68 S ATOM 21677 SG CYS 6 46 113.130 85.248 163.964 1.00 22.63 S ATOM 21700 SG CYS 6 49 116.234 84.180 162.548 1.00 35.44 S ATOM 21971 SG CYS 6 85 114.738 87.034 160.821 1.00 22.11 S ATOM 21552 SG CYS 6 30 119.231 94.547 149.853 1.00 19.69 S ATOM 21573 SG CYS 6 33 119.054 94.292 146.163 1.00 21.17 S ATOM 21868 SG CYS 6 72 118.082 97.514 147.463 1.00 15.15 S ATOM 21892 SG CYS 6 75 115.423 94.777 147.914 1.00 15.21 S ATOM 24361 SG CYS C 408 82.505 77.256 106.009 1.00 93.55 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASN 2 624 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN 2 624 " occ=0.00 residue: pdb=" N ALA 2 625 " occ=0.00 ... (2 atoms not shown) pdb=" O ALA 2 625 " occ=0.00 residue: pdb=" N HIS 2 626 " occ=0.00 ... (2 atoms not shown) pdb=" O HIS 2 626 " occ=0.00 residue: pdb=" N LYS 2 627 " occ=0.00 ... (2 atoms not shown) pdb=" O LYS 2 627 " occ=0.00 Time building chain proxies: 18.94, per 1000 atoms: 0.63 Number of scatterers: 30236 At special positions: 0 Unit cell: (184.79, 190.225, 227.183, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 116 16.00 P 146 15.00 O 6465 8.00 N 5676 7.00 C 17829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.26 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 6 201 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 61 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 23 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 26 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 58 " pdb=" ZN 6 202 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 46 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 85 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 49 " pdb=" ZN 6 203 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 33 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 30 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 72 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 75 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 425 " pdb="ZN ZN C1000 " - pdb=" ND1 HIS C 431 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 408 " Number of angles added : 18 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4928 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 41 sheets defined 38.0% alpha, 19.9% beta 33 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 11.80 Creating SS restraints... Processing helix chain '1' and resid 491 through 499 removed outlier: 3.615A pdb=" N ARG 1 495 " --> pdb=" O GLU 1 491 " (cutoff:3.500A) Processing helix chain '1' and resid 499 through 506 Processing helix chain '1' and resid 508 through 527 removed outlier: 4.761A pdb=" N ARG 1 524 " --> pdb=" O THR 1 520 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLU 1 525 " --> pdb=" O ASP 1 521 " (cutoff:3.500A) Processing helix chain '1' and resid 527 through 540 Proline residue: 1 537 - end of helix Processing helix chain '1' and resid 545 through 562 Processing helix chain '1' and resid 567 through 569 No H-bonds generated for 'chain '1' and resid 567 through 569' Processing helix chain '1' and resid 570 through 579 Processing helix chain '1' and resid 586 through 604 Processing helix chain '1' and resid 605 through 614 Processing helix chain '1' and resid 615 through 618 removed outlier: 3.817A pdb=" N ASP 1 618 " --> pdb=" O PRO 1 615 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 615 through 618' Processing helix chain '1' and resid 621 through 640 removed outlier: 3.517A pdb=" N ARG 1 625 " --> pdb=" O ASP 1 621 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN 1 626 " --> pdb=" O GLU 1 622 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR 1 627 " --> pdb=" O TYR 1 623 " (cutoff:3.500A) Processing helix chain '1' and resid 644 through 652 Processing helix chain '1' and resid 657 through 676 removed outlier: 4.010A pdb=" N ARG 1 661 " --> pdb=" O SER 1 657 " (cutoff:3.500A) Processing helix chain '1' and resid 677 through 681 removed outlier: 3.876A pdb=" N LEU 1 680 " --> pdb=" O CYS 1 677 " (cutoff:3.500A) Proline residue: 1 681 - end of helix No H-bonds generated for 'chain '1' and resid 677 through 681' Processing helix chain '1' and resid 682 through 691 Processing helix chain '1' and resid 692 through 696 removed outlier: 3.757A pdb=" N VAL 1 695 " --> pdb=" O HIS 1 692 " (cutoff:3.500A) Processing helix chain '1' and resid 698 through 717 Processing helix chain '1' and resid 727 through 738 Processing helix chain '1' and resid 740 through 754 Processing helix chain '1' and resid 755 through 757 No H-bonds generated for 'chain '1' and resid 755 through 757' Processing helix chain '1' and resid 758 through 777 removed outlier: 3.652A pdb=" N GLU 1 768 " --> pdb=" O TYR 1 764 " (cutoff:3.500A) Processing helix chain '1' and resid 781 through 796 removed outlier: 3.544A pdb=" N LYS 1 785 " --> pdb=" O ASP 1 781 " (cutoff:3.500A) Processing helix chain '1' and resid 802 through 810 Processing helix chain '1' and resid 810 through 818 Processing helix chain '1' and resid 820 through 826 removed outlier: 3.605A pdb=" N ALA 1 824 " --> pdb=" O GLN 1 820 " (cutoff:3.500A) Processing helix chain '1' and resid 829 through 845 removed outlier: 3.831A pdb=" N LYS 1 843 " --> pdb=" O GLU 1 839 " (cutoff:3.500A) Processing helix chain '1' and resid 845 through 855 removed outlier: 4.201A pdb=" N ILE 1 849 " --> pdb=" O GLY 1 845 " (cutoff:3.500A) Processing helix chain '1' and resid 861 through 879 removed outlier: 3.516A pdb=" N ARG 1 865 " --> pdb=" O ALA 1 861 " (cutoff:3.500A) Processing helix chain '1' and resid 885 through 902 Processing helix chain '1' and resid 907 through 922 removed outlier: 3.891A pdb=" N LEU 1 911 " --> pdb=" O ASP 1 907 " (cutoff:3.500A) Processing helix chain '1' and resid 923 through 925 No H-bonds generated for 'chain '1' and resid 923 through 925' Processing helix chain '1' and resid 927 through 942 removed outlier: 4.429A pdb=" N ASN 1 942 " --> pdb=" O TRP 1 938 " (cutoff:3.500A) Processing helix chain '1' and resid 945 through 965 removed outlier: 3.587A pdb=" N GLN 1 950 " --> pdb=" O LYS 1 946 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL 1 960 " --> pdb=" O SER 1 956 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL 1 961 " --> pdb=" O ARG 1 957 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS 1 965 " --> pdb=" O VAL 1 961 " (cutoff:3.500A) Processing helix chain '1' and resid 968 through 981 Processing helix chain '1' and resid 986 through 1004 Processing helix chain '1' and resid 1012 through 1021 Proline residue: 11018 - end of helix Processing helix chain '1' and resid 1022 through 1026 removed outlier: 3.533A pdb=" N LYS 11025 " --> pdb=" O PRO 11022 " (cutoff:3.500A) Processing helix chain '1' and resid 1028 through 1046 Processing helix chain '1' and resid 1047 through 1050 removed outlier: 3.937A pdb=" N VAL 11050 " --> pdb=" O ALA 11047 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1047 through 1050' Processing helix chain '1' and resid 1051 through 1063 Processing helix chain '1' and resid 1064 through 1068 removed outlier: 3.623A pdb=" N LYS 11067 " --> pdb=" O GLU 11064 " (cutoff:3.500A) Processing helix chain '1' and resid 1070 through 1089 Processing helix chain '1' and resid 1089 through 1103 removed outlier: 4.187A pdb=" N VAL 11093 " --> pdb=" O GLY 11089 " (cutoff:3.500A) Processing helix chain '1' and resid 1105 through 1123 Processing helix chain '1' and resid 1124 through 1127 Processing helix chain '1' and resid 1128 through 1136 removed outlier: 3.574A pdb=" N TYR 11136 " --> pdb=" O LEU 11132 " (cutoff:3.500A) Processing helix chain '1' and resid 1143 through 1159 Processing helix chain '1' and resid 1160 through 1164 removed outlier: 3.871A pdb=" N ASP 11164 " --> pdb=" O MET 11161 " (cutoff:3.500A) Processing helix chain '1' and resid 1165 through 1178 removed outlier: 3.697A pdb=" N VAL 11169 " --> pdb=" O TYR 11165 " (cutoff:3.500A) Proline residue: 11171 - end of helix Processing helix chain '1' and resid 1181 through 1199 removed outlier: 3.607A pdb=" N ARG 11185 " --> pdb=" O ASP 11181 " (cutoff:3.500A) Processing helix chain '1' and resid 1204 through 1216 removed outlier: 3.604A pdb=" N LEU 11208 " --> pdb=" O CYS 11204 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR 11214 " --> pdb=" O HIS 11210 " (cutoff:3.500A) Processing helix chain '1' and resid 1217 through 1221 removed outlier: 4.211A pdb=" N PHE 11220 " --> pdb=" O PRO 11217 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU 11221 " --> pdb=" O ASN 11218 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1217 through 1221' Processing helix chain '1' and resid 1223 through 1241 removed outlier: 3.604A pdb=" N VAL 11239 " --> pdb=" O GLU 11235 " (cutoff:3.500A) Processing helix chain '1' and resid 1242 through 1251 removed outlier: 3.724A pdb=" N MET 11246 " --> pdb=" O GLY 11242 " (cutoff:3.500A) Processing helix chain '1' and resid 1252 through 1254 No H-bonds generated for 'chain '1' and resid 1252 through 1254' Processing helix chain '1' and resid 1258 through 1275 removed outlier: 3.687A pdb=" N GLY 11275 " --> pdb=" O SER 11271 " (cutoff:3.500A) Processing helix chain '1' and resid 1278 through 1283 Processing helix chain '1' and resid 1298 through 1302 Processing helix chain '2' and resid 461 through 469 removed outlier: 3.613A pdb=" N LEU 2 468 " --> pdb=" O GLU 2 464 " (cutoff:3.500A) Processing helix chain '2' and resid 471 through 475 removed outlier: 3.741A pdb=" N VAL 2 474 " --> pdb=" O ARG 2 471 " (cutoff:3.500A) Processing helix chain '2' and resid 476 through 482 removed outlier: 4.026A pdb=" N VAL 2 480 " --> pdb=" O MET 2 477 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA 2 482 " --> pdb=" O ASP 2 479 " (cutoff:3.500A) Processing helix chain '2' and resid 484 through 493 Processing helix chain '2' and resid 525 through 530 removed outlier: 3.967A pdb=" N LYS 2 529 " --> pdb=" O PRO 2 525 " (cutoff:3.500A) Processing helix chain '2' and resid 568 through 578 Processing helix chain '2' and resid 610 through 618 removed outlier: 3.565A pdb=" N GLY 2 618 " --> pdb=" O ARG 2 614 " (cutoff:3.500A) Processing helix chain '2' and resid 632 through 640 removed outlier: 3.712A pdb=" N MET 2 636 " --> pdb=" O TRP 2 632 " (cutoff:3.500A) Processing helix chain '3' and resid 190 through 194 Processing helix chain '3' and resid 429 through 432 removed outlier: 3.521A pdb=" N ARG 3 432 " --> pdb=" O ARG 3 429 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 429 through 432' Processing helix chain '3' and resid 808 through 825 removed outlier: 3.674A pdb=" N GLU 3 825 " --> pdb=" O GLU 3 821 " (cutoff:3.500A) Processing helix chain '3' and resid 838 through 843 Processing helix chain '3' and resid 848 through 853 Processing helix chain '3' and resid 1134 through 1152 removed outlier: 3.576A pdb=" N HIS 31138 " --> pdb=" O SER 31134 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER 31150 " --> pdb=" O MET 31146 " (cutoff:3.500A) Processing helix chain '3' and resid 1159 through 1164 Processing helix chain '3' and resid 1176 through 1180 Processing helix chain '3' and resid 1181 through 1185 Processing helix chain '3' and resid 1186 through 1195 Processing helix chain '3' and resid 1200 through 1216 removed outlier: 3.642A pdb=" N ILE 31211 " --> pdb=" O LYS 31207 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG 31212 " --> pdb=" O LEU 31208 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR 31215 " --> pdb=" O ILE 31211 " (cutoff:3.500A) Processing helix chain '4' and resid 25 through 33 removed outlier: 3.701A pdb=" N TRP 4 30 " --> pdb=" O GLU 4 26 " (cutoff:3.500A) Processing helix chain '4' and resid 63 through 74 removed outlier: 3.513A pdb=" N ALA 4 67 " --> pdb=" O SER 4 63 " (cutoff:3.500A) Processing helix chain '4' and resid 112 through 121 Processing helix chain '4' and resid 151 through 161 removed outlier: 3.665A pdb=" N SER 4 155 " --> pdb=" O SER 4 151 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 18 removed outlier: 3.604A pdb=" N SER 5 16 " --> pdb=" O GLU 5 12 " (cutoff:3.500A) Processing helix chain '5' and resid 27 through 46 Processing helix chain '5' and resid 46 through 57 removed outlier: 3.617A pdb=" N LEU 5 50 " --> pdb=" O HIS 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 60 through 73 removed outlier: 4.162A pdb=" N LEU 5 73 " --> pdb=" O MET 5 69 " (cutoff:3.500A) Processing helix chain '6' and resid 51 through 55 Processing helix chain '6' and resid 73 through 78 Processing helix chain '6' and resid 79 through 83 removed outlier: 4.076A pdb=" N ASP 6 83 " --> pdb=" O LYS 6 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.896A pdb=" N GLN A 190 " --> pdb=" O MET A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 218 Processing helix chain 'A' and resid 235 through 272 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'C' and resid 5 through 28 Processing helix chain 'C' and resid 32 through 59 removed outlier: 3.660A pdb=" N ASP C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 72 removed outlier: 4.717A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU C 70 " --> pdb=" O GLY C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 102 through 109 removed outlier: 3.556A pdb=" N MET C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.561A pdb=" N VAL C 128 " --> pdb=" O GLN C 125 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU C 129 " --> pdb=" O ASN C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 129' Processing helix chain 'C' and resid 142 through 154 Processing helix chain 'C' and resid 159 through 168 Processing helix chain 'C' and resid 181 through 201 removed outlier: 4.001A pdb=" N TYR C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 220 Processing helix chain 'C' and resid 221 through 224 removed outlier: 4.105A pdb=" N GLY C 224 " --> pdb=" O TRP C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 224' Processing helix chain 'C' and resid 293 through 302 removed outlier: 4.109A pdb=" N ALA C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.532A pdb=" N LYS C 308 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 334 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 352 through 362 removed outlier: 3.510A pdb=" N GLU C 362 " --> pdb=" O GLU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 400 removed outlier: 3.584A pdb=" N LYS C 398 " --> pdb=" O TYR C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 425 removed outlier: 3.668A pdb=" N ARG C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 439 removed outlier: 4.095A pdb=" N LEU C 438 " --> pdb=" O GLY C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 removed outlier: 3.623A pdb=" N ALA C 447 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 470 Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.565A pdb=" N PHE D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 202 removed outlier: 3.876A pdb=" N VAL D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 246 Processing helix chain 'E' and resid 70 through 77 Processing helix chain 'E' and resid 115 through 137 Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 155 through 167 Processing helix chain 'F' and resid 5 through 11 Processing helix chain 'F' and resid 36 through 40 removed outlier: 4.208A pdb=" N ALA F 39 " --> pdb=" O ASN F 36 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR F 40 " --> pdb=" O LEU F 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 36 through 40' Processing helix chain 'F' and resid 82 through 87 removed outlier: 3.528A pdb=" N ALA F 86 " --> pdb=" O GLY F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.722A pdb=" N ASP F 105 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Proline residue: F 108 - end of helix removed outlier: 3.603A pdb=" N SER F 111 " --> pdb=" O PRO F 108 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 139 Processing helix chain 'F' and resid 151 through 161 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 61 through 72 removed outlier: 3.510A pdb=" N SER G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 99 Processing helix chain 'G' and resid 163 through 172 Processing helix chain 'G' and resid 196 through 207 Processing helix chain 'a' and resid 20 through 27 Processing helix chain 'a' and resid 28 through 38 removed outlier: 3.699A pdb=" N LEU a 32 " --> pdb=" O PRO a 28 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER a 35 " --> pdb=" O VAL a 31 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN a 38 " --> pdb=" O GLN a 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 6 through 14 Processing helix chain 'c' and resid 16 through 28 Processing helix chain 'e' and resid 4 through 13 Processing helix chain 'g' and resid 2 through 9 removed outlier: 3.873A pdb=" N PHE g 6 " --> pdb=" O LYS g 2 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 80 Processing sheet with id=AA1, first strand: chain '2' and resid 648 through 649 Processing sheet with id=AA2, first strand: chain '3' and resid 1101 through 1108 removed outlier: 3.746A pdb=" N SER 31103 " --> pdb=" O THR 31120 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N GLU 31115 " --> pdb=" O PRO 31131 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE 31128 " --> pdb=" O THR 3 7 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N THR 3 7 " --> pdb=" O ILE 31128 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL 31130 " --> pdb=" O ASN 3 5 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASN 3 5 " --> pdb=" O VAL 31130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 16 through 20 removed outlier: 3.667A pdb=" N PHE 3 16 " --> pdb=" O SER 3 33 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU 3 54 " --> pdb=" O LEU 3 40 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG 3 42 " --> pdb=" O THR 3 52 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N THR 3 52 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 62 through 68 removed outlier: 4.401A pdb=" N SER 3 82 " --> pdb=" O ARG 3 86 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG 3 86 " --> pdb=" O SER 3 82 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE 3 87 " --> pdb=" O GLN 3 104 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN 3 104 " --> pdb=" O ILE 3 87 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE 3 89 " --> pdb=" O ILE 3 102 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET 3 98 " --> pdb=" O GLN 3 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 120 through 123 Processing sheet with id=AA6, first strand: chain '3' and resid 120 through 123 Processing sheet with id=AA7, first strand: chain '3' and resid 165 through 173 removed outlier: 5.654A pdb=" N VAL 3 167 " --> pdb=" O MET 3 187 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N MET 3 187 " --> pdb=" O VAL 3 167 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS 3 169 " --> pdb=" O LEU 3 185 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET 3 181 " --> pdb=" O VAL 3 173 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU 3 208 " --> pdb=" O SER 3 225 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER 3 225 " --> pdb=" O LEU 3 208 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE 3 210 " --> pdb=" O LYS 3 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS 3 219 " --> pdb=" O ASP 3 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 232 through 237 removed outlier: 4.492A pdb=" N PHE 3 234 " --> pdb=" O CYS 3 251 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR 3 255 " --> pdb=" O SER 3 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 273 through 274 removed outlier: 6.353A pdb=" N ARG 3 273 " --> pdb=" O PHE 3 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '3' and resid 287 through 294 removed outlier: 6.874A pdb=" N GLN 3 304 " --> pdb=" O VAL 3 288 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER 3 290 " --> pdb=" O LEU 3 302 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU 3 302 " --> pdb=" O SER 3 290 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N THR 3 292 " --> pdb=" O PHE 3 300 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE 3 300 " --> pdb=" O THR 3 292 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE 3 299 " --> pdb=" O LEU 3 315 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU 3 315 " --> pdb=" O PHE 3 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP 3 309 " --> pdb=" O THR 3 305 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE 3 310 " --> pdb=" O PHE 3 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 336 through 342 removed outlier: 3.689A pdb=" N ALA 3 338 " --> pdb=" O ALA 3 350 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N HIS 3 356 " --> pdb=" O GLU 3 400 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU 3 400 " --> pdb=" O HIS 3 356 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU 3 358 " --> pdb=" O VAL 3 398 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 407 through 413 Processing sheet with id=AB4, first strand: chain '3' and resid 444 through 449 removed outlier: 6.379A pdb=" N ILE 3 764 " --> pdb=" O MET 3 447 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 461 through 462 removed outlier: 3.501A pdb=" N VAL 3 462 " --> pdb=" O TYR 3 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '3' and resid 507 through 510 removed outlier: 3.822A pdb=" N GLN 3 518 " --> pdb=" O ARG 3 525 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '3' and resid 546 through 548 removed outlier: 4.331A pdb=" N LYS 3 546 " --> pdb=" O ALA 3 557 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL 3 564 " --> pdb=" O ILE 3 556 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '3' and resid 587 through 592 removed outlier: 3.619A pdb=" N SER 3 591 " --> pdb=" O ALA 3 606 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA 3 606 " --> pdb=" O SER 3 591 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU 3 609 " --> pdb=" O THR 3 613 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR 3 613 " --> pdb=" O LEU 3 609 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER 3 629 " --> pdb=" O ILE 3 616 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '3' and resid 637 through 643 removed outlier: 4.268A pdb=" N SER 3 639 " --> pdb=" O GLY 3 668 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS 3 641 " --> pdb=" O ASN 3 666 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU 3 669 " --> pdb=" O VAL 3 673 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL 3 673 " --> pdb=" O LEU 3 669 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU 3 674 " --> pdb=" O THR 3 689 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR 3 689 " --> pdb=" O LEU 3 674 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '3' and resid 700 through 706 removed outlier: 3.666A pdb=" N VAL 3 712 " --> pdb=" O SER 3 722 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '3' and resid 785 through 790 removed outlier: 7.110A pdb=" N ILE 3 800 " --> pdb=" O ARG 3 786 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE 3 788 " --> pdb=" O ILE 3 798 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE 3 798 " --> pdb=" O PHE 3 788 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N SER 3 864 " --> pdb=" O GLN 3 881 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLN 3 881 " --> pdb=" O SER 3 864 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE 3 866 " --> pdb=" O LEU 3 879 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU 3 879 " --> pdb=" O ILE 3 866 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL 3 868 " --> pdb=" O LEU 3 877 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '3' and resid 886 through 894 removed outlier: 6.604A pdb=" N GLY 3 908 " --> pdb=" O PHE 3 889 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL 3 891 " --> pdb=" O LEU 3 906 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU 3 906 " --> pdb=" O VAL 3 891 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL 3 893 " --> pdb=" O TYR 3 904 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR 3 904 " --> pdb=" O VAL 3 893 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS 3 941 " --> pdb=" O THR 3 927 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '3' and resid 953 through 955 removed outlier: 6.823A pdb=" N LEU 3 967 " --> pdb=" O GLU 3 982 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU 3 982 " --> pdb=" O LEU 3 967 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL 3 969 " --> pdb=" O LYS 3 980 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '3' and resid 990 through 996 removed outlier: 3.732A pdb=" N GLY 3 992 " --> pdb=" O SER 31003 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE 31009 " --> pdb=" O ASP 31026 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP 31026 " --> pdb=" O PHE 31009 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP 31011 " --> pdb=" O PHE 31024 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '3' and resid 1033 through 1038 removed outlier: 4.373A pdb=" N THR 31035 " --> pdb=" O ALA 31047 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN 31052 " --> pdb=" O ASP 31048 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET 31093 " --> pdb=" O VAL 31055 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG 31057 " --> pdb=" O VAL 31091 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL 31091 " --> pdb=" O ARG 31057 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '4' and resid 39 through 43 Processing sheet with id=AC8, first strand: chain '4' and resid 131 through 132 removed outlier: 3.540A pdb=" N LYS 4 131 " --> pdb=" O PHE 4 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '6' and resid 9 through 10 removed outlier: 3.532A pdb=" N ILE 6 9 " --> pdb=" O VAL 6 89 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '6' and resid 18 through 19 removed outlier: 4.134A pdb=" N ALA 6 18 " --> pdb=" O ILE 6 45 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 21 through 22 Processing sheet with id=AD3, first strand: chain '6' and resid 39 through 42 removed outlier: 6.228A pdb=" N TYR 6 71 " --> pdb=" O CYS 6 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 118 through 121 removed outlier: 4.004A pdb=" N LYS B 118 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 148 through 153 removed outlier: 4.029A pdb=" N GLN B 167 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 282 through 283 removed outlier: 4.093A pdb=" N ALA C 282 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 406 through 408 removed outlier: 3.617A pdb=" N TYR C 414 " --> pdb=" O CYS C 408 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 170 through 174 removed outlier: 4.596A pdb=" N ASP D 183 " --> pdb=" O TYR D 173 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 13 through 16 removed outlier: 4.136A pdb=" N ALA F 13 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG F 22 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASP F 48 " --> pdb=" O ARG F 22 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU F 24 " --> pdb=" O ASP F 48 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 47 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU F 69 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AE2, first strand: chain 'G' and resid 40 through 45 Processing sheet with id=AE3, first strand: chain 'G' and resid 76 through 77 Processing sheet with id=AE4, first strand: chain 'G' and resid 177 through 181 removed outlier: 3.651A pdb=" N GLU G 179 " --> pdb=" O GLU G 193 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'e' and resid 56 through 57 removed outlier: 3.841A pdb=" N GLN e 60 " --> pdb=" O ALA d 72 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS d 20 " --> pdb=" O ILE d 68 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU d 70 " --> pdb=" O SER d 18 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER d 18 " --> pdb=" O LEU d 70 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA d 72 " --> pdb=" O LYS d 16 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LYS d 16 " --> pdb=" O ALA d 72 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N HIS d 26 " --> pdb=" O MET d 48 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE d 30 " --> pdb=" O GLU d 44 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLU d 44 " --> pdb=" O ILE d 30 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLY d 58 " --> pdb=" O GLU d 44 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL d 46 " --> pdb=" O ASN d 56 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN d 56 " --> pdb=" O VAL d 46 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N MET d 48 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN d 54 " --> pdb=" O MET d 48 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N MET d 59 " --> pdb=" O SER c 89 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER c 89 " --> pdb=" O MET d 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU c 86 " --> pdb=" O TRP c 34 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU c 35 " --> pdb=" O MET c 41 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N MET c 41 " --> pdb=" O LEU c 35 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N CYS c 46 " --> pdb=" O ASP c 60 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP c 60 " --> pdb=" O CYS c 46 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL c 57 " --> pdb=" O MET c 78 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET c 78 " --> pdb=" O VAL c 57 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP c 59 " --> pdb=" O ARG c 76 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG c 76 " --> pdb=" O ASP c 59 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA c 61 " --> pdb=" O LEU c 74 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ARG c 76 " --> pdb=" O GLY b 74 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY b 74 " --> pdb=" O ARG c 76 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE b 72 " --> pdb=" O MET c 78 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N MET b 27 " --> pdb=" O LEU b 23 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TYR b 32 " --> pdb=" O ASN b 46 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ASN b 46 " --> pdb=" O TYR b 32 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL b 34 " --> pdb=" O LEU b 44 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU b 44 " --> pdb=" O VAL b 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL b 36 " --> pdb=" O MET b 42 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET b 42 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN b 43 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL b 62 " --> pdb=" O GLN b 43 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA b 45 " --> pdb=" O GLY b 60 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY b 60 " --> pdb=" O ALA b 45 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR b 47 " --> pdb=" O HIS b 58 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N HIS b 58 " --> pdb=" O THR b 47 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU b 49 " --> pdb=" O SER b 56 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG a 55 " --> pdb=" O ASN a 69 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASN a 69 " --> pdb=" O ARG a 55 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS a 57 " --> pdb=" O LEU a 67 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU a 67 " --> pdb=" O LYS a 57 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER a 97 " --> pdb=" O ASN a 69 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS a 71 " --> pdb=" O TYR a 95 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR a 95 " --> pdb=" O LYS a 71 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET a 73 " --> pdb=" O ASP a 93 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP a 93 " --> pdb=" O MET a 73 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR a 75 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN a 91 " --> pdb=" O THR a 75 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS a 98 " --> pdb=" O LEU g 70 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU g 70 " --> pdb=" O LYS a 98 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU g 13 " --> pdb=" O ILE g 29 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL g 25 " --> pdb=" O MET g 45 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET g 45 " --> pdb=" O VAL g 25 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY g 27 " --> pdb=" O VAL g 43 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL g 43 " --> pdb=" O GLY g 27 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE g 29 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS g 41 " --> pdb=" O ILE g 29 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N HIS g 39 " --> pdb=" O SER g 59 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER g 59 " --> pdb=" O HIS g 39 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS g 41 " --> pdb=" O THR g 57 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR g 57 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR g 57 " --> pdb=" O VAL f 82 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL f 82 " --> pdb=" O THR g 57 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER f 79 " --> pdb=" O ILE f 20 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR f 15 " --> pdb=" O PHE f 31 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N THR f 30 " --> pdb=" O ASP f 44 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASP f 44 " --> pdb=" O THR f 30 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ILE f 41 " --> pdb=" O LEU f 72 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU f 72 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N CYS f 43 " --> pdb=" O VAL f 70 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL f 70 " --> pdb=" O CYS f 43 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU f 47 " --> pdb=" O VAL f 66 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL f 66 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU f 69 " --> pdb=" O LEU e 73 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS e 31 " --> pdb=" O ASN e 45 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN e 45 " --> pdb=" O LYS e 31 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE e 33 " --> pdb=" O MET e 43 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N MET e 43 " --> pdb=" O ILE e 33 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA e 35 " --> pdb=" O CYS e 41 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N CYS e 41 " --> pdb=" O ALA e 35 " (cutoff:3.500A) 1450 hydrogen bonds defined for protein. 4104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 19.38 Time building geometry restraints manager: 9.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5578 1.32 - 1.45: 8467 1.45 - 1.57: 16547 1.57 - 1.69: 288 1.69 - 1.81: 179 Bond restraints: 31059 Sorted by residual: bond pdb=" C PRO 5 78 " pdb=" N PRO 5 79 " ideal model delta sigma weight residual 1.334 1.503 -0.169 2.34e-02 1.83e+03 5.22e+01 bond pdb=" C16 9B0 11500 " pdb=" C17 9B0 11500 " ideal model delta sigma weight residual 1.450 1.322 0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" O3' C H 45 " pdb=" P U H 46 " ideal model delta sigma weight residual 1.607 1.522 0.085 1.50e-02 4.44e+03 3.23e+01 bond pdb=" N GLU D 252 " pdb=" CA GLU D 252 " ideal model delta sigma weight residual 1.457 1.488 -0.031 6.40e-03 2.44e+04 2.38e+01 bond pdb=" P U H 55 " pdb=" OP2 U H 55 " ideal model delta sigma weight residual 1.485 1.580 -0.095 2.00e-02 2.50e+03 2.27e+01 ... (remaining 31054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 41932 3.63 - 7.27: 191 7.27 - 10.90: 17 10.90 - 14.53: 6 14.53 - 18.17: 2 Bond angle restraints: 42148 Sorted by residual: angle pdb=" O2' C H 28 " pdb=" C2' C H 28 " pdb=" C1' C H 28 " ideal model delta sigma weight residual 108.40 90.23 18.17 1.50e+00 4.44e-01 1.47e+02 angle pdb=" C PRO 5 78 " pdb=" N PRO 5 79 " pdb=" CA PRO 5 79 " ideal model delta sigma weight residual 119.84 134.29 -14.45 1.25e+00 6.40e-01 1.34e+02 angle pdb=" C4' G H 42 " pdb=" C3' G H 42 " pdb=" O3' G H 42 " ideal model delta sigma weight residual 113.00 127.68 -14.68 1.50e+00 4.44e-01 9.57e+01 angle pdb=" C2' C H 28 " pdb=" C1' C H 28 " pdb=" N1 C H 28 " ideal model delta sigma weight residual 112.00 98.96 13.04 1.50e+00 4.44e-01 7.55e+01 angle pdb=" C3' U H 27 " pdb=" C2' U H 27 " pdb=" C1' U H 27 " ideal model delta sigma weight residual 101.30 107.14 -5.84 1.00e+00 1.00e+00 3.41e+01 ... (remaining 42143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.95: 15675 30.95 - 61.90: 991 61.90 - 92.84: 181 92.84 - 123.79: 12 123.79 - 154.74: 7 Dihedral angle restraints: 16866 sinusoidal: 7674 harmonic: 9192 Sorted by residual: dihedral pdb=" O4' U H 47 " pdb=" C1' U H 47 " pdb=" N1 U H 47 " pdb=" C2 U H 47 " ideal model delta sinusoidal sigma weight residual 200.00 45.26 154.74 1 1.50e+01 4.44e-03 8.13e+01 dihedral pdb=" CA GLU 3 136 " pdb=" C GLU 3 136 " pdb=" N LYS 3 137 " pdb=" CA LYS 3 137 " ideal model delta harmonic sigma weight residual 180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ILE 3 996 " pdb=" C ILE 3 996 " pdb=" N GLY 3 997 " pdb=" CA GLY 3 997 " ideal model delta harmonic sigma weight residual 180.00 -153.13 -26.87 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 16863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3882 0.136 - 0.273: 58 0.273 - 0.409: 4 0.409 - 0.545: 0 0.545 - 0.681: 1 Chirality restraints: 3945 Sorted by residual: chirality pdb=" C3' G H 42 " pdb=" C4' G H 42 " pdb=" O3' G H 42 " pdb=" C2' G H 42 " both_signs ideal model delta sigma weight residual False -2.48 -1.80 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C3' U H 43 " pdb=" C4' U H 43 " pdb=" O3' U H 43 " pdb=" C2' U H 43 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA TYR C 394 " pdb=" N TYR C 394 " pdb=" C TYR C 394 " pdb=" CB TYR C 394 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 3942 not shown) Planarity restraints: 5471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 9B0 11500 " 0.190 2.00e-02 2.50e+03 1.73e-01 2.99e+02 pdb=" C17 9B0 11500 " -0.204 2.00e-02 2.50e+03 pdb=" C18 9B0 11500 " -0.137 2.00e-02 2.50e+03 pdb=" C19 9B0 11500 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U H 43 " -0.025 2.00e-02 2.50e+03 9.03e-02 1.84e+02 pdb=" N1 U H 43 " 0.067 2.00e-02 2.50e+03 pdb=" C2 U H 43 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U H 43 " -0.046 2.00e-02 2.50e+03 pdb=" N3 U H 43 " -0.000 2.00e-02 2.50e+03 pdb=" C4 U H 43 " 0.055 2.00e-02 2.50e+03 pdb=" O4 U H 43 " 0.039 2.00e-02 2.50e+03 pdb=" C5 U H 43 " -0.214 2.00e-02 2.50e+03 pdb=" C6 U H 43 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 9B0 11500 " 0.099 2.00e-02 2.50e+03 9.30e-02 8.66e+01 pdb=" C11 9B0 11500 " -0.094 2.00e-02 2.50e+03 pdb=" C8 9B0 11500 " -0.092 2.00e-02 2.50e+03 pdb=" C9 9B0 11500 " 0.087 2.00e-02 2.50e+03 ... (remaining 5468 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 5 1.99 - 2.72: 1414 2.72 - 3.44: 38861 3.44 - 4.17: 69168 4.17 - 4.90: 115029 Nonbonded interactions: 224477 Sorted by model distance: nonbonded pdb=" OE2 GLU 1 622 " pdb=" OE2 GLU E 77 " model vdw 1.262 3.040 nonbonded pdb=" NH1 ARG 1 828 " pdb=" OE1 GLU E 71 " model vdw 1.325 3.120 nonbonded pdb=" NZ LYS 1 741 " pdb=" O PHE E 76 " model vdw 1.465 3.120 nonbonded pdb=" OE2 GLU 1 622 " pdb=" CD GLU E 77 " model vdw 1.832 3.270 nonbonded pdb=" NH2 ARG 1 828 " pdb=" CB GLU E 71 " model vdw 1.873 3.520 ... (remaining 224472 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.120 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 94.350 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:13.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 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 : 0.005 0.308 31074 Z= 0.291 Angle : 0.834 29.225 42166 Z= 0.498 Chirality : 0.051 0.681 3945 Planarity : 0.006 0.173 5471 Dihedral : 18.694 154.741 11938 Min Nonbonded Distance : 1.262 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 5.96 % Allowed : 21.55 % Favored : 72.48 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.11), residues: 4127 helix: -1.69 (0.11), residues: 1429 sheet: -1.00 (0.17), residues: 901 loop : -2.40 (0.12), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 395 HIS 0.012 0.001 HIS C 425 PHE 0.018 0.002 PHE D 168 TYR 0.018 0.001 TYR C 394 ARG 0.006 0.000 ARG 3 728 Details of bonding type rmsd hydrogen bonds : bond 0.15422 ( 1530) hydrogen bonds : angle 6.61308 ( 4276) metal coordination : bond 0.14033 ( 15) metal coordination : angle 12.26467 ( 18) covalent geometry : bond 0.00437 (31059) covalent geometry : angle 0.79435 (42148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 483 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 505 LYS cc_start: 0.6145 (ttpp) cc_final: 0.5904 (ttmt) REVERT: 1 572 HIS cc_start: 0.7572 (t70) cc_final: 0.7333 (t70) REVERT: 1 584 ASP cc_start: 0.6448 (t70) cc_final: 0.6235 (t0) REVERT: 1 768 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7358 (mt-10) REVERT: 1 770 MET cc_start: 0.6482 (tpp) cc_final: 0.6274 (tpp) REVERT: 1 789 LEU cc_start: 0.8036 (mt) cc_final: 0.7478 (mt) REVERT: 1 838 VAL cc_start: 0.8060 (t) cc_final: 0.7822 (m) REVERT: 1 908 SER cc_start: 0.6402 (OUTLIER) cc_final: 0.5929 (m) REVERT: 1 947 VAL cc_start: 0.7912 (t) cc_final: 0.7558 (t) REVERT: 1 1056 MET cc_start: 0.8020 (mmm) cc_final: 0.7765 (tpt) REVERT: 2 483 GLN cc_start: 0.6713 (mt0) cc_final: 0.5569 (mp10) REVERT: 2 509 LYS cc_start: 0.6407 (mttm) cc_final: 0.5978 (pttp) REVERT: 3 513 ASP cc_start: 0.2730 (OUTLIER) cc_final: 0.2307 (p0) REVERT: 3 629 SER cc_start: 0.1643 (OUTLIER) cc_final: 0.1418 (p) REVERT: 5 38 ASP cc_start: 0.7648 (p0) cc_final: 0.7330 (p0) REVERT: C 409 GLU cc_start: 0.6405 (mt-10) cc_final: 0.6167 (mp0) REVERT: D 147 ASP cc_start: 0.7016 (m-30) cc_final: 0.6412 (t70) REVERT: D 214 GLU cc_start: 0.6934 (pt0) cc_final: 0.6377 (pt0) REVERT: E 145 LYS cc_start: 0.4861 (OUTLIER) cc_final: 0.4442 (tptp) outliers start: 135 outliers final: 25 residues processed: 590 average time/residue: 1.3625 time to fit residues: 945.2719 Evaluate side-chains 341 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 311 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 557 ASP Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 618 ASP Chi-restraints excluded: chain 1 residue 768 GLU Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 908 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 513 ASP Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 590 MET Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 712 VAL Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 864 SER Chi-restraints excluded: chain 3 residue 872 ILE Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 145 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 361 optimal weight: 10.0000 chunk 324 optimal weight: 20.0000 chunk 180 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 335 optimal weight: 0.4980 chunk 129 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 388 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 518 GLN 1 599 ASN 1 901 GLN 11002 ASN 11007 HIS 11091 HIS 11099 ASN 11144 GLN 11252 GLN 11256 HIS 11293 ASN 2 490 HIS 3 46 ASN 3 194 ASN 3 264 GLN 3 363 HIS 3 480 ASN 3 594 ASN 3 612 ASN 3 776 GLN 3 796 ASN 3 817 GLN 3 916 ASN 3 983 ASN 31052 ASN ** 31147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 13 HIS C 400 HIS C 403 ASN C 405 ASN C 445 HIS C 472 GLN D 134 ASN D 179 ASN E 68 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.257468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.193699 restraints weight = 36308.109| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 2.58 r_work: 0.3511 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31074 Z= 0.152 Angle : 0.637 12.237 42166 Z= 0.320 Chirality : 0.044 0.174 3945 Planarity : 0.005 0.059 5471 Dihedral : 15.384 155.245 6836 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.66 % Favored : 96.32 % Rotamer: Outliers : 6.23 % Allowed : 23.37 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.12), residues: 4127 helix: 0.14 (0.13), residues: 1442 sheet: -0.51 (0.17), residues: 903 loop : -1.82 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 31032 HIS 0.008 0.002 HIS C 425 PHE 0.018 0.002 PHE D 168 TYR 0.014 0.002 TYR D 136 ARG 0.009 0.001 ARG 11041 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 1530) hydrogen bonds : angle 4.65143 ( 4276) metal coordination : bond 0.00820 ( 15) metal coordination : angle 3.32911 ( 18) covalent geometry : bond 0.00338 (31059) covalent geometry : angle 0.63334 (42148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 334 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 498 MET cc_start: 0.4622 (ppp) cc_final: 0.3698 (ptt) REVERT: 1 505 LYS cc_start: 0.6214 (ttpp) cc_final: 0.5904 (ttmt) REVERT: 1 546 ASP cc_start: 0.5966 (OUTLIER) cc_final: 0.5449 (t70) REVERT: 1 572 HIS cc_start: 0.7712 (t70) cc_final: 0.7383 (t70) REVERT: 1 584 ASP cc_start: 0.6954 (t70) cc_final: 0.6668 (t0) REVERT: 1 585 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: 1 807 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7063 (ptpp) REVERT: 1 830 TYR cc_start: 0.7228 (t80) cc_final: 0.6982 (t80) REVERT: 1 832 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6846 (tm-30) REVERT: 1 838 VAL cc_start: 0.8145 (t) cc_final: 0.7838 (m) REVERT: 1 864 TYR cc_start: 0.7178 (t80) cc_final: 0.6861 (t80) REVERT: 1 867 MET cc_start: 0.7493 (ttp) cc_final: 0.7223 (ttp) REVERT: 1 873 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7516 (pp20) REVERT: 1 947 VAL cc_start: 0.7971 (t) cc_final: 0.7623 (t) REVERT: 1 1056 MET cc_start: 0.8551 (mmm) cc_final: 0.8146 (tpt) REVERT: 1 1075 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7616 (ttm-80) REVERT: 1 1277 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: 2 502 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8101 (ttm170) REVERT: 3 8 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8662 (mp) REVERT: 3 629 SER cc_start: 0.1668 (OUTLIER) cc_final: 0.1373 (p) REVERT: 3 706 MET cc_start: 0.3993 (OUTLIER) cc_final: 0.3398 (ttt) REVERT: 3 731 LEU cc_start: 0.8385 (tp) cc_final: 0.8016 (tt) REVERT: 3 1090 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8381 (pt0) REVERT: C 472 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7007 (mp-120) REVERT: D 147 ASP cc_start: 0.7081 (m-30) cc_final: 0.6424 (t70) REVERT: D 168 PHE cc_start: 0.6649 (OUTLIER) cc_final: 0.5473 (m-80) REVERT: D 214 GLU cc_start: 0.6811 (pt0) cc_final: 0.6274 (tp30) REVERT: D 245 LYS cc_start: 0.6341 (mtpt) cc_final: 0.5638 (mmtt) REVERT: E 120 MET cc_start: 0.3704 (mmm) cc_final: 0.3300 (mmm) REVERT: E 148 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6508 (mtm180) REVERT: E 164 MET cc_start: 0.5679 (OUTLIER) cc_final: 0.4161 (tpt) outliers start: 141 outliers final: 46 residues processed: 441 average time/residue: 2.0703 time to fit residues: 1096.9839 Evaluate side-chains 362 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 300 time to evaluate : 4.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 546 ASP Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 807 LYS Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 873 GLU Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1075 ARG Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1277 GLN Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 57 GLU Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 372 GLU Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 590 MET Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 706 MET Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1090 GLU Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 164 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 394 optimal weight: 50.0000 chunk 296 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 297 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 chunk 106 optimal weight: 0.0270 chunk 177 optimal weight: 20.0000 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11002 ASN 3 104 GLN 3 805 ASN 3 844 ASN 31061 ASN 31147 HIS C 403 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.255873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.192013 restraints weight = 36125.810| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.65 r_work: 0.3474 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31074 Z= 0.158 Angle : 0.617 11.993 42166 Z= 0.312 Chirality : 0.044 0.217 3945 Planarity : 0.005 0.061 5471 Dihedral : 14.934 155.060 6809 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.52 % Allowed : 23.10 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 4127 helix: 0.96 (0.14), residues: 1427 sheet: -0.39 (0.17), residues: 913 loop : -1.53 (0.13), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 471 HIS 0.010 0.001 HIS C 425 PHE 0.017 0.002 PHE D 168 TYR 0.019 0.002 TYR 1 979 ARG 0.012 0.001 ARG 2 495 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 1530) hydrogen bonds : angle 4.32537 ( 4276) metal coordination : bond 0.00537 ( 15) metal coordination : angle 3.56919 ( 18) covalent geometry : bond 0.00368 (31059) covalent geometry : angle 0.61246 (42148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 316 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 505 LYS cc_start: 0.6319 (ttpp) cc_final: 0.5963 (ttmt) REVERT: 1 540 MET cc_start: 0.6318 (tpp) cc_final: 0.5947 (tpt) REVERT: 1 768 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: 1 830 TYR cc_start: 0.7340 (t80) cc_final: 0.7013 (t80) REVERT: 1 832 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: 1 838 VAL cc_start: 0.8268 (t) cc_final: 0.7951 (m) REVERT: 1 864 TYR cc_start: 0.7225 (t80) cc_final: 0.6958 (t80) REVERT: 1 1056 MET cc_start: 0.8469 (mmm) cc_final: 0.8078 (tpt) REVERT: 1 1075 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7746 (ttm-80) REVERT: 1 1277 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: 2 458 ASN cc_start: 0.5801 (p0) cc_final: 0.5118 (p0) REVERT: 2 477 MET cc_start: 0.8355 (tpt) cc_final: 0.8124 (tpp) REVERT: 2 502 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8071 (ptp-170) REVERT: 2 511 LEU cc_start: 0.3749 (OUTLIER) cc_final: 0.3517 (pp) REVERT: 3 8 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8717 (mp) REVERT: 3 34 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8092 (mpt-90) REVERT: 3 197 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8712 (t) REVERT: 3 377 MET cc_start: 0.7421 (mtp) cc_final: 0.7183 (mtm) REVERT: 3 463 ARG cc_start: 0.2763 (OUTLIER) cc_final: 0.2292 (ttm-80) REVERT: 3 531 LYS cc_start: 0.0822 (OUTLIER) cc_final: 0.0066 (mmmt) REVERT: 3 625 LEU cc_start: 0.3657 (OUTLIER) cc_final: 0.3316 (tp) REVERT: 3 715 MET cc_start: 0.7040 (mpt) cc_final: 0.6792 (mpp) REVERT: 3 731 LEU cc_start: 0.8498 (tp) cc_final: 0.8156 (tt) REVERT: 3 749 GLN cc_start: 0.0504 (OUTLIER) cc_final: -0.0146 (tp40) REVERT: 3 816 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7964 (tttm) REVERT: 5 17 LYS cc_start: 0.7760 (mmpt) cc_final: 0.7455 (tptp) REVERT: C 406 TYR cc_start: 0.6247 (m-80) cc_final: 0.5986 (m-80) REVERT: D 147 ASP cc_start: 0.7111 (m-30) cc_final: 0.6460 (t70) REVERT: D 214 GLU cc_start: 0.6587 (pt0) cc_final: 0.6244 (tp30) REVERT: D 245 LYS cc_start: 0.6288 (mtpt) cc_final: 0.5585 (mmtt) REVERT: D 247 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6882 (mp) REVERT: E 120 MET cc_start: 0.3614 (mmm) cc_final: 0.3113 (mmm) REVERT: E 164 MET cc_start: 0.5805 (OUTLIER) cc_final: 0.4416 (tpt) outliers start: 125 outliers final: 54 residues processed: 413 average time/residue: 1.2955 time to fit residues: 640.1727 Evaluate side-chains 361 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 291 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 526 PHE Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 567 VAL Chi-restraints excluded: chain 1 residue 606 LEU Chi-restraints excluded: chain 1 residue 651 VAL Chi-restraints excluded: chain 1 residue 768 GLU Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1075 ARG Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1277 GLN Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 511 LEU Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 57 GLU Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 266 ASP Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 589 CYS Chi-restraints excluded: chain 3 residue 590 MET Chi-restraints excluded: chain 3 residue 625 LEU Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 816 LYS Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1196 GLU Chi-restraints excluded: chain 3 residue 1198 ASP Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 164 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 159 optimal weight: 9.9990 chunk 382 optimal weight: 50.0000 chunk 306 optimal weight: 0.0980 chunk 413 optimal weight: 0.8980 chunk 226 optimal weight: 2.9990 chunk 400 optimal weight: 50.0000 chunk 229 optimal weight: 2.9990 chunk 345 optimal weight: 30.0000 chunk 90 optimal weight: 1.9990 chunk 243 optimal weight: 50.0000 chunk 14 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11209 ASN 2 467 GLN 3 46 ASN 3 203 ASN ** 3 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 ASN C 472 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.255798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.190511 restraints weight = 36123.728| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.57 r_work: 0.3474 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 31074 Z= 0.142 Angle : 0.587 11.078 42166 Z= 0.294 Chirality : 0.042 0.190 3945 Planarity : 0.004 0.061 5471 Dihedral : 14.735 154.650 6807 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.83 % Allowed : 22.92 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 4127 helix: 1.36 (0.14), residues: 1431 sheet: -0.22 (0.17), residues: 899 loop : -1.37 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 31032 HIS 0.011 0.001 HIS C 425 PHE 0.016 0.002 PHE D 168 TYR 0.019 0.002 TYR 1 570 ARG 0.005 0.000 ARG 31016 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 1530) hydrogen bonds : angle 4.14895 ( 4276) metal coordination : bond 0.00457 ( 15) metal coordination : angle 3.14873 ( 18) covalent geometry : bond 0.00327 (31059) covalent geometry : angle 0.58338 (42148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 318 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 498 MET cc_start: 0.4671 (ppp) cc_final: 0.4111 (tmm) REVERT: 1 505 LYS cc_start: 0.6299 (ttpp) cc_final: 0.5963 (ttmt) REVERT: 1 540 MET cc_start: 0.6308 (tpp) cc_final: 0.6031 (tpt) REVERT: 1 584 ASP cc_start: 0.7334 (t0) cc_final: 0.7033 (t0) REVERT: 1 587 TYR cc_start: 0.7328 (t80) cc_final: 0.6965 (t80) REVERT: 1 722 GLU cc_start: 0.8011 (mp0) cc_final: 0.7437 (pm20) REVERT: 1 832 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.7046 (tm-30) REVERT: 1 838 VAL cc_start: 0.8332 (t) cc_final: 0.8019 (m) REVERT: 1 864 TYR cc_start: 0.7442 (t80) cc_final: 0.7192 (t80) REVERT: 1 873 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7505 (pp20) REVERT: 1 958 THR cc_start: 0.8448 (p) cc_final: 0.8185 (t) REVERT: 1 1056 MET cc_start: 0.8450 (mmm) cc_final: 0.8094 (tpt) REVERT: 1 1075 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7800 (ttm-80) REVERT: 1 1277 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: 2 458 ASN cc_start: 0.5718 (p0) cc_final: 0.5090 (p0) REVERT: 2 477 MET cc_start: 0.8463 (tpt) cc_final: 0.8249 (tpp) REVERT: 2 502 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7954 (ptp-170) REVERT: 3 34 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8079 (mpt-90) REVERT: 3 86 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8662 (mtt-85) REVERT: 3 197 THR cc_start: 0.8923 (p) cc_final: 0.8703 (t) REVERT: 3 531 LYS cc_start: 0.0794 (OUTLIER) cc_final: 0.0007 (mmmt) REVERT: 3 583 MET cc_start: 0.4329 (OUTLIER) cc_final: 0.4044 (mmp) REVERT: 3 731 LEU cc_start: 0.8531 (tp) cc_final: 0.8207 (tt) REVERT: 3 1018 GLU cc_start: 0.8008 (mp0) cc_final: 0.7571 (mp0) REVERT: 5 17 LYS cc_start: 0.7725 (mmpt) cc_final: 0.7444 (tptp) REVERT: 6 90 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7435 (p0) REVERT: C 406 TYR cc_start: 0.6336 (m-80) cc_final: 0.5825 (m-80) REVERT: D 147 ASP cc_start: 0.7285 (m-30) cc_final: 0.6597 (t70) REVERT: D 168 PHE cc_start: 0.6648 (OUTLIER) cc_final: 0.5407 (m-80) REVERT: D 214 GLU cc_start: 0.6661 (pt0) cc_final: 0.6233 (tp30) REVERT: D 245 LYS cc_start: 0.6291 (mtpt) cc_final: 0.5574 (mmtt) REVERT: D 247 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6793 (mp) REVERT: E 120 MET cc_start: 0.3743 (mmm) cc_final: 0.3217 (mmm) REVERT: E 164 MET cc_start: 0.5750 (OUTLIER) cc_final: 0.4393 (tpt) outliers start: 132 outliers final: 67 residues processed: 421 average time/residue: 1.1983 time to fit residues: 605.5892 Evaluate side-chains 378 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 298 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 567 VAL Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 606 LEU Chi-restraints excluded: chain 1 residue 695 VAL Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 873 GLU Chi-restraints excluded: chain 1 residue 949 GLN Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1070 LYS Chi-restraints excluded: chain 1 residue 1075 ARG Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1277 GLN Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 467 GLN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 57 GLU Chi-restraints excluded: chain 3 residue 71 THR Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 86 ARG Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 420 THR Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 558 LEU Chi-restraints excluded: chain 3 residue 583 MET Chi-restraints excluded: chain 3 residue 589 CYS Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1090 GLU Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1198 ASP Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 16 SER Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 164 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 409 optimal weight: 20.0000 chunk 257 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 216 optimal weight: 0.1980 chunk 13 optimal weight: 50.0000 chunk 357 optimal weight: 30.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 692 HIS 11209 ASN 3 46 ASN D 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.257022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.194119 restraints weight = 36318.264| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.45 r_work: 0.3549 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31074 Z= 0.110 Angle : 0.556 12.727 42166 Z= 0.276 Chirality : 0.041 0.189 3945 Planarity : 0.004 0.057 5471 Dihedral : 14.611 154.357 6804 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.59 % Allowed : 24.51 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 4127 helix: 1.65 (0.14), residues: 1430 sheet: -0.07 (0.17), residues: 897 loop : -1.22 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 1 732 HIS 0.011 0.001 HIS C 425 PHE 0.016 0.001 PHE D 168 TYR 0.021 0.001 TYR 1 570 ARG 0.005 0.000 ARG 31016 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 1530) hydrogen bonds : angle 4.01373 ( 4276) metal coordination : bond 0.00367 ( 15) metal coordination : angle 2.77055 ( 18) covalent geometry : bond 0.00243 (31059) covalent geometry : angle 0.55289 (42148) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 307 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 498 MET cc_start: 0.4684 (ppp) cc_final: 0.4042 (ttm) REVERT: 1 505 LYS cc_start: 0.6372 (ttpp) cc_final: 0.5989 (ttmt) REVERT: 1 584 ASP cc_start: 0.7166 (t0) cc_final: 0.6882 (t0) REVERT: 1 830 TYR cc_start: 0.7504 (t80) cc_final: 0.7056 (t80) REVERT: 1 832 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6653 (tm130) REVERT: 1 838 VAL cc_start: 0.8301 (t) cc_final: 0.7991 (m) REVERT: 1 864 TYR cc_start: 0.7415 (t80) cc_final: 0.7159 (t80) REVERT: 1 873 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7531 (pp20) REVERT: 1 958 THR cc_start: 0.8469 (p) cc_final: 0.8246 (t) REVERT: 1 1003 VAL cc_start: 0.6701 (OUTLIER) cc_final: 0.6438 (t) REVERT: 1 1013 ILE cc_start: 0.7867 (mp) cc_final: 0.7614 (mt) REVERT: 1 1053 ARG cc_start: 0.8101 (mtp-110) cc_final: 0.7888 (mtp85) REVERT: 1 1056 MET cc_start: 0.8371 (mmm) cc_final: 0.8032 (tpt) REVERT: 1 1075 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7734 (ttm-80) REVERT: 1 1277 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: 2 458 ASN cc_start: 0.5702 (p0) cc_final: 0.5086 (p0) REVERT: 3 34 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7906 (mpt-90) REVERT: 3 86 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8539 (mtt-85) REVERT: 3 145 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8787 (t0) REVERT: 3 197 THR cc_start: 0.8882 (p) cc_final: 0.8665 (t) REVERT: 3 531 LYS cc_start: 0.0744 (OUTLIER) cc_final: -0.0337 (mmpt) REVERT: 3 568 MET cc_start: 0.2078 (mmp) cc_final: 0.1224 (mpm) REVERT: 3 583 MET cc_start: 0.4414 (OUTLIER) cc_final: 0.4151 (mmp) REVERT: 3 629 SER cc_start: 0.1790 (OUTLIER) cc_final: 0.1503 (p) REVERT: 3 731 LEU cc_start: 0.8431 (tp) cc_final: 0.8162 (tt) REVERT: 3 818 GLN cc_start: 0.8224 (tt0) cc_final: 0.8005 (tt0) REVERT: 3 1018 GLU cc_start: 0.7879 (mp0) cc_final: 0.7460 (mp0) REVERT: 5 17 LYS cc_start: 0.7687 (mmpt) cc_final: 0.7437 (tptp) REVERT: 6 90 ASN cc_start: 0.7801 (p0) cc_final: 0.7495 (p0) REVERT: C 406 TYR cc_start: 0.6358 (m-80) cc_final: 0.5713 (m-80) REVERT: D 147 ASP cc_start: 0.7177 (m-30) cc_final: 0.6537 (t70) REVERT: D 168 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.5313 (m-80) REVERT: D 214 GLU cc_start: 0.6590 (pt0) cc_final: 0.6199 (tp30) REVERT: D 245 LYS cc_start: 0.6117 (mtpt) cc_final: 0.5679 (pttp) REVERT: D 247 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6690 (mp) REVERT: E 120 MET cc_start: 0.3754 (mmm) cc_final: 0.3270 (mmm) outliers start: 104 outliers final: 58 residues processed: 387 average time/residue: 1.2500 time to fit residues: 580.0495 Evaluate side-chains 360 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 289 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 606 LEU Chi-restraints excluded: chain 1 residue 695 VAL Chi-restraints excluded: chain 1 residue 722 GLU Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 873 GLU Chi-restraints excluded: chain 1 residue 949 GLN Chi-restraints excluded: chain 1 residue 962 MET Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1075 ARG Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1180 ARG Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1277 GLN Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 86 ARG Chi-restraints excluded: chain 3 residue 145 ASN Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 266 ASP Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 583 MET Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 712 VAL Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1198 ASP Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 154 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 332 optimal weight: 3.9990 chunk 287 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 297 optimal weight: 7.9990 chunk 5 optimal weight: 40.0000 chunk 298 optimal weight: 40.0000 chunk 378 optimal weight: 50.0000 chunk 137 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 chunk 381 optimal weight: 0.0060 chunk 385 optimal weight: 0.9980 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 692 HIS 11209 ASN 2 467 GLN 3 46 ASN 3 998 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.255919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.193997 restraints weight = 36145.773| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.40 r_work: 0.3528 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 31074 Z= 0.163 Angle : 0.604 11.833 42166 Z= 0.301 Chirality : 0.043 0.198 3945 Planarity : 0.004 0.061 5471 Dihedral : 14.547 154.221 6800 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.74 % Allowed : 23.50 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.13), residues: 4127 helix: 1.69 (0.14), residues: 1434 sheet: -0.05 (0.17), residues: 904 loop : -1.18 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 1 819 HIS 0.011 0.001 HIS C 425 PHE 0.017 0.002 PHE 31182 TYR 0.022 0.002 TYR 1 570 ARG 0.005 0.001 ARG 1 517 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 1530) hydrogen bonds : angle 4.03905 ( 4276) metal coordination : bond 0.00484 ( 15) metal coordination : angle 3.24163 ( 18) covalent geometry : bond 0.00384 (31059) covalent geometry : angle 0.60014 (42148) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 297 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 498 MET cc_start: 0.4737 (ppp) cc_final: 0.3947 (ttm) REVERT: 1 584 ASP cc_start: 0.7147 (t0) cc_final: 0.6850 (t0) REVERT: 1 722 GLU cc_start: 0.7690 (mp0) cc_final: 0.7388 (mp0) REVERT: 1 802 GLU cc_start: 0.5483 (OUTLIER) cc_final: 0.5020 (mp0) REVERT: 1 832 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6735 (tm130) REVERT: 1 838 VAL cc_start: 0.8316 (t) cc_final: 0.7986 (m) REVERT: 1 864 TYR cc_start: 0.7515 (t80) cc_final: 0.7239 (t80) REVERT: 1 873 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7486 (pp20) REVERT: 1 958 THR cc_start: 0.8630 (p) cc_final: 0.8357 (t) REVERT: 1 1003 VAL cc_start: 0.6846 (OUTLIER) cc_final: 0.6571 (t) REVERT: 1 1013 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7565 (mt) REVERT: 1 1053 ARG cc_start: 0.8109 (mtp-110) cc_final: 0.7887 (mtp85) REVERT: 1 1056 MET cc_start: 0.8498 (mmm) cc_final: 0.8108 (tpt) REVERT: 1 1075 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7855 (ttm-80) REVERT: 2 458 ASN cc_start: 0.5769 (p0) cc_final: 0.5198 (p0) REVERT: 2 502 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7890 (ptp-170) REVERT: 3 1 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7984 (ttt) REVERT: 3 34 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8212 (mpt-90) REVERT: 3 86 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8619 (mtt-85) REVERT: 3 197 THR cc_start: 0.8907 (p) cc_final: 0.8689 (t) REVERT: 3 274 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7161 (mtm180) REVERT: 3 463 ARG cc_start: 0.3120 (OUTLIER) cc_final: 0.2054 (ptm160) REVERT: 3 531 LYS cc_start: 0.0885 (OUTLIER) cc_final: -0.0149 (mmpt) REVERT: 3 583 MET cc_start: 0.4361 (OUTLIER) cc_final: 0.4063 (mmp) REVERT: 3 629 SER cc_start: 0.1902 (OUTLIER) cc_final: 0.1577 (p) REVERT: 3 715 MET cc_start: 0.6301 (mmp) cc_final: 0.6065 (mmp) REVERT: 3 731 LEU cc_start: 0.8487 (tp) cc_final: 0.8178 (tt) REVERT: 3 749 GLN cc_start: 0.0176 (OUTLIER) cc_final: -0.0542 (pp30) REVERT: 3 1018 GLU cc_start: 0.7886 (mp0) cc_final: 0.7526 (mp0) REVERT: 5 17 LYS cc_start: 0.7751 (mmpt) cc_final: 0.7484 (tptp) REVERT: 6 90 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7535 (p0) REVERT: C 400 HIS cc_start: 0.6510 (OUTLIER) cc_final: 0.5542 (t70) REVERT: C 406 TYR cc_start: 0.6546 (m-80) cc_final: 0.5923 (m-80) REVERT: D 147 ASP cc_start: 0.7220 (m-30) cc_final: 0.6542 (t70) REVERT: D 214 GLU cc_start: 0.6654 (pt0) cc_final: 0.6244 (tp30) REVERT: D 245 LYS cc_start: 0.6187 (mtpt) cc_final: 0.5470 (mttt) REVERT: D 247 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6938 (mp) REVERT: E 120 MET cc_start: 0.3703 (mmm) cc_final: 0.3223 (mmm) outliers start: 130 outliers final: 73 residues processed: 402 average time/residue: 1.2184 time to fit residues: 588.2935 Evaluate side-chains 386 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 294 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 548 GLU Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 606 LEU Chi-restraints excluded: chain 1 residue 695 VAL Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 802 GLU Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 873 GLU Chi-restraints excluded: chain 1 residue 949 GLN Chi-restraints excluded: chain 1 residue 962 MET Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1013 ILE Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1075 ARG Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 467 GLN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 572 HIS Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 71 THR Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 86 ARG Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 266 ASP Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 420 THR Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 492 GLU Chi-restraints excluded: chain 3 residue 506 LEU Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 558 LEU Chi-restraints excluded: chain 3 residue 583 MET Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 712 VAL Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 850 SER Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1196 GLU Chi-restraints excluded: chain 3 residue 1198 ASP Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 154 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 218 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 110 optimal weight: 30.0000 chunk 270 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 351 optimal weight: 0.0020 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 50.0000 chunk 216 optimal weight: 4.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 692 HIS 11209 ASN 3 46 ASN 3 518 GLN ** 3 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 575 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.256378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.195260 restraints weight = 36281.893| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.34 r_work: 0.3555 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31074 Z= 0.128 Angle : 0.564 11.114 42166 Z= 0.281 Chirality : 0.042 0.183 3945 Planarity : 0.004 0.060 5471 Dihedral : 14.508 153.956 6800 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.99 % Allowed : 24.82 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.13), residues: 4127 helix: 1.78 (0.14), residues: 1436 sheet: 0.07 (0.18), residues: 902 loop : -1.07 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 819 HIS 0.012 0.001 HIS C 425 PHE 0.015 0.001 PHE 3 788 TYR 0.017 0.001 TYR D 136 ARG 0.006 0.000 ARG 3 429 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 1530) hydrogen bonds : angle 3.97323 ( 4276) metal coordination : bond 0.00527 ( 15) metal coordination : angle 2.92048 ( 18) covalent geometry : bond 0.00295 (31059) covalent geometry : angle 0.56053 (42148) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 296 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 498 MET cc_start: 0.4755 (ppp) cc_final: 0.4041 (ttm) REVERT: 1 584 ASP cc_start: 0.7185 (t0) cc_final: 0.6952 (t0) REVERT: 1 802 GLU cc_start: 0.5609 (OUTLIER) cc_final: 0.5284 (mp0) REVERT: 1 832 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6733 (tm130) REVERT: 1 838 VAL cc_start: 0.8363 (t) cc_final: 0.8037 (m) REVERT: 1 864 TYR cc_start: 0.7487 (t80) cc_final: 0.7209 (t80) REVERT: 1 873 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7472 (pp20) REVERT: 1 958 THR cc_start: 0.8652 (p) cc_final: 0.8381 (t) REVERT: 1 1003 VAL cc_start: 0.6821 (OUTLIER) cc_final: 0.6545 (t) REVERT: 1 1056 MET cc_start: 0.8408 (mmm) cc_final: 0.7998 (tpt) REVERT: 1 1075 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7818 (ttm-80) REVERT: 2 458 ASN cc_start: 0.5779 (p0) cc_final: 0.5219 (p0) REVERT: 2 502 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7809 (ptp-170) REVERT: 3 1 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7907 (ttt) REVERT: 3 34 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8045 (mpt-90) REVERT: 3 86 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8570 (mtt-85) REVERT: 3 197 THR cc_start: 0.8896 (p) cc_final: 0.8675 (t) REVERT: 3 274 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7044 (mtm180) REVERT: 3 447 MET cc_start: 0.2579 (ttm) cc_final: 0.1169 (tpp) REVERT: 3 531 LYS cc_start: 0.1039 (OUTLIER) cc_final: 0.0054 (mmmt) REVERT: 3 575 ASN cc_start: 0.3632 (OUTLIER) cc_final: 0.3100 (p0) REVERT: 3 583 MET cc_start: 0.4653 (OUTLIER) cc_final: 0.4322 (mmp) REVERT: 3 629 SER cc_start: 0.1881 (OUTLIER) cc_final: 0.1560 (p) REVERT: 3 731 LEU cc_start: 0.8497 (tp) cc_final: 0.8202 (tt) REVERT: 3 1018 GLU cc_start: 0.7893 (mp0) cc_final: 0.7496 (mp0) REVERT: 5 17 LYS cc_start: 0.7656 (mmpt) cc_final: 0.7426 (tptp) REVERT: 6 90 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7496 (p0) REVERT: C 406 TYR cc_start: 0.6543 (m-80) cc_final: 0.5994 (m-80) REVERT: D 147 ASP cc_start: 0.7160 (m-30) cc_final: 0.6479 (t70) REVERT: D 214 GLU cc_start: 0.6661 (pt0) cc_final: 0.6265 (tp30) REVERT: D 245 LYS cc_start: 0.6193 (mtpt) cc_final: 0.5437 (mmtt) REVERT: D 247 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6834 (mp) REVERT: E 120 MET cc_start: 0.3718 (mmm) cc_final: 0.3215 (mmm) outliers start: 113 outliers final: 66 residues processed: 386 average time/residue: 1.4584 time to fit residues: 680.8036 Evaluate side-chains 367 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 285 time to evaluate : 6.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 548 GLU Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 695 VAL Chi-restraints excluded: chain 1 residue 725 ASP Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 802 GLU Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 873 GLU Chi-restraints excluded: chain 1 residue 949 GLN Chi-restraints excluded: chain 1 residue 962 MET Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1075 ARG Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1180 ARG Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 572 HIS Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 86 ARG Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 266 ASP Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 492 GLU Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 558 LEU Chi-restraints excluded: chain 3 residue 575 ASN Chi-restraints excluded: chain 3 residue 583 MET Chi-restraints excluded: chain 3 residue 589 CYS Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 850 SER Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1198 ASP Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 154 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 235 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 246 optimal weight: 0.0470 chunk 351 optimal weight: 0.0370 chunk 109 optimal weight: 2.9990 chunk 11 optimal weight: 50.0000 chunk 78 optimal weight: 0.6980 chunk 193 optimal weight: 10.0000 chunk 242 optimal weight: 0.3980 chunk 231 optimal weight: 50.0000 chunk 42 optimal weight: 10.0000 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 692 HIS 11209 ASN 11283 HIS 3 46 ASN ** 3 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 575 ASN 3 670 GLN C 403 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.257920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.196712 restraints weight = 36568.893| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 2.46 r_work: 0.3586 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31074 Z= 0.098 Angle : 0.527 10.983 42166 Z= 0.263 Chirality : 0.040 0.165 3945 Planarity : 0.004 0.055 5471 Dihedral : 14.434 153.778 6800 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.93 % Allowed : 25.75 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.13), residues: 4127 helix: 1.98 (0.14), residues: 1433 sheet: 0.15 (0.18), residues: 906 loop : -0.95 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 1 732 HIS 0.013 0.001 HIS C 425 PHE 0.013 0.001 PHE 3 788 TYR 0.017 0.001 TYR D 209 ARG 0.010 0.000 ARG 1 495 Details of bonding type rmsd hydrogen bonds : bond 0.03065 ( 1530) hydrogen bonds : angle 3.85007 ( 4276) metal coordination : bond 0.00722 ( 15) metal coordination : angle 2.61940 ( 18) covalent geometry : bond 0.00211 (31059) covalent geometry : angle 0.52431 (42148) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 303 time to evaluate : 6.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 498 MET cc_start: 0.4693 (ppp) cc_final: 0.4029 (ttm) REVERT: 1 561 TYR cc_start: 0.7609 (t80) cc_final: 0.7318 (t80) REVERT: 1 584 ASP cc_start: 0.7276 (t0) cc_final: 0.7058 (t0) REVERT: 1 802 GLU cc_start: 0.5611 (OUTLIER) cc_final: 0.5332 (mp0) REVERT: 1 820 GLN cc_start: 0.3796 (OUTLIER) cc_final: 0.3517 (mt0) REVERT: 1 830 TYR cc_start: 0.7468 (t80) cc_final: 0.7042 (t80) REVERT: 1 832 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.6815 (tm130) REVERT: 1 838 VAL cc_start: 0.8380 (t) cc_final: 0.8062 (m) REVERT: 1 864 TYR cc_start: 0.7414 (t80) cc_final: 0.7172 (t80) REVERT: 1 873 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7511 (pp20) REVERT: 1 947 VAL cc_start: 0.7954 (t) cc_final: 0.7749 (m) REVERT: 1 958 THR cc_start: 0.8595 (p) cc_final: 0.8362 (t) REVERT: 1 1003 VAL cc_start: 0.6670 (OUTLIER) cc_final: 0.6394 (t) REVERT: 1 1056 MET cc_start: 0.8375 (mmm) cc_final: 0.8016 (tpt) REVERT: 1 1075 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7758 (ttm-80) REVERT: 2 502 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7832 (ptp-170) REVERT: 3 34 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7838 (mpt-90) REVERT: 3 197 THR cc_start: 0.8869 (p) cc_final: 0.8654 (t) REVERT: 3 442 LEU cc_start: 0.7641 (mm) cc_final: 0.7378 (mm) REVERT: 3 447 MET cc_start: 0.2076 (ttm) cc_final: 0.1264 (tpp) REVERT: 3 531 LYS cc_start: 0.0957 (OUTLIER) cc_final: -0.0093 (mmmt) REVERT: 3 575 ASN cc_start: 0.3609 (OUTLIER) cc_final: 0.3357 (p0) REVERT: 3 583 MET cc_start: 0.4570 (OUTLIER) cc_final: 0.4223 (mmp) REVERT: 3 629 SER cc_start: 0.1798 (OUTLIER) cc_final: 0.1487 (p) REVERT: 3 645 MET cc_start: 0.1889 (tpp) cc_final: 0.1238 (ptt) REVERT: 3 731 LEU cc_start: 0.8469 (tp) cc_final: 0.8215 (tt) REVERT: 3 749 GLN cc_start: 0.0179 (OUTLIER) cc_final: -0.0804 (tp-100) REVERT: 3 809 GLU cc_start: 0.7041 (pm20) cc_final: 0.6736 (pm20) REVERT: 3 817 GLN cc_start: 0.7973 (tp-100) cc_final: 0.7769 (mm-40) REVERT: 3 818 GLN cc_start: 0.8347 (tt0) cc_final: 0.8086 (tt0) REVERT: 3 1018 GLU cc_start: 0.7979 (mp0) cc_final: 0.7508 (mp0) REVERT: 6 90 ASN cc_start: 0.7821 (p0) cc_final: 0.7515 (p0) REVERT: C 406 TYR cc_start: 0.6503 (m-80) cc_final: 0.5713 (m-80) REVERT: D 147 ASP cc_start: 0.7145 (m-30) cc_final: 0.6524 (t70) REVERT: D 214 GLU cc_start: 0.6606 (pt0) cc_final: 0.6227 (tp30) REVERT: D 245 LYS cc_start: 0.6117 (mtpt) cc_final: 0.5691 (pttp) REVERT: D 247 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6725 (mp) REVERT: E 120 MET cc_start: 0.3728 (mmm) cc_final: 0.3210 (mmm) REVERT: E 131 MET cc_start: 0.1427 (mmt) cc_final: 0.0216 (mmm) outliers start: 89 outliers final: 52 residues processed: 374 average time/residue: 2.0684 time to fit residues: 936.2119 Evaluate side-chains 357 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 291 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 548 GLU Chi-restraints excluded: chain 1 residue 695 VAL Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 802 GLU Chi-restraints excluded: chain 1 residue 820 GLN Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 873 GLU Chi-restraints excluded: chain 1 residue 949 GLN Chi-restraints excluded: chain 1 residue 962 MET Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1075 ARG Chi-restraints excluded: chain 1 residue 1180 ARG Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 572 HIS Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 506 LEU Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 575 ASN Chi-restraints excluded: chain 3 residue 583 MET Chi-restraints excluded: chain 3 residue 589 CYS Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 147 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 412 optimal weight: 0.0470 chunk 211 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 208 optimal weight: 0.0270 chunk 364 optimal weight: 40.0000 chunk 268 optimal weight: 40.0000 chunk 131 optimal weight: 1.9990 chunk 185 optimal weight: 20.0000 chunk 334 optimal weight: 3.9990 chunk 415 optimal weight: 50.0000 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 692 HIS 1 829 ASN 11209 ASN 2 458 ASN 2 467 GLN 3 46 ASN ** 3 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 575 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.255726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.195007 restraints weight = 36004.544| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.36 r_work: 0.3539 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31074 Z= 0.163 Angle : 0.599 12.713 42166 Z= 0.300 Chirality : 0.043 0.192 3945 Planarity : 0.004 0.059 5471 Dihedral : 14.445 153.988 6796 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.42 % Allowed : 25.40 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.13), residues: 4127 helix: 1.89 (0.14), residues: 1439 sheet: 0.14 (0.18), residues: 906 loop : -0.98 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 1 819 HIS 0.012 0.001 HIS C 425 PHE 0.017 0.002 PHE 11155 TYR 0.019 0.002 TYR 11049 ARG 0.014 0.001 ARG 1 495 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 1530) hydrogen bonds : angle 3.94252 ( 4276) metal coordination : bond 0.00526 ( 15) metal coordination : angle 3.17182 ( 18) covalent geometry : bond 0.00388 (31059) covalent geometry : angle 0.59565 (42148) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 290 time to evaluate : 4.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 498 MET cc_start: 0.4858 (ppp) cc_final: 0.4272 (ttm) REVERT: 1 561 TYR cc_start: 0.7611 (t80) cc_final: 0.7357 (t80) REVERT: 1 802 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5411 (mp0) REVERT: 1 830 TYR cc_start: 0.7587 (t80) cc_final: 0.7270 (t80) REVERT: 1 832 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.6803 (tm130) REVERT: 1 838 VAL cc_start: 0.8498 (t) cc_final: 0.8190 (m) REVERT: 1 873 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7429 (pp20) REVERT: 1 947 VAL cc_start: 0.8002 (OUTLIER) cc_final: 0.7796 (m) REVERT: 1 958 THR cc_start: 0.8678 (p) cc_final: 0.8389 (t) REVERT: 1 1003 VAL cc_start: 0.6831 (OUTLIER) cc_final: 0.6560 (t) REVERT: 1 1013 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7431 (mt) REVERT: 1 1049 TYR cc_start: 0.7427 (m-10) cc_final: 0.7209 (m-10) REVERT: 1 1056 MET cc_start: 0.8493 (mmm) cc_final: 0.8067 (tpt) REVERT: 1 1075 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7891 (ttm-80) REVERT: 2 502 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7979 (ptp-170) REVERT: 3 34 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8178 (mpt-90) REVERT: 3 86 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8619 (mtt-85) REVERT: 3 197 THR cc_start: 0.8914 (p) cc_final: 0.8680 (t) REVERT: 3 377 MET cc_start: 0.7600 (mtm) cc_final: 0.7226 (ptm) REVERT: 3 447 MET cc_start: 0.2411 (ttm) cc_final: 0.1320 (tpp) REVERT: 3 531 LYS cc_start: 0.0863 (OUTLIER) cc_final: 0.0163 (mmmt) REVERT: 3 629 SER cc_start: 0.2007 (OUTLIER) cc_final: 0.1632 (p) REVERT: 3 645 MET cc_start: 0.2059 (tpp) cc_final: 0.1202 (ptt) REVERT: 3 731 LEU cc_start: 0.8481 (tp) cc_final: 0.8244 (tt) REVERT: 3 749 GLN cc_start: 0.0104 (OUTLIER) cc_final: -0.0915 (tp-100) REVERT: 3 817 GLN cc_start: 0.8065 (tp-100) cc_final: 0.7841 (mm-40) REVERT: 3 1018 GLU cc_start: 0.7981 (mp0) cc_final: 0.7579 (mp0) REVERT: 6 90 ASN cc_start: 0.7850 (p0) cc_final: 0.7547 (p0) REVERT: C 406 TYR cc_start: 0.6313 (m-80) cc_final: 0.5687 (m-80) REVERT: C 414 TYR cc_start: 0.6623 (t80) cc_final: 0.5744 (t80) REVERT: D 147 ASP cc_start: 0.7276 (m-30) cc_final: 0.6549 (t70) REVERT: D 214 GLU cc_start: 0.6824 (pt0) cc_final: 0.6198 (tp30) REVERT: D 245 LYS cc_start: 0.6319 (mtpt) cc_final: 0.5809 (pttp) REVERT: D 247 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7041 (mp) REVERT: E 120 MET cc_start: 0.3677 (mmm) cc_final: 0.3191 (mmm) outliers start: 100 outliers final: 65 residues processed: 368 average time/residue: 1.5046 time to fit residues: 670.1664 Evaluate side-chains 361 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 282 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 548 GLU Chi-restraints excluded: chain 1 residue 695 VAL Chi-restraints excluded: chain 1 residue 725 ASP Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 802 GLU Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 873 GLU Chi-restraints excluded: chain 1 residue 947 VAL Chi-restraints excluded: chain 1 residue 949 GLN Chi-restraints excluded: chain 1 residue 962 MET Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1013 ILE Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1075 ARG Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1180 ARG Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 467 GLN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 572 HIS Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 71 THR Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 86 ARG Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 506 LEU Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 589 CYS Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 850 SER Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1198 ASP Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 11 LEU Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 147 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 5 optimal weight: 30.0000 chunk 123 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 379 optimal weight: 50.0000 chunk 314 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 426 optimal weight: 50.0000 chunk 355 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 692 HIS 11209 ASN 2 458 ASN 3 46 ASN ** 3 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.256153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.194476 restraints weight = 36143.152| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 2.33 r_work: 0.3555 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31074 Z= 0.135 Angle : 0.578 12.034 42166 Z= 0.289 Chirality : 0.042 0.173 3945 Planarity : 0.004 0.060 5471 Dihedral : 14.434 154.033 6796 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.75 % Allowed : 26.15 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.13), residues: 4127 helix: 1.93 (0.14), residues: 1440 sheet: 0.14 (0.18), residues: 904 loop : -0.94 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 708 HIS 0.013 0.001 HIS C 425 PHE 0.015 0.002 PHE 3 788 TYR 0.019 0.002 TYR 1 805 ARG 0.016 0.000 ARG 1 495 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 1530) hydrogen bonds : angle 3.89193 ( 4276) metal coordination : bond 0.00390 ( 15) metal coordination : angle 3.01026 ( 18) covalent geometry : bond 0.00315 (31059) covalent geometry : angle 0.57443 (42148) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 289 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 498 MET cc_start: 0.4919 (ppp) cc_final: 0.4246 (ttm) REVERT: 1 561 TYR cc_start: 0.7594 (t80) cc_final: 0.7372 (t80) REVERT: 1 802 GLU cc_start: 0.5774 (OUTLIER) cc_final: 0.5433 (mp0) REVERT: 1 830 TYR cc_start: 0.7418 (t80) cc_final: 0.6934 (t80) REVERT: 1 832 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6596 (tm130) REVERT: 1 838 VAL cc_start: 0.8371 (t) cc_final: 0.8078 (m) REVERT: 1 873 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7445 (pp20) REVERT: 1 958 THR cc_start: 0.8655 (p) cc_final: 0.8371 (t) REVERT: 1 1003 VAL cc_start: 0.6850 (OUTLIER) cc_final: 0.6563 (t) REVERT: 1 1056 MET cc_start: 0.8441 (mmm) cc_final: 0.7996 (tpt) REVERT: 1 1075 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7848 (ttm-80) REVERT: 2 458 ASN cc_start: 0.6372 (OUTLIER) cc_final: 0.5815 (p0) REVERT: 2 502 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7974 (ptp-170) REVERT: 3 34 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8039 (mpt-90) REVERT: 3 86 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8571 (mtt-85) REVERT: 3 197 THR cc_start: 0.8897 (p) cc_final: 0.8659 (t) REVERT: 3 274 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7083 (mtm180) REVERT: 3 377 MET cc_start: 0.7507 (mtm) cc_final: 0.7245 (ptm) REVERT: 3 442 LEU cc_start: 0.7611 (mm) cc_final: 0.7381 (mm) REVERT: 3 447 MET cc_start: 0.2185 (ttm) cc_final: 0.0999 (tpp) REVERT: 3 531 LYS cc_start: 0.0838 (OUTLIER) cc_final: 0.0132 (mmmt) REVERT: 3 629 SER cc_start: 0.2273 (OUTLIER) cc_final: 0.1638 (m) REVERT: 3 645 MET cc_start: 0.1676 (tpp) cc_final: 0.1025 (ptt) REVERT: 3 731 LEU cc_start: 0.8467 (tp) cc_final: 0.8258 (tt) REVERT: 3 749 GLN cc_start: 0.0401 (OUTLIER) cc_final: -0.0415 (pp30) REVERT: 3 817 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7763 (mm-40) REVERT: 3 1018 GLU cc_start: 0.7959 (mp0) cc_final: 0.7557 (mp0) REVERT: 6 90 ASN cc_start: 0.7840 (p0) cc_final: 0.7540 (p0) REVERT: C 406 TYR cc_start: 0.6552 (m-80) cc_final: 0.5856 (m-80) REVERT: D 147 ASP cc_start: 0.7280 (m-30) cc_final: 0.6543 (t70) REVERT: D 214 GLU cc_start: 0.6803 (pt0) cc_final: 0.6145 (tp30) REVERT: D 247 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6927 (mp) REVERT: E 120 MET cc_start: 0.3593 (mmm) cc_final: 0.3092 (mmm) outliers start: 85 outliers final: 55 residues processed: 357 average time/residue: 1.2080 time to fit residues: 521.6851 Evaluate side-chains 350 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 281 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 548 GLU Chi-restraints excluded: chain 1 residue 695 VAL Chi-restraints excluded: chain 1 residue 722 GLU Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 802 GLU Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 873 GLU Chi-restraints excluded: chain 1 residue 962 MET Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1075 ARG Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 458 ASN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 572 HIS Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 57 GLU Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 86 ARG Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 506 LEU Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 589 CYS Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 850 SER Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1198 ASP Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 11 LEU Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 147 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 168 optimal weight: 7.9990 chunk 412 optimal weight: 0.0470 chunk 257 optimal weight: 1.9990 chunk 332 optimal weight: 4.9990 chunk 378 optimal weight: 50.0000 chunk 75 optimal weight: 0.9980 chunk 254 optimal weight: 0.0060 chunk 356 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 358 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 692 HIS ** 1 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11209 ASN 2 458 ASN 3 46 ASN ** 3 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.256186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.196566 restraints weight = 36108.594| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.30 r_work: 0.3558 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.252 31074 Z= 0.166 Angle : 0.691 59.162 42166 Z= 0.367 Chirality : 0.044 0.958 3945 Planarity : 0.004 0.059 5471 Dihedral : 14.433 154.004 6796 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.36 % Allowed : 26.81 % Favored : 69.83 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 4127 helix: 1.94 (0.14), residues: 1440 sheet: 0.15 (0.18), residues: 903 loop : -0.94 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 732 HIS 0.013 0.001 HIS C 425 PHE 0.016 0.001 PHE 3 788 TYR 0.017 0.001 TYR 11049 ARG 0.016 0.000 ARG 1 495 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 1530) hydrogen bonds : angle 3.89188 ( 4276) metal coordination : bond 0.02493 ( 15) metal coordination : angle 3.00886 ( 18) covalent geometry : bond 0.00369 (31059) covalent geometry : angle 0.68877 (42148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39706.15 seconds wall clock time: 697 minutes 57.66 seconds (41877.66 seconds total)