Starting phenix.real_space_refine (version: dev) on Sat May 14 20:54:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4o_13811/05_2022/7q4o_13811_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4o_13811/05_2022/7q4o_13811.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4o_13811/05_2022/7q4o_13811_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4o_13811/05_2022/7q4o_13811_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4o_13811/05_2022/7q4o_13811_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4o_13811/05_2022/7q4o_13811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4o_13811/05_2022/7q4o_13811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4o_13811/05_2022/7q4o_13811_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4o_13811/05_2022/7q4o_13811_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "9 GLU 428": "OE1" <-> "OE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 114": "NH1" <-> "NH2" Residue "C TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "C TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1065": "OE1" <-> "OE2" Residue "C GLU 1099": "OE1" <-> "OE2" Residue "C PHE 1168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "G ASP 27": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 21212 Number of models: 1 Model: "" Number of chains: 20 Chain: "1" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 321 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "2" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 739 Classifications: {'RNA': 35} Modifications used: {'rna3p': 10, 'rna2p': 1, 'rna3p_pur': 12, 'rna3p_pyr': 7, 'rna2p_pur': 3, 'rna2p_pyr': 2} Link IDs: {'rna3p': 28, 'rna2p': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "9" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 782 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 6639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6639 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 35, 'TRANS': 799, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1043 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain breaks: 2 Chain: "C" Number of atoms: 9255 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1181, 9247 Classifications: {'peptide': 1181} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1120, 'PCIS': 2} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 1181, 9247 Classifications: {'peptide': 1181} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1120, 'PCIS': 2} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 9426 Chain: "E" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 531 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "F" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 745 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain: "G" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 592 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "h" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 275 Classifications: {'RNA': 13} Modifications used: {'rna3p_pyr': 6, 'rna2p_pur': 1, 'rna3p_pur': 6} Link IDs: {'rna3p': 11, 'rna2p': 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" 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: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "h" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 118 SG CYS 1 56 47.111 52.373 24.279 1.00 95.24 S ATOM 141 SG CYS 1 59 50.861 51.295 23.601 1.00 92.97 S ATOM 1183 SG CYS 9 408 72.578 28.007 41.933 1.00108.56 S ATOM 1206 SG CYS 9 411 69.232 26.603 39.890 1.00110.39 S ATOM 20210 SG CYS G 30 54.883 79.862 61.930 1.00 49.61 S ATOM 20231 SG CYS G 33 53.921 77.253 59.858 1.00 52.86 S ATOM 20513 SG CYS G 72 52.244 77.183 63.288 1.00 38.79 S ATOM 20537 SG CYS G 75 55.787 76.633 62.802 1.00 43.71 S ATOM 20080 SG CYS G 11 69.989 85.530 62.875 1.00 73.10 S ATOM 20335 SG CYS G 46 69.644 88.054 64.908 1.00 67.15 S ATOM 20358 SG CYS G 49 68.451 89.512 62.400 1.00 85.43 S ATOM 20616 SG CYS G 85 66.902 86.872 64.085 1.00 60.88 S ATOM 20167 SG CYS G 23 54.959 92.962 56.014 1.00 73.78 S ATOM 20183 SG CYS G 26 55.044 89.893 54.985 1.00 77.31 S ATOM 20417 SG CYS G 58 57.443 91.409 57.957 1.00 85.09 S ATOM 20438 SG CYS G 61 57.790 91.933 54.306 1.00 86.66 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AMET C 1 " occ=0.40 ... (14 atoms not shown) pdb=" CE BMET C 1 " occ=0.60 Time building chain proxies: 16.46, per 1000 atoms: 0.78 Number of scatterers: 21212 At special positions: 0 Unit cell: (121.6, 142.72, 158.08, 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 5 29.99 S 117 16.00 P 48 15.00 O 4303 8.00 N 3598 7.00 C 13141 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 - 3.50 Amino acid : False - 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: 9.32 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN 1 501 " pdb="ZN ZN 1 501 " - pdb=" SG CYS 1 59 " pdb="ZN ZN 1 501 " - pdb=" SG CYS 1 56 " pdb="ZN ZN 1 501 " - pdb=" NE2 HIS 1 72 " pdb="ZN ZN 1 501 " - pdb=" ND1 HIS 1 78 " pdb=" ZN 9 601 " pdb="ZN ZN 9 601 " - pdb=" NE2 HIS 9 425 " pdb="ZN ZN 9 601 " - pdb=" SG CYS 9 408 " pdb="ZN ZN 9 601 " - pdb=" ND1 HIS 9 431 " pdb="ZN ZN 9 601 " - pdb=" SG CYS 9 411 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 33 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 75 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 30 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 72 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 46 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 49 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 11 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 85 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 23 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 61 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 26 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 58 " Number of angles added : 20 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4714 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 25 sheets defined 38.1% alpha, 19.6% beta 8 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 9.66 Creating SS restraints... Processing helix chain '1' and resid 66 through 73 Processing helix chain '1' and resid 76 through 82 Processing helix chain '9' and resid 396 through 399 No H-bonds generated for 'chain '9' and resid 396 through 399' Processing helix chain '9' and resid 419 through 427 removed outlier: 3.834A pdb=" N PHE 9 426 " --> pdb=" O PHE 9 422 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ALA 9 427 " --> pdb=" O GLN 9 423 " (cutoff:3.500A) Processing helix chain '9' and resid 429 through 438 Processing helix chain '9' and resid 444 through 446 No H-bonds generated for 'chain '9' and resid 444 through 446' Processing helix chain '9' and resid 452 through 469 Processing helix chain '9' and resid 473 through 476 No H-bonds generated for 'chain '9' and resid 473 through 476' Processing helix chain 'A' and resid 401 through 407 removed outlier: 3.710A pdb=" N MET A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 505 removed outlier: 3.789A pdb=" N LYS A 503 " --> pdb=" O LYS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 539 removed outlier: 5.044A pdb=" N ARG A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Proline residue: A 530 - end of helix Proline residue: A 537 - end of helix Processing helix chain 'A' and resid 546 through 578 removed outlier: 3.737A pdb=" N ARG A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP A 565 " --> pdb=" O TYR A 561 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU A 566 " --> pdb=" O LYS A 562 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ARG A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Proline residue: A 569 - end of helix removed outlier: 5.438A pdb=" N HIS A 572 " --> pdb=" O ARG A 568 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LYS A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 577 " --> pdb=" O LYS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 603 Processing helix chain 'A' and resid 606 through 613 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 622 through 637 Processing helix chain 'A' and resid 641 through 653 Proline residue: A 646 - end of helix removed outlier: 4.391A pdb=" N LYS A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 694 removed outlier: 7.504A pdb=" N CYS A 677 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ALA A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE A 679 " --> pdb=" O MET A 675 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU A 680 " --> pdb=" O GLY A 676 " (cutoff:3.500A) Proline residue: A 681 - end of helix removed outlier: 5.036A pdb=" N ARG A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N HIS A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU A 694 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 716 Processing helix chain 'A' and resid 721 through 723 No H-bonds generated for 'chain 'A' and resid 721 through 723' Processing helix chain 'A' and resid 725 through 737 removed outlier: 4.476A pdb=" N LYS A 729 " --> pdb=" O ASP A 725 " (cutoff:3.500A) Proline residue: A 730 - end of helix Processing helix chain 'A' and resid 740 through 756 Proline residue: A 755 - end of helix Processing helix chain 'A' and resid 759 through 778 removed outlier: 3.641A pdb=" N LEU A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 797 Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 811 through 818 Processing helix chain 'A' and resid 821 through 825 removed outlier: 3.528A pdb=" N LEU A 825 " --> pdb=" O ARG A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 844 removed outlier: 3.775A pdb=" N LYS A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 858 removed outlier: 3.792A pdb=" N ARG A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASP A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASP A 856 " --> pdb=" O ARG A 852 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS A 858 " --> pdb=" O VAL A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 879 removed outlier: 3.563A pdb=" N ASN A 878 " --> pdb=" O LYS A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 901 Processing helix chain 'A' and resid 908 through 927 removed outlier: 6.387A pdb=" N LYS A 923 " --> pdb=" O ASN A 919 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG A 924 " --> pdb=" O ALA A 920 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL A 925 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS A 926 " --> pdb=" O GLY A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix Processing helix chain 'A' and resid 929 through 941 Processing helix chain 'A' and resid 945 through 962 removed outlier: 5.194A pdb=" N VAL A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL A 961 " --> pdb=" O ARG A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 983 removed outlier: 3.774A pdb=" N HIS A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY A 983 " --> pdb=" O TYR A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1003 removed outlier: 3.530A pdb=" N SER A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1025 Proline residue: A1018 - end of helix Proline residue: A1022 - end of helix Processing helix chain 'A' and resid 1029 through 1045 Processing helix chain 'A' and resid 1047 through 1049 No H-bonds generated for 'chain 'A' and resid 1047 through 1049' Processing helix chain 'A' and resid 1052 through 1067 removed outlier: 4.538A pdb=" N LYS A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1088 Processing helix chain 'A' and resid 1090 through 1102 removed outlier: 4.451A pdb=" N LYS A1102 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1122 Processing helix chain 'A' and resid 1125 through 1137 Proline residue: A1130 - end of helix removed outlier: 3.540A pdb=" N ARG A1137 " --> pdb=" O MET A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1177 removed outlier: 7.128A pdb=" N GLU A1160 " --> pdb=" O GLU A1156 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N MET A1161 " --> pdb=" O TYR A1157 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY A1162 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS A1163 " --> pdb=" O GLY A1159 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASP A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR A1165 " --> pdb=" O MET A1161 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR A1167 " --> pdb=" O LYS A1163 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ALA A1168 " --> pdb=" O ASP A1164 " (cutoff:3.500A) Proline residue: A1171 - end of helix Processing helix chain 'A' and resid 1182 through 1198 Processing helix chain 'A' and resid 1205 through 1220 removed outlier: 3.641A pdb=" N TYR A1214 " --> pdb=" O HIS A1210 " (cutoff:3.500A) Proline residue: A1217 - end of helix removed outlier: 5.202A pdb=" N PHE A1220 " --> pdb=" O TRP A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1241 removed outlier: 3.521A pdb=" N VAL A1239 " --> pdb=" O GLU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1253 removed outlier: 5.029A pdb=" N GLN A1252 " --> pdb=" O GLN A1248 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLY A1253 " --> pdb=" O TYR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1275 Processing helix chain 'A' and resid 1277 through 1283 removed outlier: 3.823A pdb=" N ILE A1281 " --> pdb=" O GLN A1277 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA A1282 " --> pdb=" O ASP A1278 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS A1283 " --> pdb=" O ALA A1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1277 through 1283' Processing helix chain 'A' and resid 1299 through 1301 No H-bonds generated for 'chain 'A' and resid 1299 through 1301' Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.513A pdb=" N GLN B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 485 through 492 Processing helix chain 'B' and resid 502 through 505 removed outlier: 4.244A pdb=" N CYS B 505 " --> pdb=" O ARG B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 505' Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 533 through 536 No H-bonds generated for 'chain 'B' and resid 533 through 536' Processing helix chain 'B' and resid 568 through 576 removed outlier: 3.916A pdb=" N PHE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 430 through 432 No H-bonds generated for 'chain 'C' and resid 430 through 432' Processing helix chain 'C' and resid 809 through 825 Processing helix chain 'C' and resid 830 through 844 removed outlier: 3.508A pdb=" N ALA C 836 " --> pdb=" O GLU C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 852 No H-bonds generated for 'chain 'C' and resid 849 through 852' Processing helix chain 'C' and resid 1135 through 1151 removed outlier: 3.732A pdb=" N SER C1150 " --> pdb=" O MET C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 Processing helix chain 'C' and resid 1176 through 1184 removed outlier: 3.608A pdb=" N GLN C1181 " --> pdb=" O ASP C1177 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE C1182 " --> pdb=" O LEU C1178 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ASN C1183 " --> pdb=" O CYS C1179 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER C1184 " --> pdb=" O GLU C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1187 through 1196 Processing helix chain 'C' and resid 1201 through 1214 Processing helix chain 'E' and resid 28 through 45 Processing helix chain 'E' and resid 47 through 56 Processing helix chain 'E' and resid 61 through 72 Processing helix chain 'F' and resid 32 through 42 removed outlier: 3.694A pdb=" N LYS F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR F 42 " --> pdb=" O ILE F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 77 Processing helix chain 'F' and resid 94 through 97 No H-bonds generated for 'chain 'F' and resid 94 through 97' Processing helix chain 'G' and resid 47 through 50 No H-bonds generated for 'chain 'G' and resid 47 through 50' Processing helix chain 'G' and resid 52 through 54 No H-bonds generated for 'chain 'G' and resid 52 through 54' Processing helix chain 'G' and resid 73 through 77 Processing helix chain 'G' and resid 80 through 82 No H-bonds generated for 'chain 'G' and resid 80 through 82' Processing sheet with id= A, first strand: chain '1' and resid 46 through 48 removed outlier: 3.535A pdb=" N THR 1 61 " --> pdb=" O CYS 1 56 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 1173 through 1175 removed outlier: 6.772A pdb=" N LEU C 3 " --> pdb=" O ILE C1174 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE C1126 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER C1103 " --> pdb=" O THR C1120 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 16 through 20 removed outlier: 3.640A pdb=" N PHE C 16 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 54 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG C 42 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N THR C 52 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP C 44 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL C 50 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 62 through 68 removed outlier: 6.472A pdb=" N GLY C 81 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU C 65 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA C 67 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR C 77 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER C 82 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARG C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU C 91 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS C 101 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLN C 93 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N PHE C 99 " --> pdb=" O GLN C 93 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 120 through 123 Processing sheet with id= F, first strand: chain 'C' and resid 144 through 146 Processing sheet with id= G, first strand: chain 'C' and resid 165 through 173 removed outlier: 6.651A pdb=" N LEU C 185 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL C 170 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 183 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY C 172 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N MET C 181 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU C 212 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ARG C 222 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP C 214 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL C 220 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 267 through 270 removed outlier: 3.574A pdb=" N PHE C 234 " --> pdb=" O CYS C 251 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 287 through 294 removed outlier: 6.911A pdb=" N GLN C 304 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER C 290 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU C 302 " --> pdb=" O SER C 290 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N THR C 292 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE C 300 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE C 299 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU C 315 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP C 331 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LYS C 312 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TYR C 329 " --> pdb=" O LYS C 312 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR C 314 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU C 327 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU C 316 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE C 325 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 336 through 342 removed outlier: 7.026A pdb=" N ALA C 350 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET C 339 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE C 348 " --> pdb=" O MET C 339 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL C 341 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE C 346 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLN C 360 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU C 397 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.626A pdb=" N PHE C 409 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 481 through 485 Processing sheet with id= M, first strand: chain 'C' and resid 533 through 537 removed outlier: 5.949A pdb=" N VAL C 517 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU C 510 " --> pdb=" O VAL C 517 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL C 519 " --> pdb=" O CYS C 508 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N CYS C 508 " --> pdb=" O VAL C 519 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 573 through 576 removed outlier: 3.911A pdb=" N GLN C 573 " --> pdb=" O ASP C 569 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 587 through 592 removed outlier: 6.795A pdb=" N GLY C 608 " --> pdb=" O VAL C 588 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET C 590 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA C 606 " --> pdb=" O MET C 590 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU C 592 " --> pdb=" O PHE C 604 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE C 604 " --> pdb=" O LEU C 592 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER C 629 " --> pdb=" O ILE C 616 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N SER C 618 " --> pdb=" O PRO C 627 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 686 through 690 removed outlier: 5.540A pdb=" N VAL C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU C 669 " --> pdb=" O VAL C 673 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 701 through 706 removed outlier: 8.800A pdb=" N GLU C 710 " --> pdb=" O SER C 724 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER C 724 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 741 through 745 removed outlier: 6.482A pdb=" N ALA C 766 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLU C 446 " --> pdb=" O ALA C 766 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 785 through 790 removed outlier: 7.153A pdb=" N ILE C 800 " --> pdb=" O ARG C 786 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE C 788 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 798 " --> pdb=" O PHE C 788 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 886 through 894 removed outlier: 6.613A pdb=" N GLY C 908 " --> pdb=" O PHE C 889 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL C 891 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU C 906 " --> pdb=" O VAL C 891 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL C 893 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR C 904 " --> pdb=" O VAL C 893 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TRP C 903 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS C 929 " --> pdb=" O PHE C 939 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N PHE C 939 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL C 931 " --> pdb=" O LEU C 937 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU C 937 " --> pdb=" O VAL C 931 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 949 through 955 removed outlier: 6.690A pdb=" N GLY C 962 " --> pdb=" O ALA C 950 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE C 952 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU C 960 " --> pdb=" O ILE C 952 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG C 958 " --> pdb=" O PRO C 954 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP C 971 " --> pdb=" O ARG C 979 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ARG C 979 " --> pdb=" O ASP C 971 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 990 through 996 removed outlier: 6.466A pdb=" N SER C1003 " --> pdb=" O SER C 991 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE C 993 " --> pdb=" O ILE C1001 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE C1001 " --> pdb=" O ILE C 993 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR C 995 " --> pdb=" O ARG C 999 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG C 999 " --> pdb=" O THR C 995 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG C1013 " --> pdb=" O ILE C1023 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE C1023 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS C1015 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU C1021 " --> pdb=" O LYS C1015 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 1033 through 1038 removed outlier: 6.691A pdb=" N ALA C1047 " --> pdb=" O THR C1034 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA C1036 " --> pdb=" O ALA C1045 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA C1045 " --> pdb=" O ALA C1036 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU C1038 " --> pdb=" O THR C1043 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR C1043 " --> pdb=" O LEU C1038 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN C1052 " --> pdb=" O ASP C1048 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG C1057 " --> pdb=" O VAL C1091 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL C1091 " --> pdb=" O ARG C1057 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 88 through 91 removed outlier: 3.532A pdb=" N VAL F 88 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 39 through 42 removed outlier: 6.268A pdb=" N TYR G 71 " --> pdb=" O CYS G 40 " (cutoff:3.500A) 806 hydrogen bonds defined for protein. 2301 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 10.44 Time building geometry restraints manager: 9.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3386 1.30 - 1.43: 5725 1.43 - 1.56: 12067 1.56 - 1.70: 94 1.70 - 1.83: 179 Bond restraints: 21451 Sorted by residual: bond pdb=" C TRP A1216 " pdb=" O TRP A1216 " ideal model delta sigma weight residual 1.244 1.169 0.075 9.80e-03 1.04e+04 5.81e+01 bond pdb=" C5 OMU 2 47 " pdb=" C6 OMU 2 47 " ideal model delta sigma weight residual 1.480 1.343 0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C2 OMC 2 61 " pdb=" N3 OMC 2 61 " ideal model delta sigma weight residual 1.490 1.360 0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" C2 OMC 2 40 " pdb=" N3 OMC 2 40 " ideal model delta sigma weight residual 1.490 1.361 0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" C2 OMU 2 47 " pdb=" N3 OMU 2 47 " ideal model delta sigma weight residual 1.499 1.375 0.124 2.00e-02 2.50e+03 3.84e+01 ... (remaining 21446 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.30: 913 106.30 - 113.56: 10848 113.56 - 120.81: 10250 120.81 - 128.06: 7097 128.06 - 135.31: 168 Bond angle restraints: 29276 Sorted by residual: angle pdb=" CA LYS 1 77 " pdb=" C LYS 1 77 " pdb=" N HIS 1 78 " ideal model delta sigma weight residual 117.30 105.73 11.57 1.16e+00 7.43e-01 9.94e+01 angle pdb=" C HIS 1 78 " pdb=" N GLN 1 79 " pdb=" CA GLN 1 79 " ideal model delta sigma weight residual 120.28 132.21 -11.93 1.34e+00 5.57e-01 7.92e+01 angle pdb=" O HIS 1 78 " pdb=" C HIS 1 78 " pdb=" N GLN 1 79 " ideal model delta sigma weight residual 122.09 112.69 9.40 1.08e+00 8.57e-01 7.58e+01 angle pdb=" CA HIS 1 78 " pdb=" C HIS 1 78 " pdb=" N GLN 1 79 " ideal model delta sigma weight residual 117.17 126.37 -9.20 1.18e+00 7.18e-01 6.08e+01 angle pdb=" C LYS 1 77 " pdb=" N HIS 1 78 " pdb=" CA HIS 1 78 " ideal model delta sigma weight residual 120.44 110.16 10.28 1.36e+00 5.41e-01 5.71e+01 ... (remaining 29271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.54: 12340 31.54 - 63.08: 446 63.08 - 94.62: 45 94.62 - 126.16: 0 126.16 - 157.69: 3 Dihedral angle restraints: 12834 sinusoidal: 5517 harmonic: 7317 Sorted by residual: dihedral pdb=" O4* PSU 2 43 " pdb=" C1* PSU 2 43 " pdb=" C5 PSU 2 43 " pdb=" C4 PSU 2 43 " ideal model delta sinusoidal sigma weight residual 200.00 42.31 157.69 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" O4* PSU 2 44 " pdb=" C1* PSU 2 44 " pdb=" C5 PSU 2 44 " pdb=" C4 PSU 2 44 " ideal model delta sinusoidal sigma weight residual 200.00 46.69 153.31 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" C HIS 1 78 " pdb=" N HIS 1 78 " pdb=" CA HIS 1 78 " pdb=" CB HIS 1 78 " ideal model delta harmonic sigma weight residual -122.60 -137.96 15.36 0 2.50e+00 1.60e-01 3.77e+01 ... (remaining 12831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 2519 0.128 - 0.256: 709 0.256 - 0.384: 66 0.384 - 0.512: 13 0.512 - 0.640: 3 Chirality restraints: 3310 Sorted by residual: chirality pdb=" CA HIS 1 78 " pdb=" N HIS 1 78 " pdb=" C HIS 1 78 " pdb=" CB HIS 1 78 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P C h 1 " pdb=" OP1 C h 1 " pdb=" OP2 C h 1 " pdb=" O5' C h 1 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.09e+00 chirality pdb=" P A 2 29 " pdb=" OP1 A 2 29 " pdb=" OP2 A 2 29 " pdb=" O5' A 2 29 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.01e+00 ... (remaining 3307 not shown) Planarity restraints: 3611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC 2 40 " 0.201 2.00e-02 2.50e+03 5.59e-01 7.02e+03 pdb=" C4' OMC 2 40 " -0.432 2.00e-02 2.50e+03 pdb=" O4' OMC 2 40 " -0.961 2.00e-02 2.50e+03 pdb=" C3' OMC 2 40 " 0.569 2.00e-02 2.50e+03 pdb=" O3' OMC 2 40 " 0.315 2.00e-02 2.50e+03 pdb=" C2' OMC 2 40 " 0.311 2.00e-02 2.50e+03 pdb=" O2' OMC 2 40 " -0.566 2.00e-02 2.50e+03 pdb=" C1' OMC 2 40 " -0.292 2.00e-02 2.50e+03 pdb=" N1 OMC 2 40 " 0.856 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 2 61 " -0.077 2.00e-02 2.50e+03 5.30e-01 6.32e+03 pdb=" C4' OMC 2 61 " 0.431 2.00e-02 2.50e+03 pdb=" O4' OMC 2 61 " 0.680 2.00e-02 2.50e+03 pdb=" C3' OMC 2 61 " -0.560 2.00e-02 2.50e+03 pdb=" O3' OMC 2 61 " -0.435 2.00e-02 2.50e+03 pdb=" C2' OMC 2 61 " -0.252 2.00e-02 2.50e+03 pdb=" O2' OMC 2 61 " 0.772 2.00e-02 2.50e+03 pdb=" C1' OMC 2 61 " 0.247 2.00e-02 2.50e+03 pdb=" N1 OMC 2 61 " -0.807 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 587 " 0.091 2.00e-02 2.50e+03 5.16e-02 5.33e+01 pdb=" CG TYR A 587 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 587 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR A 587 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 587 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 587 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR A 587 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR A 587 " 0.085 2.00e-02 2.50e+03 ... (remaining 3608 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 400 2.68 - 3.23: 19926 3.23 - 3.79: 36144 3.79 - 4.34: 49613 4.34 - 4.90: 77222 Nonbonded interactions: 183305 Sorted by model distance: nonbonded pdb=" N GLU C 369 " pdb=" OE1 GLU C 369 " model vdw 2.125 2.520 nonbonded pdb=" OE1 GLU C 352 " pdb=" NH2 ARG C 429 " model vdw 2.327 2.520 nonbonded pdb=" O GLU C1209 " pdb=" OG1 THR C1213 " model vdw 2.337 2.440 nonbonded pdb=" NH2 ARG C 429 " pdb=" O GLU E 59 " model vdw 2.339 2.520 nonbonded pdb=" N LYS 1 77 " pdb=" N HIS 1 78 " model vdw 2.376 2.560 ... (remaining 183300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 48 5.49 5 S 117 5.16 5 C 13141 2.51 5 N 3598 2.21 5 O 4303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 24.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 61.130 Check model and map are aligned: 0.360 Convert atoms to be neutral: 0.210 Process input model: 77.010 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 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 : 0.009 0.137 21451 Z= 0.601 Angle : 1.494 11.928 29276 Z= 1.001 Chirality : 0.113 0.640 3310 Planarity : 0.015 0.559 3611 Dihedral : 15.759 157.695 8120 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 4.50 % Cbeta Deviations : 0.81 % Peptide Plane: Cis-proline : 2.48 % 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: -0.66 (0.16), residues: 2483 helix: -0.55 (0.16), residues: 927 sheet: 0.27 (0.23), residues: 483 loop : -0.49 (0.18), residues: 1073 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 310 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 24 residues processed: 385 average time/residue: 1.5355 time to fit residues: 663.1272 Evaluate side-chains 238 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 214 time to evaluate : 2.259 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 6 average time/residue: 0.6114 time to fit residues: 8.0351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN 1 65 ASN 1 81 ASN ** 9 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN A 550 HIS A 659 GLN A 662 HIS B 496 ASN ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 218 ASN C 670 GLN C 776 GLN C 782 GLN C 844 ASN C 846 ASN C 941 HIS C 985 HIS C 988 ASN F 25 ASN F 72 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 21451 Z= 0.284 Angle : 0.714 13.663 29276 Z= 0.392 Chirality : 0.048 0.458 3310 Planarity : 0.006 0.124 3611 Dihedral : 10.263 159.208 3294 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 0.54 (0.17), residues: 2483 helix: 0.83 (0.17), residues: 935 sheet: 0.34 (0.23), residues: 498 loop : 0.10 (0.19), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 231 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 17 residues processed: 268 average time/residue: 1.4664 time to fit residues: 445.1237 Evaluate side-chains 222 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 2.447 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 6 average time/residue: 1.0047 time to fit residues: 10.5133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 228 optimal weight: 0.0970 chunk 78 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN ** 9 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A1194 HIS B 483 GLN ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 ASN C 844 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.138 21451 Z= 0.375 Angle : 0.702 12.680 29276 Z= 0.384 Chirality : 0.047 0.304 3310 Planarity : 0.006 0.129 3611 Dihedral : 9.941 159.307 3294 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 0.71 (0.17), residues: 2483 helix: 1.01 (0.17), residues: 939 sheet: 0.28 (0.22), residues: 507 loop : 0.26 (0.19), residues: 1037 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 223 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 20 residues processed: 249 average time/residue: 1.4693 time to fit residues: 416.7570 Evaluate side-chains 225 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 205 time to evaluate : 2.431 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 8 average time/residue: 0.2380 time to fit residues: 6.7289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 0.8980 chunk 173 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 218 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 GLN A1091 HIS B 483 GLN ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 846 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.121 21451 Z= 0.224 Angle : 0.641 13.234 29276 Z= 0.350 Chirality : 0.044 0.458 3310 Planarity : 0.005 0.121 3611 Dihedral : 9.823 160.329 3294 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 0.83 (0.17), residues: 2483 helix: 1.13 (0.17), residues: 934 sheet: 0.30 (0.22), residues: 510 loop : 0.33 (0.19), residues: 1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 211 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 15 residues processed: 232 average time/residue: 1.4822 time to fit residues: 390.8321 Evaluate side-chains 217 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 2.516 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.7830 time to fit residues: 5.3647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 219 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 81 ASN ** 9 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 846 ASN G 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.126 21451 Z= 0.238 Angle : 0.637 13.127 29276 Z= 0.347 Chirality : 0.044 0.395 3310 Planarity : 0.005 0.122 3611 Dihedral : 9.710 161.254 3294 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 0.85 (0.17), residues: 2483 helix: 1.17 (0.17), residues: 934 sheet: 0.32 (0.22), residues: 514 loop : 0.30 (0.19), residues: 1035 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 209 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 18 residues processed: 230 average time/residue: 1.4518 time to fit residues: 379.5459 Evaluate side-chains 219 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 2.429 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.4431 time to fit residues: 6.4287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 82 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 GLN B 483 GLN C 846 ASN C1181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.145 21451 Z= 0.383 Angle : 0.682 12.884 29276 Z= 0.368 Chirality : 0.046 0.345 3310 Planarity : 0.006 0.126 3611 Dihedral : 9.687 160.901 3294 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 0.83 (0.17), residues: 2483 helix: 1.12 (0.17), residues: 936 sheet: 0.33 (0.22), residues: 523 loop : 0.30 (0.19), residues: 1024 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 204 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 230 average time/residue: 1.4447 time to fit residues: 378.2796 Evaluate side-chains 223 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 2.652 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 6 average time/residue: 0.2932 time to fit residues: 6.5601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 139 optimal weight: 0.7980 chunk 178 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 243 optimal weight: 30.0000 chunk 152 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 HIS B 483 GLN ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 846 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.092 21451 Z= 0.189 Angle : 0.629 13.342 29276 Z= 0.340 Chirality : 0.043 0.397 3310 Planarity : 0.005 0.121 3611 Dihedral : 9.588 161.368 3294 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 0.89 (0.17), residues: 2483 helix: 1.22 (0.17), residues: 932 sheet: 0.34 (0.22), residues: 517 loop : 0.30 (0.19), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 209 time to evaluate : 2.380 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 outliers start: 30 outliers final: 18 residues processed: 229 average time/residue: 1.5228 time to fit residues: 396.8736 Evaluate side-chains 222 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 2.697 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.5536 time to fit residues: 6.4833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 150 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 191 optimal weight: 0.3980 chunk 221 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 451 GLN ** 9 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 846 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.165 21451 Z= 0.224 Angle : 0.636 13.263 29276 Z= 0.345 Chirality : 0.043 0.382 3310 Planarity : 0.005 0.122 3611 Dihedral : 9.542 161.560 3294 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 0.88 (0.17), residues: 2483 helix: 1.23 (0.17), residues: 928 sheet: 0.30 (0.22), residues: 518 loop : 0.31 (0.19), residues: 1037 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 222 average time/residue: 1.4568 time to fit residues: 366.4098 Evaluate side-chains 223 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 206 time to evaluate : 2.384 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 4 average time/residue: 0.5077 time to fit residues: 6.0965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 233 optimal weight: 0.6980 chunk 213 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 205 optimal weight: 0.9980 chunk 214 optimal weight: 0.2980 chunk 226 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 HIS B 483 GLN ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 GLN C 846 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.116 21451 Z= 0.209 Angle : 0.635 13.327 29276 Z= 0.343 Chirality : 0.043 0.378 3310 Planarity : 0.005 0.122 3611 Dihedral : 9.474 161.945 3294 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 0.88 (0.17), residues: 2483 helix: 1.24 (0.17), residues: 924 sheet: 0.35 (0.23), residues: 504 loop : 0.27 (0.19), residues: 1055 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 205 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 222 average time/residue: 1.4581 time to fit residues: 370.2140 Evaluate side-chains 215 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 200 time to evaluate : 2.463 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 2 average time/residue: 0.3573 time to fit residues: 4.1859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 240 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 200 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 chunk 159 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 ASN B 483 GLN C 575 ASN C 730 HIS G 50 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.199 21451 Z= 0.294 Angle : 0.673 15.330 29276 Z= 0.363 Chirality : 0.044 0.336 3310 Planarity : 0.006 0.124 3611 Dihedral : 9.410 162.103 3294 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 0.85 (0.17), residues: 2483 helix: 1.19 (0.17), residues: 927 sheet: 0.32 (0.22), residues: 511 loop : 0.28 (0.19), residues: 1045 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 201 time to evaluate : 2.544 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 outliers start: 20 outliers final: 16 residues processed: 215 average time/residue: 1.5194 time to fit residues: 372.8141 Evaluate side-chains 217 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 201 time to evaluate : 2.587 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 3 average time/residue: 0.2896 time to fit residues: 5.1236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 185 optimal weight: 0.9980 chunk 29 optimal weight: 40.0000 chunk 55 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 206 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN C 846 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.156245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.084115 restraints weight = 33644.804| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.09 r_work: 0.3066 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.3031 rms_B_bonded: 1.93 restraints_weight: 0.1250 r_work: 0.3013 rms_B_bonded: 1.99 restraints_weight: 0.0625 r_work: 0.2995 rms_B_bonded: 2.09 restraints_weight: 0.0312 r_work: 0.2976 rms_B_bonded: 2.21 restraints_weight: 0.0156 r_work: 0.2955 rms_B_bonded: 2.36 restraints_weight: 0.0078 r_work: 0.2934 rms_B_bonded: 2.55 restraints_weight: 0.0039 r_work: 0.2911 rms_B_bonded: 2.77 restraints_weight: 0.0020 r_work: 0.2888 rms_B_bonded: 3.03 restraints_weight: 0.0010 r_work: 0.2863 rms_B_bonded: 3.35 restraints_weight: 0.0005 r_work: 0.2837 rms_B_bonded: 3.71 restraints_weight: 0.0002 r_work: 0.2811 rms_B_bonded: 4.13 restraints_weight: 0.0001 r_work: 0.2785 rms_B_bonded: 4.62 restraints_weight: 0.0001 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4283 r_free = 0.4283 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4282 r_free = 0.4282 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.158 21451 Z= 0.229 Angle : 0.648 13.567 29276 Z= 0.350 Chirality : 0.043 0.357 3310 Planarity : 0.005 0.122 3611 Dihedral : 9.366 162.373 3294 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 0.87 (0.17), residues: 2483 helix: 1.20 (0.17), residues: 924 sheet: 0.37 (0.23), residues: 502 loop : 0.30 (0.19), residues: 1057 =============================================================================== Job complete usr+sys time: 8955.37 seconds wall clock time: 160 minutes 59.47 seconds (9659.47 seconds total)