Starting phenix.real_space_refine on Sat Feb 17 15:53:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oep_20033/02_2024/6oep_20033.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oep_20033/02_2024/6oep_20033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oep_20033/02_2024/6oep_20033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oep_20033/02_2024/6oep_20033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oep_20033/02_2024/6oep_20033.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oep_20033/02_2024/6oep_20033.pdb" } resolution = 3.7 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= 0.001 sd= 0.006 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 Zn 2 6.06 5 P 204 5.49 5 S 106 5.16 5 C 11503 2.51 5 N 3384 2.21 5 O 3996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "A GLU 719": "OE1" <-> "OE2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 838": "NH1" <-> "NH2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 915": "NH1" <-> "NH2" Residue "A ARG 927": "NH1" <-> "NH2" Residue "A ARG 969": "NH1" <-> "NH2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C GLU 597": "OE1" <-> "OE2" Residue "C PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 649": "OE1" <-> "OE2" Residue "C GLU 680": "OE1" <-> "OE2" Residue "C GLU 709": "OE1" <-> "OE2" Residue "C GLU 771": "OE1" <-> "OE2" Residue "C ARG 773": "NH1" <-> "NH2" Residue "C GLU 824": "OE1" <-> "OE2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" Residue "C GLU 873": "OE1" <-> "OE2" Residue "C GLU 877": "OE1" <-> "OE2" Residue "C ARG 915": "NH1" <-> "NH2" Residue "C ARG 927": "NH1" <-> "NH2" Residue "C GLU 948": "OE1" <-> "OE2" Residue "C ARG 970": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19198 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 604, 4788 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 578} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 604, 4788 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 578} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 4883 Chain: "B" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2673 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 4859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4859 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 586} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "D" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2671 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 938 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 936 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "G" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1154 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1171 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2520 SG CYS A 727 95.273 49.915 96.252 1.00 86.00 S ATOM 2541 SG CYS A 730 97.682 47.308 97.987 1.00 93.67 S ATOM 10043 SG CYS C 727 35.644 107.070 98.576 1.00 79.44 S ATOM 10064 SG CYS C 730 33.216 109.426 99.791 1.00 87.30 S Time building chain proxies: 12.53, per 1000 atoms: 0.65 Number of scatterers: 19198 At special positions: 0 Unit cell: (126.26, 159.43, 160.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 3 19.99 S 106 16.00 P 204 15.00 O 3996 8.00 N 3384 7.00 C 11503 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: 8.73 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " Number of angles added : 4 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 20 sheets defined 36.7% alpha, 20.4% beta 96 base pairs and 172 stacking pairs defined. Time for finding SS restraints: 7.42 Creating SS restraints... Processing helix chain 'A' and resid 401 through 408 removed outlier: 3.899A pdb=" N LEU A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 Processing helix chain 'A' and resid 426 through 441 removed outlier: 3.546A pdb=" N ALA A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.832A pdb=" N ALA A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 479 through 493 removed outlier: 3.664A pdb=" N LYS A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 505 Processing helix chain 'A' and resid 559 through 568 removed outlier: 3.697A pdb=" N SER A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 682 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 733 through 738 removed outlier: 3.876A pdb=" N SER A 738 " --> pdb=" O ARG A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 763 Processing helix chain 'A' and resid 768 through 777 removed outlier: 3.998A pdb=" N ASP A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 813 removed outlier: 3.630A pdb=" N ASP A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 842 removed outlier: 3.985A pdb=" N ARG A 828 " --> pdb=" O GLU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 858 removed outlier: 3.600A pdb=" N ALA A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 870 Processing helix chain 'A' and resid 873 through 890 removed outlier: 3.746A pdb=" N GLU A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 895 removed outlier: 3.534A pdb=" N SER A 895 " --> pdb=" O PRO A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 923 removed outlier: 5.347A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N PHE A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 916 " --> pdb=" O ASN A 912 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.591A pdb=" N HIS A 937 " --> pdb=" O THR A 933 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 950 removed outlier: 4.292A pdb=" N GLU A 948 " --> pdb=" O PRO A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 Processing helix chain 'A' and resid 964 through 975 removed outlier: 3.549A pdb=" N PHE A 968 " --> pdb=" O GLY A 964 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 969 " --> pdb=" O ASN A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.786A pdb=" N VAL A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 988 " --> pdb=" O MET A 984 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1001 removed outlier: 3.773A pdb=" N GLN A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.698A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'C' and resid 408 through 422 Processing helix chain 'C' and resid 426 through 441 Processing helix chain 'C' and resid 444 through 457 removed outlier: 4.004A pdb=" N ALA C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 removed outlier: 3.849A pdb=" N CYS C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 499 through 509 removed outlier: 3.952A pdb=" N VAL C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 664 through 682 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 683 through 685 No H-bonds generated for 'chain 'C' and resid 683 through 685' Processing helix chain 'C' and resid 708 through 716 removed outlier: 3.691A pdb=" N ARG C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 750 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 812 removed outlier: 3.573A pdb=" N CYS C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS C 806 " --> pdb=" O ALA C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 841 Processing helix chain 'C' and resid 850 through 858 removed outlier: 3.735A pdb=" N MET C 858 " --> pdb=" O ALA C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 867 Processing helix chain 'C' and resid 868 through 870 No H-bonds generated for 'chain 'C' and resid 868 through 870' Processing helix chain 'C' and resid 873 through 890 Processing helix chain 'C' and resid 897 through 902 removed outlier: 3.623A pdb=" N CYS C 902 " --> pdb=" O PRO C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 907 Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 942 through 950 removed outlier: 3.844A pdb=" N ILE C 946 " --> pdb=" O HIS C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 974 removed outlier: 3.523A pdb=" N MET C 974 " --> pdb=" O ARG C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 994 Processing helix chain 'C' and resid 996 through 1004 removed outlier: 3.646A pdb=" N GLN C1000 " --> pdb=" O SER C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1008 removed outlier: 3.875A pdb=" N ALA C1008 " --> pdb=" O ALA C1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1005 through 1008' Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.877A pdb=" N LEU D 14 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.956A pdb=" N TRP D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 520 removed outlier: 6.174A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 600 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 520 removed outlier: 6.174A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 600 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N HIS A 633 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASN A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 6 removed outlier: 4.657A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 24 removed outlier: 4.155A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 7.329A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 212 removed outlier: 4.448A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 267 removed outlier: 7.227A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.830A pdb=" N GLU C 518 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR C 705 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLU C 597 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.830A pdb=" N GLU C 518 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR C 705 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLU C 597 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN C 636 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 5 removed outlier: 3.981A pdb=" N TYR D 346 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 24 Processing sheet with id=AB5, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.214A pdb=" N LYS D 51 " --> pdb=" O HIS D 54 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 80 Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.237A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB9, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.629A pdb=" N ILE D 210 " --> pdb=" O TYR D 217 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 234 through 235 Processing sheet with id=AC2, first strand: chain 'D' and resid 262 through 267 removed outlier: 6.800A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) 638 hydrogen bonds defined for protein. 1772 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 238 hydrogen bonds 472 hydrogen bond angles 0 basepair planarities 96 basepair parallelities 172 stacking parallelities Total time for adding SS restraints: 10.25 Time building geometry restraints manager: 9.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4680 1.33 - 1.46: 5947 1.46 - 1.58: 8848 1.58 - 1.71: 403 1.71 - 1.83: 161 Bond restraints: 20039 Sorted by residual: bond pdb=" N VAL C 605 " pdb=" CA VAL C 605 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.51e+00 bond pdb=" N ILE C 953 " pdb=" CA ILE C 953 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.47e+00 bond pdb=" N VAL C 615 " pdb=" CA VAL C 615 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.23e-02 6.61e+03 6.97e+00 bond pdb=" N GLU C 607 " pdb=" CA GLU C 607 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.72e+00 bond pdb=" N HIS C 609 " pdb=" CA HIS C 609 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.16e-02 7.43e+03 6.58e+00 ... (remaining 20034 not shown) Histogram of bond angle deviations from ideal: 95.10 - 102.93: 477 102.93 - 110.77: 7639 110.77 - 118.60: 8649 118.60 - 126.44: 10386 126.44 - 134.27: 837 Bond angle restraints: 27988 Sorted by residual: angle pdb=" C GLU A 803 " pdb=" N PHE A 804 " pdb=" CA PHE A 804 " ideal model delta sigma weight residual 122.06 111.99 10.07 1.86e+00 2.89e-01 2.93e+01 angle pdb=" C ASN D 268 " pdb=" N ASP D 269 " pdb=" CA ASP D 269 " ideal model delta sigma weight residual 122.46 129.43 -6.97 1.41e+00 5.03e-01 2.44e+01 angle pdb=" N VAL A 742 " pdb=" CA VAL A 742 " pdb=" C VAL A 742 " ideal model delta sigma weight residual 106.42 113.82 -7.40 1.51e+00 4.39e-01 2.40e+01 angle pdb=" C ARG B 212 " pdb=" N ASN B 213 " pdb=" CA ASN B 213 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.24e+01 angle pdb=" C PRO A 819 " pdb=" N ASN A 820 " pdb=" CA ASN A 820 " ideal model delta sigma weight residual 122.82 129.51 -6.69 1.42e+00 4.96e-01 2.22e+01 ... (remaining 27983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 10393 35.65 - 71.31: 1096 71.31 - 106.96: 18 106.96 - 142.61: 2 142.61 - 178.27: 3 Dihedral angle restraints: 11512 sinusoidal: 5966 harmonic: 5546 Sorted by residual: dihedral pdb=" CA GLN C 520 " pdb=" C GLN C 520 " pdb=" N PRO C 521 " pdb=" CA PRO C 521 " ideal model delta harmonic sigma weight residual 180.00 146.55 33.45 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA THR B 169 " pdb=" C THR B 169 " pdb=" N GLU B 170 " pdb=" CA GLU B 170 " ideal model delta harmonic sigma weight residual 180.00 154.51 25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ARG B 212 " pdb=" C ARG B 212 " pdb=" N ASN B 213 " pdb=" CA ASN B 213 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 11509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2409 0.063 - 0.127: 566 0.127 - 0.190: 101 0.190 - 0.253: 18 0.253 - 0.317: 2 Chirality restraints: 3096 Sorted by residual: chirality pdb=" CB VAL A 943 " pdb=" CA VAL A 943 " pdb=" CG1 VAL A 943 " pdb=" CG2 VAL A 943 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA PHE A 804 " pdb=" N PHE A 804 " pdb=" C PHE A 804 " pdb=" CB PHE A 804 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA VAL A 943 " pdb=" N VAL A 943 " pdb=" C VAL A 943 " pdb=" CB VAL A 943 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 3093 not shown) Planarity restraints: 2883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 212 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ARG B 212 " 0.065 2.00e-02 2.50e+03 pdb=" O ARG B 212 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN B 213 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 317 " 0.024 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP B 317 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP B 317 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 317 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 317 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 317 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 317 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 317 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 317 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " 0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO D 99 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.046 5.00e-02 4.00e+02 ... (remaining 2880 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 995 2.70 - 3.25: 16638 3.25 - 3.80: 32825 3.80 - 4.35: 38797 4.35 - 4.90: 62265 Nonbonded interactions: 151520 Sorted by model distance: nonbonded pdb=" OD2 ASP A 600 " pdb="CA CA A1101 " model vdw 2.147 2.510 nonbonded pdb=" OE1 GLN A 962 " pdb="CA CA A1101 " model vdw 2.238 2.510 nonbonded pdb=" OG SER B 147 " pdb=" OD1 ASP B 214 " model vdw 2.248 2.440 nonbonded pdb=" OD2 ASP C 600 " pdb="CA CA C1101 " model vdw 2.260 2.510 nonbonded pdb=" OH TYR A 559 " pdb=" OE2 GLU A 597 " model vdw 2.268 2.440 ... (remaining 151515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 401 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB )) or resid 408 through 427 or (resid 428 through 429 \ and (name N or name CA or name C or name O or name CB )) or resid 430 or resid 4 \ 32 through 457 or (resid 458 and (name N or name CA or name C or name O or name \ CB )) or resid 459 through 519 or (resid 520 and (name N or name CA or name C or \ name O or name CB )) or resid 521 through 584 or (resid 585 and (name N or name \ CA or name C or name O or name CB )) or resid 586 through 607 or (resid 608 and \ (name N or name CA or name C or name O or name CB )) or resid 613 through 846 o \ r (resid 847 through 848 and (name N or name CA or name C or name O or name CB ) \ ) or resid 849 through 903 or (resid 904 and (name N or name CA or name C or nam \ e O or name CB )) or resid 905 through 913 or (resid 914 and (name N or name CA \ or name C or name O or name CB )) or resid 915 through 917 or (resid 918 and (na \ me N or name CA or name C or name O or name CB )) or resid 919 through 924 or (r \ esid 925 and (name N or name CA or name C or name O or name CB )) or resid 926 t \ hrough 958 or (resid 961 and (name N or name CA or name C or name O or name CB ) \ ) or resid 962 through 1008 or resid 1101 through 1102)) selection = (chain 'C' and (resid 401 through 430 or resid 432 through 523 or (resid 524 and \ (name N or name CA or name C or name O or name CB )) or resid 525 through 568 o \ r (resid 569 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 70 through 571 or (resid 572 and (name N or name CA or name C or name O or name \ CB )) or resid 573 through 603 or (resid 604 and (name N or name CA or name C or \ name O or name CB )) or resid 605 through 608 or resid 613 through 631 or (resi \ d 632 and (name N or name CA or name C or name O or name CB )) or resid 633 thro \ ugh 813 or (resid 814 and (name N or name CA or name C or name O or name CB )) o \ r resid 815 through 816 or (resid 817 and (name N or name CA or name C or name O \ or name CB )) or resid 818 through 822 or (resid 823 through 824 and (name N or \ name CA or name C or name O or name CB )) or resid 825 through 826 or (resid 82 \ 7 through 828 and (name N or name CA or name C or name O or name CB )) or resid \ 829 through 834 or (resid 835 and (name N or name CA or name C or name O or name \ CB )) or resid 836 through 838 or (resid 839 and (name N or name CA or name C o \ r name O or name CB )) or resid 840 through 854 or (resid 855 and (name N or nam \ e CA or name C or name O or name CB )) or resid 856 through 860 or (resid 861 an \ d (name N or name CA or name C or name O or name CB )) or resid 862 through 867 \ or (resid 868 and (name N or name CA or name C or name O or name CB )) or resid \ 869 through 947 or (resid 948 and (name N or name CA or name C or name O or name \ CB )) or resid 949 through 979 or (resid 980 and (name N or name CA or name C o \ r name O or name CB )) or resid 981 through 1008 or resid 1101 through 1102)) } ncs_group { reference = (chain 'B' and (resid 1 through 334 or (resid 335 through 338 and (name N or nam \ e CA or name C or name O or name CB )) or resid 339 through 351)) selection = (chain 'D' and (resid 1 through 339 or (resid 340 through 342 and (name N or nam \ e CA or name C or name O or name CB )) or resid 343 through 351)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.010 Extract box with map and model: 5.730 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 66.870 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 20039 Z= 0.502 Angle : 0.993 11.882 27988 Z= 0.571 Chirality : 0.057 0.317 3096 Planarity : 0.007 0.084 2883 Dihedral : 22.733 178.268 7936 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.61 % Favored : 92.07 % Rotamer: Outliers : 0.55 % Allowed : 10.78 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 1.15 % 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: -4.10 (0.15), residues: 1893 helix: -2.87 (0.14), residues: 633 sheet: -1.54 (0.26), residues: 333 loop : -3.08 (0.17), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP B 317 HIS 0.009 0.002 HIS A 942 PHE 0.024 0.003 PHE C 591 TYR 0.027 0.002 TYR C 998 ARG 0.008 0.001 ARG A 558 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 184 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 MET cc_start: 0.9122 (ptp) cc_final: 0.8769 (ptm) REVERT: A 602 MET cc_start: 0.8397 (ptm) cc_final: 0.7570 (ppp) REVERT: A 962 GLN cc_start: 0.8240 (tp40) cc_final: 0.7999 (tm-30) REVERT: B 162 MET cc_start: 0.8803 (mmt) cc_final: 0.8393 (mmm) REVERT: C 445 HIS cc_start: 0.8541 (m-70) cc_final: 0.8282 (m-70) REVERT: C 597 GLU cc_start: 0.7545 (tp30) cc_final: 0.7225 (tp30) REVERT: D 249 CYS cc_start: 0.8684 (t) cc_final: 0.8045 (t) REVERT: D 287 CYS cc_start: 0.7966 (m) cc_final: 0.7243 (m) REVERT: D 298 GLU cc_start: 0.7687 (tp30) cc_final: 0.7395 (tp30) outliers start: 9 outliers final: 3 residues processed: 191 average time/residue: 0.3556 time to fit residues: 101.1790 Evaluate side-chains 134 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 609 HIS Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 952 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 53 optimal weight: 0.0370 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 HIS A 876 HIS A 965 ASN A 975 ASN A1007 ASN B 89 HIS B 101 ASN B 222 HIS C 501 HIS C 588 ASN ** C 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN C1000 GLN ** C1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN D 89 HIS D 94 HIS D 222 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20039 Z= 0.240 Angle : 0.629 10.694 27988 Z= 0.349 Chirality : 0.042 0.205 3096 Planarity : 0.005 0.056 2883 Dihedral : 25.514 173.674 4343 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.50 % Favored : 93.39 % Rotamer: Outliers : 1.72 % Allowed : 14.90 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -2.84 (0.17), residues: 1893 helix: -1.16 (0.19), residues: 646 sheet: -1.16 (0.26), residues: 377 loop : -2.80 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 317 HIS 0.009 0.001 HIS A 515 PHE 0.020 0.001 PHE A 804 TYR 0.017 0.001 TYR C 998 ARG 0.004 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 LYS cc_start: 0.8391 (ptpp) cc_final: 0.8132 (ptpt) REVERT: A 602 MET cc_start: 0.8306 (ptm) cc_final: 0.7142 (ppp) REVERT: A 691 MET cc_start: 0.7724 (mmt) cc_final: 0.7508 (tpt) REVERT: A 716 GLU cc_start: 0.7847 (tp30) cc_final: 0.7577 (tp30) REVERT: B 270 GLU cc_start: 0.7407 (tm-30) cc_final: 0.6658 (tm-30) REVERT: B 285 MET cc_start: 0.8262 (mmm) cc_final: 0.7452 (mmm) REVERT: C 451 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8465 (mp) REVERT: C 503 LEU cc_start: 0.9081 (tp) cc_final: 0.8830 (tp) REVERT: C 597 GLU cc_start: 0.7511 (tp30) cc_final: 0.7123 (tp30) REVERT: C 609 HIS cc_start: 0.6933 (OUTLIER) cc_final: 0.6416 (m-70) REVERT: C 662 GLU cc_start: 0.8575 (tt0) cc_final: 0.8251 (tm-30) REVERT: D 5 MET cc_start: 0.8473 (tpp) cc_final: 0.7923 (tpp) REVERT: D 126 GLU cc_start: 0.8542 (pp20) cc_final: 0.8277 (pp20) REVERT: D 287 CYS cc_start: 0.7931 (m) cc_final: 0.7311 (m) REVERT: D 298 GLU cc_start: 0.7807 (tp30) cc_final: 0.7495 (tp30) outliers start: 28 outliers final: 15 residues processed: 170 average time/residue: 0.2751 time to fit residues: 76.6205 Evaluate side-chains 146 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 609 HIS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 156 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS A 753 ASN C1004 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20039 Z= 0.375 Angle : 0.683 11.579 27988 Z= 0.371 Chirality : 0.043 0.237 3096 Planarity : 0.005 0.055 2883 Dihedral : 25.511 176.244 4342 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.46 % Favored : 91.49 % Rotamer: Outliers : 3.26 % Allowed : 16.93 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -2.32 (0.18), residues: 1893 helix: -0.60 (0.20), residues: 649 sheet: -0.83 (0.27), residues: 364 loop : -2.62 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 317 HIS 0.007 0.001 HIS A 942 PHE 0.026 0.002 PHE C 418 TYR 0.021 0.002 TYR C 757 ARG 0.003 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 128 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.8357 (ptm) cc_final: 0.7163 (ppp) REVERT: A 691 MET cc_start: 0.7875 (mmt) cc_final: 0.7654 (tpt) REVERT: A 716 GLU cc_start: 0.8097 (tp30) cc_final: 0.7756 (tp30) REVERT: C 451 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8468 (mp) REVERT: C 772 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8502 (tm) REVERT: D 5 MET cc_start: 0.8469 (tpp) cc_final: 0.8108 (tpp) REVERT: D 126 GLU cc_start: 0.8562 (pp20) cc_final: 0.8280 (pp20) REVERT: D 298 GLU cc_start: 0.7825 (tp30) cc_final: 0.7501 (tp30) REVERT: D 302 MET cc_start: 0.6583 (ptm) cc_final: 0.6027 (ptm) REVERT: D 303 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8069 (pm20) outliers start: 53 outliers final: 32 residues processed: 171 average time/residue: 0.2589 time to fit residues: 74.7359 Evaluate side-chains 156 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 121 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20039 Z= 0.344 Angle : 0.660 10.876 27988 Z= 0.361 Chirality : 0.043 0.259 3096 Planarity : 0.004 0.051 2883 Dihedral : 25.455 174.794 4340 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.82 % Favored : 92.12 % Rotamer: Outliers : 3.63 % Allowed : 18.47 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.97 (0.19), residues: 1893 helix: -0.30 (0.20), residues: 647 sheet: -0.49 (0.30), residues: 332 loop : -2.44 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 317 HIS 0.006 0.001 HIS A 942 PHE 0.047 0.002 PHE C 418 TYR 0.018 0.002 TYR C 998 ARG 0.003 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 126 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 ARG cc_start: 0.8522 (tmt170) cc_final: 0.8127 (tmm-80) REVERT: A 421 LYS cc_start: 0.8337 (ptpp) cc_final: 0.8039 (ptpt) REVERT: A 602 MET cc_start: 0.8361 (ptm) cc_final: 0.7145 (ppp) REVERT: A 716 GLU cc_start: 0.8088 (tp30) cc_final: 0.7784 (tp30) REVERT: B 270 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7251 (tm-30) REVERT: C 451 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8274 (mp) REVERT: C 772 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8616 (tm) REVERT: D 5 MET cc_start: 0.8443 (tpp) cc_final: 0.8101 (tpp) REVERT: D 126 GLU cc_start: 0.8550 (pp20) cc_final: 0.8231 (pp20) REVERT: D 298 GLU cc_start: 0.7806 (tp30) cc_final: 0.7511 (tp30) REVERT: D 302 MET cc_start: 0.6521 (ptm) cc_final: 0.6129 (ptm) REVERT: D 303 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7624 (pm20) outliers start: 59 outliers final: 39 residues processed: 172 average time/residue: 0.2939 time to fit residues: 82.6839 Evaluate side-chains 164 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 122 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 7.9990 chunk 113 optimal weight: 0.0970 chunk 2 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 0.0970 chunk 170 optimal weight: 0.3980 chunk 138 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 102 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 overall best weight: 1.1178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20039 Z= 0.180 Angle : 0.582 10.577 27988 Z= 0.321 Chirality : 0.040 0.237 3096 Planarity : 0.004 0.046 2883 Dihedral : 25.254 175.468 4340 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.92 % Rotamer: Outliers : 2.89 % Allowed : 19.77 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.54 (0.19), residues: 1893 helix: 0.12 (0.20), residues: 642 sheet: -0.28 (0.30), residues: 338 loop : -2.21 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 36 HIS 0.004 0.001 HIS A 515 PHE 0.039 0.001 PHE C 418 TYR 0.014 0.001 TYR A 757 ARG 0.003 0.000 ARG D 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 143 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.8309 (ptm) cc_final: 0.7138 (ppp) REVERT: A 691 MET cc_start: 0.7623 (mmt) cc_final: 0.7380 (tpt) REVERT: A 716 GLU cc_start: 0.7994 (tp30) cc_final: 0.7606 (tp30) REVERT: A 856 LYS cc_start: 0.8323 (mttt) cc_final: 0.7929 (mtmm) REVERT: B 270 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7327 (tm-30) REVERT: C 662 GLU cc_start: 0.8616 (tt0) cc_final: 0.8246 (tm-30) REVERT: C 806 LYS cc_start: 0.9005 (mmpt) cc_final: 0.8653 (mmtp) REVERT: D 5 MET cc_start: 0.8331 (tpp) cc_final: 0.8062 (tpp) REVERT: D 126 GLU cc_start: 0.8416 (pp20) cc_final: 0.8067 (pp20) REVERT: D 298 GLU cc_start: 0.7779 (tp30) cc_final: 0.7447 (tp30) REVERT: D 302 MET cc_start: 0.6531 (ptm) cc_final: 0.5867 (ptm) REVERT: D 303 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7671 (pm20) outliers start: 47 outliers final: 27 residues processed: 181 average time/residue: 0.2660 time to fit residues: 79.2818 Evaluate side-chains 160 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 0.0570 chunk 200 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 HIS C 443 ASN C 515 HIS C 647 ASN D 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20039 Z= 0.162 Angle : 0.587 16.418 27988 Z= 0.316 Chirality : 0.040 0.225 3096 Planarity : 0.004 0.044 2883 Dihedral : 25.099 177.204 4338 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.50 % Favored : 94.45 % Rotamer: Outliers : 2.83 % Allowed : 21.24 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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 (0.19), residues: 1893 helix: 0.35 (0.20), residues: 649 sheet: -0.25 (0.30), residues: 344 loop : -2.03 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 760 HIS 0.004 0.001 HIS A 795 PHE 0.034 0.001 PHE C 418 TYR 0.014 0.001 TYR A 757 ARG 0.006 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 148 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.8282 (ptm) cc_final: 0.7132 (ppp) REVERT: A 716 GLU cc_start: 0.7970 (tp30) cc_final: 0.7493 (tp30) REVERT: A 847 MET cc_start: 0.8018 (mpp) cc_final: 0.7567 (mpp) REVERT: A 856 LYS cc_start: 0.8233 (mttt) cc_final: 0.7895 (mtmm) REVERT: B 270 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7414 (tm-30) REVERT: B 285 MET cc_start: 0.8564 (mmm) cc_final: 0.8249 (mmm) REVERT: C 662 GLU cc_start: 0.8574 (tt0) cc_final: 0.8281 (tm-30) REVERT: C 806 LYS cc_start: 0.8992 (mmpt) cc_final: 0.8705 (mmtp) REVERT: D 126 GLU cc_start: 0.8404 (pp20) cc_final: 0.8149 (pp20) REVERT: D 298 GLU cc_start: 0.7731 (tp30) cc_final: 0.7396 (tp30) REVERT: D 302 MET cc_start: 0.6431 (ptm) cc_final: 0.6073 (ptm) REVERT: D 303 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7536 (pm20) outliers start: 46 outliers final: 29 residues processed: 182 average time/residue: 0.2674 time to fit residues: 80.2185 Evaluate side-chains 160 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 609 HIS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 282 GLN Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 331 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 168 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 chunk 199 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 ASN B 281 ASN B 313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20039 Z= 0.227 Angle : 0.612 15.808 27988 Z= 0.328 Chirality : 0.041 0.262 3096 Planarity : 0.004 0.046 2883 Dihedral : 25.095 177.187 4338 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.66 % Rotamer: Outliers : 2.40 % Allowed : 22.23 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.15 (0.19), residues: 1893 helix: 0.46 (0.21), residues: 650 sheet: -0.16 (0.30), residues: 344 loop : -1.97 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 956 HIS 0.003 0.001 HIS C 937 PHE 0.015 0.001 PHE A 804 TYR 0.014 0.001 TYR C 757 ARG 0.003 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.8305 (ptm) cc_final: 0.7132 (ppp) REVERT: A 716 GLU cc_start: 0.8021 (tp30) cc_final: 0.7522 (tp30) REVERT: A 847 MET cc_start: 0.8018 (mpp) cc_final: 0.7570 (mpp) REVERT: A 856 LYS cc_start: 0.8229 (mttt) cc_final: 0.7862 (mtmm) REVERT: C 627 MET cc_start: 0.8944 (ttm) cc_final: 0.8409 (ttm) REVERT: C 662 GLU cc_start: 0.8565 (tt0) cc_final: 0.8303 (tm-30) REVERT: C 806 LYS cc_start: 0.8992 (mmpt) cc_final: 0.8683 (mmtp) REVERT: D 126 GLU cc_start: 0.8399 (pp20) cc_final: 0.8149 (pp20) REVERT: D 298 GLU cc_start: 0.7856 (tp30) cc_final: 0.7463 (tp30) REVERT: D 302 MET cc_start: 0.6510 (ptm) cc_final: 0.6128 (ptm) REVERT: D 303 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7582 (pm20) outliers start: 39 outliers final: 34 residues processed: 164 average time/residue: 0.2570 time to fit residues: 70.0508 Evaluate side-chains 160 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 975 ASN Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 249 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 331 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 10.0000 chunk 79 optimal weight: 0.0170 chunk 119 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20039 Z= 0.211 Angle : 0.601 15.976 27988 Z= 0.323 Chirality : 0.040 0.250 3096 Planarity : 0.004 0.045 2883 Dihedral : 25.069 176.934 4338 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 2.83 % Allowed : 22.11 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.04 (0.19), residues: 1893 helix: 0.53 (0.20), residues: 649 sheet: -0.09 (0.30), residues: 350 loop : -1.91 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 956 HIS 0.003 0.001 HIS C 937 PHE 0.011 0.001 PHE B 30 TYR 0.013 0.001 TYR C 757 ARG 0.003 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 126 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.8293 (ptm) cc_final: 0.7110 (ppp) REVERT: A 716 GLU cc_start: 0.7971 (tp30) cc_final: 0.7502 (tp30) REVERT: A 847 MET cc_start: 0.7998 (mpp) cc_final: 0.7543 (mpp) REVERT: A 856 LYS cc_start: 0.8233 (mttt) cc_final: 0.7881 (mtmm) REVERT: A 858 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.4577 (ptt) REVERT: C 627 MET cc_start: 0.8899 (ttm) cc_final: 0.8619 (ttm) REVERT: C 806 LYS cc_start: 0.9010 (mmpt) cc_final: 0.8692 (mmtp) REVERT: D 110 MET cc_start: 0.9085 (mmt) cc_final: 0.8762 (mmp) REVERT: D 126 GLU cc_start: 0.8379 (pp20) cc_final: 0.8146 (pp20) REVERT: D 152 MET cc_start: 0.8291 (tpp) cc_final: 0.8059 (mmp) REVERT: D 298 GLU cc_start: 0.7849 (tp30) cc_final: 0.7455 (tp30) REVERT: D 302 MET cc_start: 0.6555 (ptm) cc_final: 0.6131 (ptm) REVERT: D 303 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7578 (pm20) outliers start: 46 outliers final: 35 residues processed: 164 average time/residue: 0.2552 time to fit residues: 70.0550 Evaluate side-chains 162 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 975 ASN Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 249 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 331 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 174 optimal weight: 0.0050 chunk 185 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 overall best weight: 2.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20039 Z= 0.274 Angle : 0.637 16.218 27988 Z= 0.339 Chirality : 0.041 0.256 3096 Planarity : 0.004 0.045 2883 Dihedral : 25.108 176.689 4338 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.77 % Favored : 92.18 % Rotamer: Outliers : 3.14 % Allowed : 21.67 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.03 (0.19), residues: 1893 helix: 0.54 (0.20), residues: 646 sheet: 0.14 (0.30), residues: 338 loop : -1.98 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 317 HIS 0.004 0.001 HIS A 942 PHE 0.013 0.001 PHE B 30 TYR 0.016 0.001 TYR C 757 ARG 0.004 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 126 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.8304 (ptm) cc_final: 0.7103 (ppp) REVERT: A 716 GLU cc_start: 0.7970 (tp30) cc_final: 0.7487 (tp30) REVERT: A 847 MET cc_start: 0.8008 (mpp) cc_final: 0.7487 (mpp) REVERT: A 856 LYS cc_start: 0.8251 (mttt) cc_final: 0.7899 (mtmm) REVERT: A 858 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.4526 (ptt) REVERT: C 445 HIS cc_start: 0.8776 (m90) cc_final: 0.8520 (m-70) REVERT: C 662 GLU cc_start: 0.8593 (tt0) cc_final: 0.8322 (tm-30) REVERT: C 806 LYS cc_start: 0.9017 (mmpt) cc_final: 0.8684 (mmtp) REVERT: D 110 MET cc_start: 0.9076 (mmt) cc_final: 0.8761 (mmp) REVERT: D 126 GLU cc_start: 0.8399 (pp20) cc_final: 0.8157 (pp20) REVERT: D 152 MET cc_start: 0.8298 (tpp) cc_final: 0.8071 (mmp) REVERT: D 298 GLU cc_start: 0.7896 (tp30) cc_final: 0.7506 (tp30) REVERT: D 302 MET cc_start: 0.6653 (ptm) cc_final: 0.6211 (ptm) REVERT: D 303 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7584 (pm20) outliers start: 51 outliers final: 38 residues processed: 168 average time/residue: 0.2644 time to fit residues: 74.9890 Evaluate side-chains 166 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 126 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 975 ASN Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 249 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 331 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 130 optimal weight: 0.5980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20039 Z= 0.251 Angle : 0.629 15.892 27988 Z= 0.335 Chirality : 0.041 0.249 3096 Planarity : 0.004 0.045 2883 Dihedral : 25.088 176.496 4338 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.98 % Favored : 92.97 % Rotamer: Outliers : 2.52 % Allowed : 22.29 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.97 (0.19), residues: 1893 helix: 0.58 (0.20), residues: 646 sheet: 0.11 (0.30), residues: 347 loop : -1.92 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 317 HIS 0.003 0.001 HIS A 942 PHE 0.016 0.001 PHE C 804 TYR 0.014 0.001 TYR C 998 ARG 0.002 0.000 ARG B 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 129 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.8306 (ptm) cc_final: 0.7102 (ppp) REVERT: A 716 GLU cc_start: 0.7968 (tp30) cc_final: 0.7523 (tp30) REVERT: A 856 LYS cc_start: 0.8265 (mttt) cc_final: 0.7918 (mtmm) REVERT: A 858 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.4599 (ptt) REVERT: C 445 HIS cc_start: 0.8789 (m90) cc_final: 0.8526 (m-70) REVERT: C 662 GLU cc_start: 0.8527 (tt0) cc_final: 0.8286 (tm-30) REVERT: C 806 LYS cc_start: 0.9028 (mmpt) cc_final: 0.8695 (mmtp) REVERT: D 110 MET cc_start: 0.9085 (mmt) cc_final: 0.8766 (mmp) REVERT: D 126 GLU cc_start: 0.8391 (pp20) cc_final: 0.8158 (pp20) REVERT: D 152 MET cc_start: 0.8290 (tpp) cc_final: 0.8063 (mmp) REVERT: D 298 GLU cc_start: 0.7899 (tp30) cc_final: 0.7501 (tp30) outliers start: 41 outliers final: 38 residues processed: 163 average time/residue: 0.2680 time to fit residues: 72.6324 Evaluate side-chains 167 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 975 ASN Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 249 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 331 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 144 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.108705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.074125 restraints weight = 49956.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.075798 restraints weight = 29003.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.076121 restraints weight = 18931.378| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20039 Z= 0.162 Angle : 0.601 15.142 27988 Z= 0.322 Chirality : 0.040 0.254 3096 Planarity : 0.003 0.045 2883 Dihedral : 24.950 177.656 4338 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.66 % Rotamer: Outliers : 2.16 % Allowed : 22.72 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.79 (0.20), residues: 1893 helix: 0.74 (0.21), residues: 647 sheet: -0.02 (0.30), residues: 355 loop : -1.73 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 36 HIS 0.003 0.001 HIS C 836 PHE 0.015 0.001 PHE C 418 TYR 0.014 0.001 TYR B 80 ARG 0.004 0.000 ARG D 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3228.39 seconds wall clock time: 60 minutes 14.27 seconds (3614.27 seconds total)