Starting phenix.real_space_refine on Wed Aug 7 09:19:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oer_20035/08_2024/6oer_20035.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oer_20035/08_2024/6oer_20035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oer_20035/08_2024/6oer_20035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oer_20035/08_2024/6oer_20035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oer_20035/08_2024/6oer_20035.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oer_20035/08_2024/6oer_20035.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 4 9.91 5 Zn 2 6.06 5 P 204 5.49 5 S 108 5.16 5 C 11682 2.51 5 N 3436 2.21 5 O 4046 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 ARG 442": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 838": "NH1" <-> "NH2" Residue "A ARG 840": "NH1" <-> "NH2" 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 ARG 349": "NH1" <-> "NH2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 446": "NH1" <-> "NH2" Residue "C ARG 471": "NH1" <-> "NH2" Residue "C ARG 494": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "C ARG 558": "NH1" <-> "NH2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C ARG 621": "NH1" <-> "NH2" Residue "C ARG 773": "NH1" <-> "NH2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" Residue "C ARG 855": "NH1" <-> "NH2" Residue "C ARG 875": "NH1" <-> "NH2" Residue "C ARG 915": "NH1" <-> "NH2" Residue "C ARG 927": "NH1" <-> "NH2" Residue "C ARG 970": "NH1" <-> "NH2" Residue "C ARG 977": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 237": "NH1" <-> "NH2" 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-5409/modules/chem_data/mon_lib" Total number of atoms: 19482 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4844 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 608, 4829 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 582} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Conformer: "B" Number of residues, atoms: 608, 4829 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 582} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 bond proxies already assigned to first conformer: 4912 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: 4866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4866 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 590} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2674 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 927 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' DT:plan': 2} Unresolved non-hydrogen planarities: 18 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: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1143 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' DT:plan': 2} Unresolved non-hydrogen planarities: 18 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: "H" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 242 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2551 SG CYS A 727 100.836 25.668 65.811 1.00 60.61 S ATOM 2572 SG CYS A 730 102.666 22.653 64.452 1.00 60.71 S ATOM 10094 SG CYS C 727 55.520 91.294 61.039 1.00 63.75 S ATOM 10115 SG CYS C 730 53.507 93.903 59.647 1.00 65.17 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 816 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 816 " occ=0.50 Time building chain proxies: 12.41, per 1000 atoms: 0.64 Number of scatterers: 19482 At special positions: 0 Unit cell: (157.29, 118.77, 159.43, 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 4 19.99 S 108 16.00 P 204 15.00 O 4046 8.00 N 3436 7.00 C 11682 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: 8.39 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 730 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 730 " Number of angles added : 4 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3652 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 20 sheets defined 37.8% alpha, 19.6% beta 93 base pairs and 155 stacking pairs defined. Time for finding SS restraints: 8.06 Creating SS restraints... Processing helix chain 'A' and resid 401 through 424 removed outlier: 5.056A pdb=" N GLU A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 442 removed outlier: 4.049A pdb=" N ARG A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 457 Processing helix chain 'A' and resid 463 through 473 removed outlier: 3.522A pdb=" N CYS A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 558 through 568 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 717 removed outlier: 3.590A pdb=" N GLY A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.577A pdb=" N ASN A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 removed outlier: 4.223A pdb=" N ASP A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 813 removed outlier: 3.652A pdb=" N GLY A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 842 Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 859 through 867 Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 874 through 895 removed outlier: 4.179A pdb=" N LEU A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Proline residue: A 891 - end of helix Processing helix chain 'A' and resid 897 through 901 removed outlier: 3.783A pdb=" N GLU A 901 " --> pdb=" O PRO A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 924 removed outlier: 4.960A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N PHE A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 942 removed outlier: 4.403A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 removed outlier: 4.152A pdb=" N GLU A 948 " --> pdb=" O PRO A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.676A pdb=" N GLY A 964 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A 965 " --> pdb=" O ASN A 961 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 996 removed outlier: 4.070A pdb=" N GLU A 985 " --> pdb=" O CYS A 981 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1004 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 423 Processing helix chain 'C' and resid 427 through 441 Processing helix chain 'C' and resid 444 through 456 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 500 through 509 removed outlier: 3.517A pdb=" N ALA C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 3.739A 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 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 735 through 740 removed outlier: 3.533A pdb=" N GLN C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 763 Processing helix chain 'C' and resid 768 through 777 removed outlier: 4.265A pdb=" N ASP C 774 " --> pdb=" O GLU C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 813 Processing helix chain 'C' and resid 824 through 841 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.782A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) 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 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 902 through 923 removed outlier: 4.631A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE C 911 " --> pdb=" O CYS C 907 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 958 through 964 removed outlier: 3.914A pdb=" N GLY C 964 " --> pdb=" O GLY C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 975 Processing helix chain 'C' and resid 981 through 995 removed outlier: 4.161A pdb=" N GLU C 985 " --> pdb=" O CYS C 981 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL C 987 " --> pdb=" O GLU C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 999 through 1004 Processing helix chain 'D' and resid 11 through 15 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'H' and resid 102 through 107 removed outlier: 4.132A pdb=" N SER H 107 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 115 Processing helix chain 'H' and resid 123 through 136 removed outlier: 3.966A pdb=" N LYS H 128 " --> pdb=" O ASP H 124 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU H 129 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR H 136 " --> pdb=" O MET H 132 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 10.017A pdb=" N PHE A 591 " --> pdb=" O PHE A 700 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N PHE A 702 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N VAL A 593 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N GLY A 704 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 10.722A pdb=" N VAL A 595 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N GLY A 706 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU A 597 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU A 632 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 596 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL A 626 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER A 598 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE A 624 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASP A 600 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE A 622 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU A 655 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 519 removed outlier: 10.017A pdb=" N PHE A 591 " --> pdb=" O PHE A 700 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N PHE A 702 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N VAL A 593 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N GLY A 704 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 10.722A pdb=" N VAL A 595 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N GLY A 706 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU A 597 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU A 632 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 596 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL A 626 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER A 598 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE A 624 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASP A 600 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE A 622 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS A 633 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASN A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 24 removed outlier: 5.483A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N LEU B 55 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 349 " --> pdb=" O SER B 2 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 346 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.826A pdb=" N TYR B 108 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS B 127 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N MET B 110 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR B 125 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL B 112 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG B 123 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.842A pdb=" N GLU B 102 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.460A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.028A 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: 3.631A pdb=" N ARG B 212 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 267 removed outlier: 5.803A pdb=" N GLN B 265 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 272 " --> pdb=" O GLN B 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 277 through 279 removed outlier: 6.418A pdb=" N GLN B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 517 through 520 removed outlier: 6.798A pdb=" N ILE C 631 " --> pdb=" O LYS C 639 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS C 639 " --> pdb=" O ILE C 631 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 534 through 536 removed outlier: 7.199A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG C 621 " --> pdb=" O ASP C 600 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 2 through 5 removed outlier: 3.962A pdb=" N PHE D 318 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 7 through 8 removed outlier: 7.244A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 80 removed outlier: 5.165A pdb=" N TYR D 108 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS D 127 " --> pdb=" O TYR D 108 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N MET D 110 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR D 125 " --> pdb=" O MET D 110 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N VAL D 112 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG D 123 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 97 through 98 removed outlier: 3.767A pdb=" N GLU D 102 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.440A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 156 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AC1, first strand: chain 'D' and resid 208 through 212 removed outlier: 3.876A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 262 through 267 removed outlier: 6.972A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 229 hydrogen bonds 454 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 155 stacking parallelities Total time for adding SS restraints: 10.10 Time building geometry restraints manager: 9.13 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: 4914 1.33 - 1.45: 4819 1.45 - 1.57: 10028 1.57 - 1.69: 406 1.69 - 1.81: 164 Bond restraints: 20331 Sorted by residual: bond pdb=" N ARG C 848 " pdb=" CA ARG C 848 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.19e-02 7.06e+03 7.10e+00 bond pdb=" N MET C 602 " pdb=" CA MET C 602 " ideal model delta sigma weight residual 1.454 1.485 -0.030 1.15e-02 7.56e+03 7.03e+00 bond pdb=" N GLU A 597 " pdb=" CA GLU A 597 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.21e-02 6.83e+03 6.38e+00 bond pdb=" N GLN C 962 " pdb=" CA GLN C 962 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.12e+00 bond pdb=" N ARG A 713 " pdb=" CA ARG A 713 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.28e-02 6.10e+03 5.94e+00 ... (remaining 20326 not shown) Histogram of bond angle deviations from ideal: 97.83 - 105.10: 1145 105.10 - 112.37: 10755 112.37 - 119.64: 6582 119.64 - 126.91: 9205 126.91 - 134.18: 696 Bond angle restraints: 28383 Sorted by residual: angle pdb=" N ILE H 113 " pdb=" CA ILE H 113 " pdb=" C ILE H 113 " ideal model delta sigma weight residual 113.71 108.78 4.93 9.50e-01 1.11e+00 2.69e+01 angle pdb=" N GLY B 275 " pdb=" CA GLY B 275 " pdb=" C GLY B 275 " ideal model delta sigma weight residual 111.03 116.79 -5.76 1.40e+00 5.10e-01 1.69e+01 angle pdb=" O3' DT G 41 " pdb=" C3' DT G 41 " pdb=" C2' DT G 41 " ideal model delta sigma weight residual 111.50 105.50 6.00 1.50e+00 4.44e-01 1.60e+01 angle pdb=" C ARG D 212 " pdb=" N ASN D 213 " pdb=" CA ASN D 213 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" O3' DT G 42 " pdb=" C3' DT G 42 " pdb=" C2' DT G 42 " ideal model delta sigma weight residual 111.50 117.05 -5.55 1.50e+00 4.44e-01 1.37e+01 ... (remaining 28378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 10788 35.86 - 71.72: 879 71.72 - 107.57: 10 107.57 - 143.43: 0 143.43 - 179.29: 5 Dihedral angle restraints: 11682 sinusoidal: 6012 harmonic: 5670 Sorted by residual: dihedral pdb=" CA ARG A 458 " pdb=" C ARG A 458 " pdb=" N GLY A 459 " pdb=" CA GLY A 459 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ARG C 838 " pdb=" C ARG C 838 " pdb=" N LYS C 839 " pdb=" CA LYS C 839 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+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 180.00 154.96 25.04 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 11679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2087 0.042 - 0.084: 788 0.084 - 0.126: 220 0.126 - 0.167: 33 0.167 - 0.209: 5 Chirality restraints: 3133 Sorted by residual: chirality pdb=" CG LEU C 411 " pdb=" CB LEU C 411 " pdb=" CD1 LEU C 411 " pdb=" CD2 LEU C 411 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' DT G 42 " pdb=" C4' DT G 42 " pdb=" O3' DT G 42 " pdb=" C2' DT G 42 " both_signs ideal model delta sigma weight residual False -2.66 -2.46 -0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CA ARG A 848 " pdb=" N ARG A 848 " pdb=" C ARG A 848 " pdb=" CB ARG A 848 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 3130 not shown) Planarity restraints: 2944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 18 " 0.043 2.00e-02 2.50e+03 1.71e-02 8.08e+00 pdb=" N9 DA I 18 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 18 " -0.014 2.00e-02 2.50e+03 pdb=" N7 DA I 18 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 18 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 18 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 18 " 0.018 2.00e-02 2.50e+03 pdb=" N1 DA I 18 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 18 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 18 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DA I 18 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 515 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO C 516 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 516 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 516 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 18 " 0.035 2.00e-02 2.50e+03 1.42e-02 5.55e+00 pdb=" N9 DA J 18 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DA J 18 " -0.010 2.00e-02 2.50e+03 pdb=" N7 DA J 18 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA J 18 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA J 18 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA J 18 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DA J 18 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA J 18 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA J 18 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DA J 18 " -0.009 2.00e-02 2.50e+03 ... (remaining 2941 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 40 2.35 - 2.99: 10011 2.99 - 3.62: 29724 3.62 - 4.26: 47253 4.26 - 4.90: 73921 Nonbonded interactions: 160949 Sorted by model distance: nonbonded pdb=" OD2 ASP A 708 " pdb="CA CA A1102 " model vdw 1.709 2.510 nonbonded pdb=" OD2 ASP C 708 " pdb="CA CA C1102 " model vdw 1.920 2.510 nonbonded pdb=" OD2 ASP C 600 " pdb="CA CA C1103 " model vdw 1.966 2.510 nonbonded pdb=" O GLN A 962 " pdb=" NE2 GLN A 962 " model vdw 2.165 3.120 nonbonded pdb=" NH2 ARG D 73 " pdb=" OD1 ASN D 101 " model vdw 2.196 3.120 ... (remaining 160944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' 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 451 or (resid 452 through 453 and (name N or name CA or name C or nam \ e O or name CB )) or resid 454 or (resid 455 through 456 and (name N or name CA \ or name C or name O or name CB )) or resid 457 or (resid 458 and (name N or name \ CA or name C or name O or name CB )) or resid 459 through 523 or (resid 524 and \ (name N or name CA or name C or name O or name CB )) or resid 525 through 815 o \ r resid 817 through 1008 or resid 1101 through 1103)) selection = (chain 'C' and (resid 401 through 430 or resid 432 through 815 or resid 817 thro \ ugh 860 or (resid 861 and (name N or name CA or name C or name O or name CB )) o \ r 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 1008 or resid 1101 through 1103)) } 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 116 or (resid 117 and (name N or name CA or name \ C or name O or name CB )) or resid 118 through 339 or (resid 340 through 342 an \ d (name N or name 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 67.500 Find NCS groups from input model: 0.690 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: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 : 0.007 0.107 20331 Z= 0.427 Angle : 0.778 9.029 28383 Z= 0.452 Chirality : 0.047 0.209 3133 Planarity : 0.005 0.059 2944 Dihedral : 20.065 179.289 8030 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.45 % Favored : 90.34 % Rotamer: Outliers : 0.30 % Allowed : 2.67 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -4.65 (0.15), residues: 1940 helix: -2.29 (0.16), residues: 682 sheet: -3.15 (0.23), residues: 352 loop : -3.70 (0.16), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 317 HIS 0.008 0.002 HIS A 942 PHE 0.033 0.003 PHE A 557 TYR 0.034 0.003 TYR D 91 ARG 0.010 0.001 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 176 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 298 GLU cc_start: 0.8086 (tt0) cc_final: 0.7571 (tm-30) REVERT: B 302 MET cc_start: 0.7316 (ptm) cc_final: 0.6874 (ptp) REVERT: C 416 LYS cc_start: 0.8056 (pptt) cc_final: 0.7776 (mtpp) REVERT: C 418 PHE cc_start: 0.8313 (t80) cc_final: 0.7205 (t80) REVERT: C 849 MET cc_start: 0.8599 (tpt) cc_final: 0.8318 (tpt) REVERT: D 298 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7621 (mp0) REVERT: D 303 GLU cc_start: 0.7391 (pm20) cc_final: 0.6977 (mp0) outliers start: 5 outliers final: 3 residues processed: 180 average time/residue: 0.3547 time to fit residues: 94.1505 Evaluate side-chains 114 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 607 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 85 optimal weight: 0.0060 chunk 164 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN A 473 ASN A 633 HIS A 739 GLN A 750 HIS ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 ASN A 990 HIS B 100 ASN B 222 HIS B 282 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 ASN C 934 ASN C 991 HIS D 181 HIS ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20331 Z= 0.240 Angle : 0.658 9.200 28383 Z= 0.362 Chirality : 0.042 0.168 3133 Planarity : 0.005 0.048 2944 Dihedral : 24.895 179.556 4395 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.30 % Favored : 93.60 % Rotamer: Outliers : 0.79 % Allowed : 5.96 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.96 (0.18), residues: 1940 helix: -0.63 (0.19), residues: 683 sheet: -2.54 (0.24), residues: 354 loop : -2.79 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 317 HIS 0.005 0.001 HIS C 406 PHE 0.028 0.002 PHE A 557 TYR 0.017 0.002 TYR C 928 ARG 0.005 0.001 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7197 (tm-30) REVERT: C 416 LYS cc_start: 0.8052 (pptt) cc_final: 0.7842 (mtpp) REVERT: D 110 MET cc_start: 0.8462 (mmm) cc_final: 0.7807 (mmm) REVERT: D 298 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7645 (mp0) REVERT: D 303 GLU cc_start: 0.7192 (pm20) cc_final: 0.6926 (mp0) REVERT: D 322 MET cc_start: 0.8925 (mtm) cc_final: 0.8604 (mtm) outliers start: 13 outliers final: 6 residues processed: 137 average time/residue: 0.3139 time to fit residues: 67.1162 Evaluate side-chains 113 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 910 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 206 optimal weight: 20.0000 chunk 170 optimal weight: 2.9990 chunk 189 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 153 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 282 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS D 222 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20331 Z= 0.206 Angle : 0.609 8.670 28383 Z= 0.336 Chirality : 0.041 0.155 3133 Planarity : 0.004 0.042 2944 Dihedral : 24.675 179.489 4392 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.63 % Favored : 94.27 % Rotamer: Outliers : 1.16 % Allowed : 6.75 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.19 (0.18), residues: 1940 helix: 0.10 (0.20), residues: 691 sheet: -2.10 (0.26), residues: 347 loop : -2.45 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 893 HIS 0.004 0.001 HIS C 406 PHE 0.021 0.001 PHE A 557 TYR 0.023 0.001 TYR A 559 ARG 0.005 0.000 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 883 MET cc_start: 0.8061 (tpt) cc_final: 0.7804 (tpt) REVERT: B 270 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7116 (tm-30) REVERT: D 298 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7627 (mp0) REVERT: D 322 MET cc_start: 0.8900 (mtm) cc_final: 0.8588 (mtm) outliers start: 19 outliers final: 7 residues processed: 130 average time/residue: 0.2903 time to fit residues: 59.8609 Evaluate side-chains 110 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 910 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20331 Z= 0.228 Angle : 0.609 10.450 28383 Z= 0.332 Chirality : 0.041 0.153 3133 Planarity : 0.004 0.038 2944 Dihedral : 24.600 179.739 4387 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.68 % Favored : 94.27 % Rotamer: Outliers : 1.09 % Allowed : 8.88 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.82 (0.19), residues: 1940 helix: 0.39 (0.20), residues: 696 sheet: -1.82 (0.26), residues: 347 loop : -2.28 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 893 HIS 0.004 0.001 HIS C 406 PHE 0.023 0.002 PHE A 418 TYR 0.020 0.001 TYR A 559 ARG 0.004 0.000 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8198 (pp) REVERT: B 270 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7245 (tm-30) REVERT: C 451 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8152 (tt) REVERT: D 298 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7657 (mp0) REVERT: D 322 MET cc_start: 0.8881 (mtm) cc_final: 0.8559 (mtm) outliers start: 18 outliers final: 12 residues processed: 123 average time/residue: 0.2931 time to fit residues: 57.9179 Evaluate side-chains 119 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain D residue 22 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 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 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20331 Z= 0.245 Angle : 0.606 9.061 28383 Z= 0.330 Chirality : 0.041 0.154 3133 Planarity : 0.004 0.038 2944 Dihedral : 24.577 179.774 4387 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 1.52 % Allowed : 9.12 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.62 (0.19), residues: 1940 helix: 0.53 (0.20), residues: 696 sheet: -1.62 (0.26), residues: 347 loop : -2.17 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 893 HIS 0.004 0.001 HIS C 406 PHE 0.031 0.002 PHE A 418 TYR 0.018 0.001 TYR A 559 ARG 0.007 0.000 ARG C 915 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7252 (tm-30) REVERT: C 418 PHE cc_start: 0.8262 (t80) cc_final: 0.8026 (t80) REVERT: C 451 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8152 (tt) REVERT: D 322 MET cc_start: 0.8866 (mtm) cc_final: 0.8590 (mtm) REVERT: D 329 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8665 (mp) outliers start: 25 outliers final: 13 residues processed: 124 average time/residue: 0.2895 time to fit residues: 58.9126 Evaluate side-chains 121 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 203 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 94 optimal weight: 40.0000 chunk 16 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20331 Z= 0.226 Angle : 0.597 8.615 28383 Z= 0.325 Chirality : 0.040 0.151 3133 Planarity : 0.004 0.039 2944 Dihedral : 24.509 179.837 4387 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.06 % Rotamer: Outliers : 1.40 % Allowed : 9.79 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.46 (0.19), residues: 1940 helix: 0.63 (0.20), residues: 696 sheet: -1.46 (0.26), residues: 349 loop : -2.09 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 893 HIS 0.004 0.001 HIS C 406 PHE 0.036 0.002 PHE A 418 TYR 0.016 0.001 TYR A 559 ARG 0.006 0.000 ARG C 970 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 883 MET cc_start: 0.8090 (tpt) cc_final: 0.7695 (tpt) REVERT: B 270 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7249 (tm-30) REVERT: C 418 PHE cc_start: 0.8173 (t80) cc_final: 0.7916 (t80) REVERT: C 451 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8099 (tt) REVERT: C 879 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.7000 (tp) REVERT: D 298 GLU cc_start: 0.7568 (mp0) cc_final: 0.7210 (mp0) REVERT: D 322 MET cc_start: 0.8862 (mtm) cc_final: 0.8612 (mtm) REVERT: D 329 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8670 (mp) outliers start: 23 outliers final: 16 residues processed: 124 average time/residue: 0.2883 time to fit residues: 57.4721 Evaluate side-chains 125 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 20331 Z= 0.340 Angle : 0.642 9.405 28383 Z= 0.346 Chirality : 0.042 0.177 3133 Planarity : 0.004 0.038 2944 Dihedral : 24.595 179.700 4387 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.51 % Favored : 93.44 % Rotamer: Outliers : 1.76 % Allowed : 9.73 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.48 (0.19), residues: 1940 helix: 0.55 (0.20), residues: 698 sheet: -1.41 (0.27), residues: 338 loop : -2.07 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 893 HIS 0.004 0.001 HIS A 991 PHE 0.037 0.002 PHE A 418 TYR 0.020 0.002 TYR A 559 ARG 0.004 0.001 ARG A 773 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 883 MET cc_start: 0.8161 (tpt) cc_final: 0.7757 (tpt) REVERT: B 270 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7205 (tm-30) REVERT: B 298 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7387 (tm-30) REVERT: C 418 PHE cc_start: 0.8166 (t80) cc_final: 0.7917 (t80) REVERT: C 451 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8111 (tt) REVERT: C 691 MET cc_start: 0.8728 (ttm) cc_final: 0.8385 (ttp) REVERT: D 298 GLU cc_start: 0.7660 (mp0) cc_final: 0.7340 (mp0) REVERT: D 322 MET cc_start: 0.8889 (mtm) cc_final: 0.8647 (mtm) REVERT: D 329 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8678 (mp) outliers start: 29 outliers final: 19 residues processed: 122 average time/residue: 0.2823 time to fit residues: 56.8060 Evaluate side-chains 120 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.261 > 50: distance: 15 - 171: 12.399 distance: 18 - 168: 7.307 distance: 27 - 157: 3.271 distance: 75 - 179: 8.597 distance: 78 - 176: 3.921 distance: 91 - 165: 3.244 distance: 94 - 162: 9.782 distance: 128 - 132: 6.779 distance: 132 - 133: 13.215 distance: 133 - 134: 23.175 distance: 133 - 136: 19.829 distance: 134 - 135: 19.925 distance: 134 - 138: 11.520 distance: 136 - 137: 10.870 distance: 138 - 139: 13.790 distance: 139 - 140: 18.355 distance: 139 - 142: 3.649 distance: 140 - 141: 4.494 distance: 140 - 147: 13.788 distance: 142 - 143: 26.045 distance: 143 - 144: 15.098 distance: 144 - 145: 16.167 distance: 145 - 146: 16.576 distance: 147 - 148: 3.579 distance: 147 - 153: 9.040 distance: 148 - 149: 12.818 distance: 148 - 151: 10.055 distance: 149 - 150: 15.550 distance: 149 - 154: 10.106 distance: 151 - 152: 3.071 distance: 152 - 153: 10.334 distance: 154 - 155: 14.669 distance: 155 - 156: 8.943 distance: 155 - 158: 10.331 distance: 156 - 157: 6.256 distance: 158 - 159: 10.211 distance: 159 - 160: 15.971 distance: 159 - 161: 21.394 distance: 162 - 163: 6.085 distance: 163 - 164: 6.519 distance: 163 - 166: 3.447 distance: 164 - 165: 4.624 distance: 166 - 167: 5.943 distance: 169 - 172: 5.839 distance: 170 - 171: 10.391 distance: 172 - 173: 6.152 distance: 173 - 174: 3.444 distance: 173 - 175: 4.949 distance: 177 - 178: 5.765 distance: 177 - 180: 4.123 distance: 180 - 181: 6.700 distance: 181 - 182: 9.407 distance: 182 - 183: 3.694 distance: 185 - 186: 9.388 distance: 185 - 188: 6.879 distance: 186 - 187: 6.436 distance: 186 - 192: 3.553 distance: 189 - 190: 3.974 distance: 189 - 191: 4.742 distance: 192 - 193: 6.767 distance: 193 - 194: 12.980 distance: 193 - 196: 5.864 distance: 194 - 195: 16.625 distance: 194 - 197: 23.994 distance: 197 - 198: 11.717 distance: 198 - 199: 10.442 distance: 198 - 201: 11.665 distance: 199 - 205: 3.771 distance: 201 - 202: 13.841 distance: 202 - 204: 3.995