Starting phenix.real_space_refine (version: dev) on Thu Feb 23 02:18:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeq_20034/02_2023/6oeq_20034.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeq_20034/02_2023/6oeq_20034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeq_20034/02_2023/6oeq_20034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeq_20034/02_2023/6oeq_20034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeq_20034/02_2023/6oeq_20034.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeq_20034/02_2023/6oeq_20034.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 Process input model Symmetric amino acids flipped Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A ARG 826": "NH1" <-> "NH2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A ARG 894": "NH1" <-> "NH2" Residue "A GLU 901": "OE1" <-> "OE2" Residue "A ARG 915": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B GLU 135": "OE1" <-> "OE2" 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 504": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "C ARG 558": "NH1" <-> "NH2" Residue "C GLU 649": "OE1" <-> "OE2" Residue "C GLU 662": "OE1" <-> "OE2" Residue "C ARG 773": "NH1" <-> "NH2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" Residue "C ARG 848": "NH1" <-> "NH2" Residue "C GLU 861": "OE1" <-> "OE2" Residue "C ARG 875": "NH1" <-> "NH2" Residue "C ARG 915": "NH1" <-> "NH2" Residue "C ARG 927": "NH1" <-> "NH2" Residue "C GLU 929": "OE1" <-> "OE2" Residue "C GLU 945": "OE1" <-> "OE2" 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19134 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4762 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2668 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 4827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4827 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 586} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 55 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: "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: "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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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 2540 SG CYS A 727 88.865 46.259 95.690 1.00176.74 S ATOM 2561 SG CYS A 730 91.881 43.361 96.831 1.00172.49 S ATOM 9974 SG CYS C 727 29.444 104.285 98.095 1.00 70.24 S ATOM 9995 SG CYS C 730 27.447 106.657 100.264 1.00 68.58 S Time building chain proxies: 11.44, per 1000 atoms: 0.60 Number of scatterers: 19134 At special positions: 0 Unit cell: (126.26, 157.29, 158.36, 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 2 19.99 S 104 16.00 P 204 15.00 O 3988 8.00 N 3376 7.00 C 11458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.55 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 942 " pdb=" ZN C1103 " pdb="ZN ZN C1103 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1103 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 727 " Number of angles added : 4 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3578 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 20 sheets defined 36.2% alpha, 21.8% beta 98 base pairs and 161 stacking pairs defined. Time for finding SS restraints: 6.83 Creating SS restraints... Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.876A pdb=" N GLN A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 Processing helix chain 'A' and resid 426 through 441 Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.817A 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 477 through 493 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.806A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 569 removed outlier: 3.520A pdb=" N ALA A 562 " --> pdb=" O ARG A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 removed outlier: 3.675A pdb=" N LEU A 668 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.723A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 removed outlier: 3.509A pdb=" N SER A 738 " --> pdb=" O ARG A 734 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 792 through 814 removed outlier: 3.950A pdb=" N CYS A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 838 removed outlier: 4.338A pdb=" N ARG A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 857 Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.640A pdb=" N VAL A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 890 Processing helix chain 'A' and resid 902 through 907 Processing helix chain 'A' and resid 908 through 923 Processing helix chain 'A' and resid 933 through 941 removed outlier: 3.730A pdb=" N HIS A 937 " --> pdb=" O THR A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 950 Processing helix chain 'A' and resid 962 through 974 removed outlier: 4.080A pdb=" N LYS A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 995 removed outlier: 3.640A pdb=" N GLU A 985 " --> pdb=" O CYS A 981 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 986 " --> pdb=" O TYR A 982 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 988 " --> pdb=" O MET A 984 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1001 Processing helix chain 'A' and resid 1002 through 1005 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 402 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 455 removed outlier: 3.804A pdb=" N ALA C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 473 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 508 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 removed outlier: 3.556A pdb=" N LEU C 668 " --> pdb=" O ASP C 664 " (cutoff:3.500A) Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 711 through 716 removed outlier: 3.682A pdb=" N GLU C 716 " --> pdb=" O VAL C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 740 removed outlier: 3.805A pdb=" N SER C 738 " --> pdb=" O ARG C 734 " (cutoff:3.500A) removed outlier: 3.938A 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 Processing helix chain 'C' and resid 792 through 813 removed outlier: 3.550A pdb=" N CYS C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY C 813 " --> pdb=" O GLN C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 841 Processing helix chain 'C' and resid 850 through 858 removed outlier: 3.901A pdb=" N MET C 858 " --> pdb=" O ALA C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.654A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 890 Processing helix chain 'C' and resid 890 through 895 removed outlier: 3.601A pdb=" N ARG C 894 " --> pdb=" O LYS C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 924 removed outlier: 4.021A pdb=" N CYS C 907 " --> pdb=" O PRO C 903 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN C 908 " --> pdb=" O GLU C 904 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR C 909 " --> pdb=" O SER C 905 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE C 911 " --> pdb=" O CYS C 907 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.610A pdb=" N HIS C 937 " --> pdb=" O THR C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 958 through 963 removed outlier: 3.531A pdb=" N GLN C 962 " --> pdb=" O SER C 958 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER C 963 " --> pdb=" O GLU C 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 958 through 963' Processing helix chain 'C' and resid 964 through 975 Processing helix chain 'C' and resid 981 through 996 removed outlier: 3.833A pdb=" N GLU C 985 " --> pdb=" O CYS C 981 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL C 987 " --> pdb=" O GLU C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1004 removed outlier: 3.638A pdb=" N GLN C1000 " --> pdb=" O SER C 996 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE C1002 " --> pdb=" O TYR C 998 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.824A pdb=" N LEU D 14 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 4.017A pdb=" N THR A 705 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.371A 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 519 removed outlier: 4.017A pdb=" N THR A 705 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 636 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.583A pdb=" N GLY B 330 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 24 removed outlier: 4.189A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 58 " --> pdb=" O HIS B 47 " (cutoff:3.500A) removed outlier: 3.742A 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 112 through 116 Processing sheet with id=AA7, first strand: chain 'B' and resid 130 through 131 removed outlier: 5.926A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 182 " --> pdb=" O TYR B 195 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA9, first strand: chain 'B' and resid 205 through 211 removed outlier: 5.139A pdb=" N HIS B 207 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY B 220 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER B 209 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE B 218 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA B 211 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL B 216 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 520 removed outlier: 6.822A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 518 through 520 removed outlier: 6.822A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AB5, first strand: chain 'D' and resid 20 through 24 Processing sheet with id=AB6, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB7, first strand: chain 'D' and resid 75 through 80 removed outlier: 3.620A pdb=" N CYS D 78 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB9, first strand: chain 'D' and resid 160 through 161 Processing sheet with id=AC1, first strand: chain 'D' and resid 207 through 212 removed outlier: 3.503A pdb=" N THR D 215 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 3.911A 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: 6.299A pdb=" N LEU D 263 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL D 274 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLN D 265 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL D 272 " --> pdb=" O GLN D 265 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 244 hydrogen bonds 488 hydrogen bond angles 0 basepair planarities 98 basepair parallelities 161 stacking parallelities Total time for adding SS restraints: 11.87 Time building geometry restraints manager: 10.07 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: 5052 1.33 - 1.46: 5945 1.46 - 1.58: 8419 1.58 - 1.71: 399 1.71 - 1.83: 158 Bond restraints: 19973 Sorted by residual: bond pdb=" CA ALA C 502 " pdb=" C ALA C 502 " ideal model delta sigma weight residual 1.522 1.455 0.067 1.40e-02 5.10e+03 2.32e+01 bond pdb=" CA THR C 728 " pdb=" C THR C 728 " ideal model delta sigma weight residual 1.523 1.461 0.062 1.41e-02 5.03e+03 1.91e+01 bond pdb=" N LEU A 906 " pdb=" CA LEU A 906 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.28e-02 6.10e+03 9.35e+00 bond pdb=" C TYR C 514 " pdb=" N HIS C 515 " ideal model delta sigma weight residual 1.333 1.252 0.080 2.74e-02 1.33e+03 8.55e+00 bond pdb=" N ASP C 600 " pdb=" CA ASP C 600 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.20e-02 6.94e+03 6.43e+00 ... (remaining 19968 not shown) Histogram of bond angle deviations from ideal: 97.12 - 104.51: 1050 104.51 - 111.90: 9898 111.90 - 119.28: 6801 119.28 - 126.67: 9391 126.67 - 134.06: 770 Bond angle restraints: 27910 Sorted by residual: angle pdb=" C TYR C 725 " pdb=" N ILE C 726 " pdb=" CA ILE C 726 " ideal model delta sigma weight residual 122.66 117.66 5.00 9.70e-01 1.06e+00 2.66e+01 angle pdb=" C ARG D 73 " pdb=" N TYR D 74 " pdb=" CA TYR D 74 " ideal model delta sigma weight residual 122.85 117.53 5.32 1.10e+00 8.26e-01 2.34e+01 angle pdb=" N LEU C 655 " pdb=" CA LEU C 655 " pdb=" C LEU C 655 " ideal model delta sigma weight residual 114.62 109.15 5.47 1.14e+00 7.69e-01 2.30e+01 angle pdb=" C ASN D 268 " pdb=" N ASP D 269 " pdb=" CA ASP D 269 " ideal model delta sigma weight residual 122.46 128.93 -6.47 1.41e+00 5.03e-01 2.10e+01 angle pdb=" C THR C 400 " pdb=" N ARG C 401 " pdb=" CA ARG C 401 " ideal model delta sigma weight residual 120.28 125.96 -5.68 1.34e+00 5.57e-01 1.80e+01 ... (remaining 27905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 10202 35.50 - 71.00: 1010 71.00 - 106.49: 17 106.49 - 141.99: 3 141.99 - 177.49: 7 Dihedral angle restraints: 11239 sinusoidal: 5692 harmonic: 5547 Sorted by residual: dihedral pdb=" CA GLU D 303 " pdb=" C GLU D 303 " pdb=" N THR D 304 " pdb=" CA THR D 304 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ASN D 101 " pdb=" C ASN D 101 " pdb=" N GLU D 102 " pdb=" CA GLU D 102 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA GLN A 581 " pdb=" C GLN A 581 " pdb=" N ASP A 582 " pdb=" CA ASP A 582 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 11236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2115 0.054 - 0.107: 757 0.107 - 0.161: 179 0.161 - 0.215: 39 0.215 - 0.268: 5 Chirality restraints: 3095 Sorted by residual: chirality pdb=" CB ILE B 50 " pdb=" CA ILE B 50 " pdb=" CG1 ILE B 50 " pdb=" CG2 ILE B 50 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CG LEU D 14 " pdb=" CB LEU D 14 " pdb=" CD1 LEU D 14 " pdb=" CD2 LEU D 14 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" P DA I 42 " pdb=" OP1 DA I 42 " pdb=" OP2 DA I 42 " pdb=" O5' DA I 42 " both_signs ideal model delta sigma weight residual True 2.35 -2.57 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 3092 not shown) Planarity restraints: 2876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 511 " -0.051 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO C 512 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 512 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 512 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 91 " -0.018 2.00e-02 2.50e+03 1.92e-02 7.39e+00 pdb=" CG TYR D 91 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR D 91 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR D 91 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR D 91 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 91 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 91 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 91 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 673 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO C 674 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 674 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 674 " 0.037 5.00e-02 4.00e+02 ... (remaining 2873 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 54 2.37 - 3.01: 9613 3.01 - 3.64: 31301 3.64 - 4.27: 44669 4.27 - 4.90: 68375 Nonbonded interactions: 154012 Sorted by model distance: nonbonded pdb=" OE1 GLN C 962 " pdb="CA CA C1102 " model vdw 1.742 2.510 nonbonded pdb=" OD1 ASP C 600 " pdb="CA CA C1101 " model vdw 1.808 2.510 nonbonded pdb=" OD2 ASP C 708 " pdb="CA CA C1101 " model vdw 1.873 2.510 nonbonded pdb=" OD2 ASP C 600 " pdb="CA CA C1102 " model vdw 1.909 2.510 nonbonded pdb=" OG SER C 872 " pdb=" OE1 GLU C 874 " model vdw 2.234 2.440 ... (remaining 154007 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 400 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 through 43 \ 1 or (resid 432 and (name N or name CA or name C or name O or name CB )) or resi \ d 433 through 435 or (resid 436 and (name N or name CA or name C or name O or na \ me CB )) or resid 437 through 451 or (resid 452 through 453 and (name N or name \ CA or name C or name O or name CB )) or resid 454 through 455 or (resid 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 52 \ 3 or (resid 524 and (name N or name CA or name C or name O or name CB )) or resi \ d 525 through 571 or (resid 572 and (name N or name CA or name C or name O or na \ me 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 614 and \ (name N or name CA or name C or name O or name CB )) or resid 615 through 813 or \ (resid 814 and (name N or name CA or name C or name O or name CB )) or resid 81 \ 5 through 816 or (resid 817 and (name N or name CA or name C or name O or name C \ B )) or resid 818 through 823 or (resid 824 and (name N or name CA or name C or \ name O or name CB )) or resid 825 through 826 or (resid 827 through 828 and (nam \ e N or name CA or name C or name O or name CB )) or resid 829 through 879 or (re \ sid 880 and (name N or name CA or name C or name O or name CB )) or resid 881 th \ rough 979 or (resid 980 and (name N or name CA or name C or name O or name CB )) \ or resid 981 through 1008)) selection = (chain 'C' and (resid 400 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB )) or resid 410 through 519 or (resid 520 and (name N \ or name CA or name C or name O or name CB )) or resid 521 through 606 or (resid \ 607 through 614 and (name N or name CA or name C or name O or name CB )) or resi \ d 615 through 638 or (resid 639 and (name N or name CA or name C or name O or na \ me CB )) or resid 640 through 751 or (resid 752 and (name N or name CA or name C \ or name O or name CB )) or resid 753 through 757 or (resid 758 and (name N or n \ ame CA or name C or name O or name CB )) or resid 759 through 810 or (resid 811 \ and (name N or name CA or name C or name O or name CB )) or resid 812 through 81 \ 9 or (resid 820 through 821 and (name N or name CA or name C or name O or name C \ B )) or resid 822 through 837 or (resid 838 through 839 and (name N or name CA o \ r name C or name O or name CB )) or resid 840 through 843 or (resid 844 and (nam \ e N or name CA or name C or name O or name CB )) or resid 845 through 846 or (re \ sid 847 and (name N or name CA or name C or name O or name CB )) or resid 848 th \ rough 860 or (resid 861 and (name N or name CA or name C or name O or name CB )) \ or resid 862 through 887 or (resid 888 and (name N or name CA or name C or name \ O or name CB )) or resid 889 through 913 or (resid 914 and (name N or name CA o \ r name C or name O or name CB )) or resid 915 through 917 or (resid 918 and (nam \ e N or name CA or name C or name O or name CB )) or resid 919 through 924 or (re \ sid 925 and (name N or name CA or name C or name O or name CB )) or resid 926 or \ (resid 927 through 928 and (name N or name CA or name C or name O or name CB )) \ or resid 929 through 957 or (resid 961 and (name N or name CA or name C or name \ O or name CB )) or resid 962 through 982 or (resid 983 and (name N or name CA o \ r name C or name O or name CB )) or resid 984 through 1008)) } ncs_group { reference = chain 'B' 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 338 or (resid 339 and (name N or \ name CA or name C or name O or name CB )) or resid 340 through 351)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 P 204 5.49 5 S 104 5.16 5 C 11458 2.51 5 N 3376 2.21 5 O 3988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 0.880 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: 6.320 Check model and map are aligned: 0.290 Process input model: 66.180 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.080 19973 Z= 0.531 Angle : 1.049 10.377 27910 Z= 0.604 Chirality : 0.058 0.268 3095 Planarity : 0.007 0.077 2876 Dihedral : 22.936 177.489 7661 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.71 % Favored : 91.18 % Rotamer Outliers : 0.62 % 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: -4.02 (0.16), residues: 1894 helix: -2.70 (0.15), residues: 604 sheet: -1.61 (0.29), residues: 307 loop : -3.04 (0.16), residues: 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 202 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 211 average time/residue: 0.3320 time to fit residues: 106.5000 Evaluate side-chains 142 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1727 time to fit residues: 3.8794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.0470 chunk 162 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN A 525 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 795 HIS ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN A 842 ASN A 860 GLN ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 HIS A1006 HIS B 4 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 ASN C 820 ASN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS D 89 HIS D 101 ASN D 222 HIS D 268 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 19973 Z= 0.198 Angle : 0.650 7.811 27910 Z= 0.361 Chirality : 0.041 0.154 3095 Planarity : 0.005 0.052 2876 Dihedral : 25.897 179.183 4120 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.12 % Favored : 94.83 % Rotamer Outliers : 0.06 % 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: -2.78 (0.17), residues: 1894 helix: -1.07 (0.19), residues: 630 sheet: -1.36 (0.29), residues: 323 loop : -2.60 (0.18), residues: 941 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 220 average time/residue: 0.3031 time to fit residues: 104.2277 Evaluate side-chains 146 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 2.074 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1713 time to fit residues: 2.9897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 HIS ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN C 876 HIS ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1007 ASN D 47 HIS D 101 ASN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 19973 Z= 0.175 Angle : 0.602 7.328 27910 Z= 0.334 Chirality : 0.040 0.151 3095 Planarity : 0.004 0.037 2876 Dihedral : 25.658 178.772 4120 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.44 % Favored : 94.51 % Rotamer Outliers : 0.12 % 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: -2.15 (0.18), residues: 1894 helix: -0.38 (0.20), residues: 635 sheet: -1.23 (0.28), residues: 331 loop : -2.27 (0.19), residues: 928 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.3012 time to fit residues: 96.9607 Evaluate side-chains 145 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.069 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 97 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 179 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A 795 HIS ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 525 ASN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS D 101 ASN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 19973 Z= 0.297 Angle : 0.665 6.921 27910 Z= 0.368 Chirality : 0.041 0.157 3095 Planarity : 0.004 0.043 2876 Dihedral : 25.628 179.898 4120 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 0.00 % 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: -2.08 (0.19), residues: 1894 helix: -0.23 (0.20), residues: 649 sheet: -1.25 (0.28), residues: 330 loop : -2.31 (0.19), residues: 915 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2967 time to fit residues: 88.6955 Evaluate side-chains 139 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.917 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 0.9980 chunk 179 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 19973 Z= 0.196 Angle : 0.599 6.748 27910 Z= 0.330 Chirality : 0.040 0.154 3095 Planarity : 0.004 0.038 2876 Dihedral : 25.564 178.465 4120 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.00 % 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: -1.71 (0.19), residues: 1894 helix: 0.07 (0.21), residues: 646 sheet: -0.98 (0.29), residues: 319 loop : -2.11 (0.20), residues: 929 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3040 time to fit residues: 93.9490 Evaluate side-chains 143 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 0.0270 chunk 200 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 19973 Z= 0.199 Angle : 0.596 7.109 27910 Z= 0.329 Chirality : 0.040 0.156 3095 Planarity : 0.004 0.040 2876 Dihedral : 25.501 178.869 4120 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 0.06 % 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: -1.59 (0.19), residues: 1894 helix: 0.14 (0.21), residues: 648 sheet: -0.86 (0.29), residues: 321 loop : -2.03 (0.20), residues: 925 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.3083 time to fit residues: 94.6659 Evaluate side-chains 146 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.078 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 111 optimal weight: 0.3980 chunk 199 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 19973 Z= 0.166 Angle : 0.583 7.068 27910 Z= 0.320 Chirality : 0.040 0.153 3095 Planarity : 0.004 0.039 2876 Dihedral : 25.389 177.907 4120 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 0.12 % 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: -1.42 (0.19), residues: 1894 helix: 0.20 (0.21), residues: 648 sheet: -0.52 (0.30), residues: 306 loop : -1.95 (0.20), residues: 940 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 203 average time/residue: 0.3104 time to fit residues: 99.1511 Evaluate side-chains 152 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.858 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.9980 chunk 79 optimal weight: 0.0770 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 0.0010 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 0.2980 chunk 135 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 19973 Z= 0.163 Angle : 0.592 8.859 27910 Z= 0.319 Chirality : 0.040 0.202 3095 Planarity : 0.004 0.037 2876 Dihedral : 25.301 177.830 4120 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 0.12 % 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: -1.22 (0.19), residues: 1894 helix: 0.40 (0.21), residues: 639 sheet: -0.34 (0.30), residues: 306 loop : -1.87 (0.20), residues: 949 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.2921 time to fit residues: 94.2229 Evaluate side-chains 154 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.137 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 185 optimal weight: 0.7980 chunk 111 optimal weight: 0.0870 chunk 80 optimal weight: 8.9990 chunk 145 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 overall best weight: 1.2560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 19973 Z= 0.186 Angle : 0.603 15.637 27910 Z= 0.325 Chirality : 0.040 0.179 3095 Planarity : 0.004 0.060 2876 Dihedral : 25.256 179.168 4120 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.07 % Favored : 93.88 % Rotamer Outliers : 0.06 % 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: -1.18 (0.19), residues: 1894 helix: 0.45 (0.21), residues: 638 sheet: -0.49 (0.30), residues: 321 loop : -1.80 (0.20), residues: 935 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.2933 time to fit residues: 94.0612 Evaluate side-chains 155 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.063 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 136 optimal weight: 0.0870 chunk 206 optimal weight: 10.0000 chunk 189 optimal weight: 20.0000 chunk 164 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 overall best weight: 2.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN ** C1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 19973 Z= 0.245 Angle : 0.631 8.194 27910 Z= 0.344 Chirality : 0.041 0.162 3095 Planarity : 0.004 0.064 2876 Dihedral : 25.292 179.782 4120 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.71 % Favored : 93.24 % Rotamer Outliers : 0.06 % 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: -1.31 (0.19), residues: 1894 helix: 0.30 (0.21), residues: 650 sheet: -0.55 (0.30), residues: 322 loop : -1.87 (0.20), residues: 922 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.3015 time to fit residues: 89.3350 Evaluate side-chains 146 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.042 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 151 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN ** C1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.079930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058767 restraints weight = 102846.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.060139 restraints weight = 56257.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.061015 restraints weight = 37401.672| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 19973 Z= 0.190 Angle : 0.599 8.089 27910 Z= 0.326 Chirality : 0.040 0.169 3095 Planarity : 0.004 0.051 2876 Dihedral : 25.259 179.080 4120 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.09 % Rotamer Outliers : 0.00 % 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: -1.25 (0.19), residues: 1894 helix: 0.35 (0.21), residues: 651 sheet: -0.54 (0.30), residues: 320 loop : -1.82 (0.20), residues: 923 =============================================================================== Job complete usr+sys time: 3177.60 seconds wall clock time: 59 minutes 0.61 seconds (3540.61 seconds total)