Starting phenix.real_space_refine (version: dev) on Sun Feb 26 04:26:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wte_32780/02_2023/7wte_32780_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wte_32780/02_2023/7wte_32780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wte_32780/02_2023/7wte_32780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wte_32780/02_2023/7wte_32780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wte_32780/02_2023/7wte_32780_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wte_32780/02_2023/7wte_32780_updated.pdb" } resolution = 3.3 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= 0.000 sd= 0.002 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 GLU 729": "OE1" <-> "OE2" Residue "A PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 946": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C GLU 353": "OE1" <-> "OE2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 621": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ARG 445": "NH1" <-> "NH2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "D GLU 863": "OE1" <-> "OE2" Residue "D GLU 1079": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 27160 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4625 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 40, 'TRANS': 559} Chain: "B" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4625 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 40, 'TRANS': 559} Chain: "C" Number of atoms: 8869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 8869 Classifications: {'peptide': 1146} Link IDs: {'PTRANS': 65, 'TRANS': 1080} Chain: "D" Number of atoms: 8877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8877 Classifications: {'peptide': 1147} Link IDs: {'PTRANS': 65, 'TRANS': 1081} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'ACO': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'ACO': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.55, per 1000 atoms: 0.57 Number of scatterers: 27160 At special positions: 0 Unit cell: (161.7, 160.6, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 152 16.00 P 12 15.00 O 5089 8.00 N 4735 7.00 C 17172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 752 " - pdb=" SG CYS A 786 " distance=2.03 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 786 " distance=2.02 Simple disulfide: pdb=" SG CYS C 752 " - pdb=" SG CYS C 786 " distance=2.02 Simple disulfide: pdb=" SG CYS D 752 " - pdb=" SG CYS D 786 " distance=2.02 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: 10.65 Conformation dependent library (CDL) restraints added in 4.5 seconds 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 23 sheets defined 39.7% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 541 through 559 Proline residue: A 550 - end of helix Processing helix chain 'A' and resid 572 through 577 Processing helix chain 'A' and resid 584 through 597 removed outlier: 3.532A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 609 through 617 removed outlier: 4.678A pdb=" N ASP A 613 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 633 removed outlier: 3.975A pdb=" N GLU A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 669 Processing helix chain 'A' and resid 683 through 696 Processing helix chain 'A' and resid 720 through 733 Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 779 through 787 Processing helix chain 'A' and resid 810 through 816 Processing helix chain 'A' and resid 828 through 842 Processing helix chain 'A' and resid 850 through 853 No H-bonds generated for 'chain 'A' and resid 850 through 853' Processing helix chain 'A' and resid 861 through 864 No H-bonds generated for 'chain 'A' and resid 861 through 864' Processing helix chain 'A' and resid 868 through 881 Processing helix chain 'A' and resid 884 through 900 removed outlier: 3.919A pdb=" N LYS A 888 " --> pdb=" O SER A 885 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU A 889 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 895 " --> pdb=" O LYS A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 923 Processing helix chain 'A' and resid 929 through 933 Processing helix chain 'A' and resid 942 through 948 Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'A' and resid 978 through 981 No H-bonds generated for 'chain 'A' and resid 978 through 981' Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1004 through 1012 Processing helix chain 'A' and resid 1014 through 1027 Processing helix chain 'A' and resid 1035 through 1039 Processing helix chain 'B' and resid 497 through 509 Processing helix chain 'B' and resid 542 through 547 Processing helix chain 'B' and resid 550 through 559 Processing helix chain 'B' and resid 572 through 577 Processing helix chain 'B' and resid 584 through 589 removed outlier: 4.495A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.701A pdb=" N HIS B 596 " --> pdb=" O PRO B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 611 No H-bonds generated for 'chain 'B' and resid 609 through 611' Processing helix chain 'B' and resid 614 through 617 No H-bonds generated for 'chain 'B' and resid 614 through 617' Processing helix chain 'B' and resid 623 through 631 removed outlier: 3.533A pdb=" N GLU B 629 " --> pdb=" O ARG B 625 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU B 630 " --> pdb=" O ARG B 626 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 669 Processing helix chain 'B' and resid 683 through 696 Processing helix chain 'B' and resid 720 through 733 removed outlier: 3.615A pdb=" N MET B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 762 removed outlier: 3.526A pdb=" N ARG B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 799 through 801 No H-bonds generated for 'chain 'B' and resid 799 through 801' Processing helix chain 'B' and resid 810 through 816 Processing helix chain 'B' and resid 828 through 845 removed outlier: 3.655A pdb=" N ASP B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR B 845 " --> pdb=" O ALA B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 864 No H-bonds generated for 'chain 'B' and resid 861 through 864' Processing helix chain 'B' and resid 868 through 880 removed outlier: 3.845A pdb=" N ASN B 873 " --> pdb=" O GLY B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 900 removed outlier: 4.133A pdb=" N VAL B 895 " --> pdb=" O LYS B 892 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU B 896 " --> pdb=" O ALA B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 924 Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 942 through 949 Processing helix chain 'B' and resid 961 through 968 Processing helix chain 'B' and resid 978 through 981 No H-bonds generated for 'chain 'B' and resid 978 through 981' Processing helix chain 'B' and resid 988 through 997 Processing helix chain 'B' and resid 1004 through 1012 Processing helix chain 'B' and resid 1014 through 1027 Processing helix chain 'B' and resid 1035 through 1039 Processing helix chain 'C' and resid 47 through 59 removed outlier: 3.523A pdb=" N LEU C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 109 removed outlier: 3.548A pdb=" N ASN C 109 " --> pdb=" O VAL C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 211 through 226 removed outlier: 3.759A pdb=" N GLU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 302 Processing helix chain 'C' and resid 333 through 339 Processing helix chain 'C' and resid 344 through 353 Processing helix chain 'C' and resid 357 through 360 No H-bonds generated for 'chain 'C' and resid 357 through 360' Processing helix chain 'C' and resid 436 through 449 Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'C' and resid 469 through 473 Processing helix chain 'C' and resid 478 through 480 No H-bonds generated for 'chain 'C' and resid 478 through 480' Processing helix chain 'C' and resid 497 through 510 removed outlier: 3.513A pdb=" N LEU C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 547 Processing helix chain 'C' and resid 550 through 559 Processing helix chain 'C' and resid 572 through 577 Processing helix chain 'C' and resid 587 through 589 No H-bonds generated for 'chain 'C' and resid 587 through 589' Processing helix chain 'C' and resid 591 through 597 removed outlier: 3.700A pdb=" N HIS C 596 " --> pdb=" O PRO C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 612 No H-bonds generated for 'chain 'C' and resid 609 through 612' Processing helix chain 'C' and resid 623 through 633 removed outlier: 4.417A pdb=" N GLU C 629 " --> pdb=" O ARG C 625 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 630 " --> pdb=" O ARG C 626 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU C 632 " --> pdb=" O GLN C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 669 Processing helix chain 'C' and resid 683 through 696 Processing helix chain 'C' and resid 720 through 733 Processing helix chain 'C' and resid 749 through 762 removed outlier: 4.327A pdb=" N ARG C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 789 Processing helix chain 'C' and resid 799 through 801 No H-bonds generated for 'chain 'C' and resid 799 through 801' Processing helix chain 'C' and resid 810 through 816 Processing helix chain 'C' and resid 828 through 845 removed outlier: 4.082A pdb=" N PHE C 832 " --> pdb=" O MET C 828 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP C 833 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU C 844 " --> pdb=" O GLY C 840 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR C 845 " --> pdb=" O ALA C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 864 No H-bonds generated for 'chain 'C' and resid 861 through 864' Processing helix chain 'C' and resid 868 through 880 removed outlier: 3.880A pdb=" N THR C 872 " --> pdb=" O GLY C 868 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASN C 873 " --> pdb=" O GLY C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 892 Processing helix chain 'C' and resid 894 through 901 Processing helix chain 'C' and resid 909 through 924 Processing helix chain 'C' and resid 928 through 933 Processing helix chain 'C' and resid 942 through 949 Processing helix chain 'C' and resid 961 through 967 Processing helix chain 'C' and resid 978 through 981 No H-bonds generated for 'chain 'C' and resid 978 through 981' Processing helix chain 'C' and resid 988 through 997 removed outlier: 3.782A pdb=" N LYS C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1012 Processing helix chain 'C' and resid 1014 through 1026 removed outlier: 3.704A pdb=" N ALA C1025 " --> pdb=" O LYS C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1039 Processing helix chain 'D' and resid 47 through 59 removed outlier: 3.510A pdb=" N LEU D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 99 through 108 Processing helix chain 'D' and resid 125 through 133 Processing helix chain 'D' and resid 143 through 149 Processing helix chain 'D' and resid 152 through 161 Processing helix chain 'D' and resid 177 through 186 Processing helix chain 'D' and resid 210 through 227 removed outlier: 3.798A pdb=" N GLU D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 302 Processing helix chain 'D' and resid 331 through 339 removed outlier: 4.056A pdb=" N THR D 334 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 353 Processing helix chain 'D' and resid 357 through 360 Processing helix chain 'D' and resid 436 through 449 Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'D' and resid 469 through 473 Processing helix chain 'D' and resid 478 through 480 No H-bonds generated for 'chain 'D' and resid 478 through 480' Processing helix chain 'D' and resid 485 through 487 No H-bonds generated for 'chain 'D' and resid 485 through 487' Processing helix chain 'D' and resid 496 through 509 removed outlier: 3.629A pdb=" N LEU D 501 " --> pdb=" O ALA D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 547 Processing helix chain 'D' and resid 550 through 559 Processing helix chain 'D' and resid 572 through 576 Processing helix chain 'D' and resid 584 through 597 removed outlier: 3.545A pdb=" N ILE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Proline residue: D 592 - end of helix Processing helix chain 'D' and resid 609 through 617 removed outlier: 3.796A pdb=" N ASP D 613 " --> pdb=" O GLY D 609 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET D 616 " --> pdb=" O PHE D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 633 Processing helix chain 'D' and resid 656 through 669 Processing helix chain 'D' and resid 683 through 696 Processing helix chain 'D' and resid 720 through 733 Processing helix chain 'D' and resid 749 through 760 Processing helix chain 'D' and resid 779 through 789 Processing helix chain 'D' and resid 810 through 817 removed outlier: 3.733A pdb=" N THR D 817 " --> pdb=" O LEU D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 828 through 845 removed outlier: 3.767A pdb=" N GLY D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR D 845 " --> pdb=" O ALA D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 852 No H-bonds generated for 'chain 'D' and resid 850 through 852' Processing helix chain 'D' and resid 868 through 870 No H-bonds generated for 'chain 'D' and resid 868 through 870' Processing helix chain 'D' and resid 872 through 881 removed outlier: 3.791A pdb=" N ALA D 878 " --> pdb=" O LEU D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 901 removed outlier: 3.731A pdb=" N TYR D 894 " --> pdb=" O VAL D 890 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL D 895 " --> pdb=" O LYS D 891 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU D 896 " --> pdb=" O LYS D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 924 Processing helix chain 'D' and resid 928 through 933 Processing helix chain 'D' and resid 942 through 949 Processing helix chain 'D' and resid 961 through 968 Processing helix chain 'D' and resid 978 through 981 No H-bonds generated for 'chain 'D' and resid 978 through 981' Processing helix chain 'D' and resid 989 through 997 Processing helix chain 'D' and resid 1004 through 1012 Processing helix chain 'D' and resid 1014 through 1026 Processing helix chain 'D' and resid 1035 through 1039 Processing sheet with id= A, first strand: chain 'A' and resid 564 through 567 Processing sheet with id= B, first strand: chain 'A' and resid 640 through 644 removed outlier: 7.361A pdb=" N VAL A 673 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU A 643 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ARG A 675 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL A 699 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL A 676 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU A 701 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE A 737 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE A 704 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS A 739 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE A 740 " --> pdb=" O PRO A 767 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N HIS A 769 " --> pdb=" O ILE A 740 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 1047 through 1050 removed outlier: 4.034A pdb=" N LEU A1058 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A1077 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL A1065 " --> pdb=" O GLN A1075 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN A1075 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 564 through 567 Processing sheet with id= E, first strand: chain 'B' and resid 640 through 644 removed outlier: 6.847A pdb=" N VAL B 673 " --> pdb=" O MET B 641 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU B 643 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG B 675 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL B 699 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL B 676 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU B 701 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE B 737 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N ILE B 740 " --> pdb=" O PRO B 767 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N HIS B 769 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ASP B 742 " --> pdb=" O HIS B 769 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N HIS B 771 " --> pdb=" O ASP B 742 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 1047 through 1051 removed outlier: 6.867A pdb=" N PHE B1077 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B1065 " --> pdb=" O GLN B1075 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN B1075 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 137 through 139 removed outlier: 6.519A pdb=" N ARG C 62 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL C 42 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL C 64 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU C 82 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR C 67 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR C 84 " --> pdb=" O TYR C 67 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 191 through 195 removed outlier: 3.771A pdb=" N GLU C 236 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 262 through 264 Processing sheet with id= J, first strand: chain 'C' and resid 249 through 251 Processing sheet with id= K, first strand: chain 'C' and resid 275 through 277 removed outlier: 3.678A pdb=" N VAL C 427 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 396 through 398 removed outlier: 4.078A pdb=" N ARG C 451 " --> pdb=" O ARG C 398 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 564 through 566 Processing sheet with id= N, first strand: chain 'C' and resid 768 through 771 removed outlier: 6.386A pdb=" N LEU C 738 " --> pdb=" O HIS C 769 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N HIS C 771 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE C 740 " --> pdb=" O HIS C 771 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE C 737 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 702 " --> pdb=" O ILE C 737 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 701 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET C 641 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 642 " --> pdb=" O ASN C 606 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 1048 through 1050 removed outlier: 3.531A pdb=" N PHE C1048 " --> pdb=" O ILE C1060 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C1060 " --> pdb=" O PHE C1048 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE C1077 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VAL C1065 " --> pdb=" O GLN C1075 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN C1075 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 1146 through 1148 removed outlier: 3.505A pdb=" N ASP C1122 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N SER C1141 " --> pdb=" O VAL C1120 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C1120 " --> pdb=" O SER C1141 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 137 through 139 removed outlier: 3.640A pdb=" N ALA D 113 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG D 62 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL D 42 " --> pdb=" O ARG D 62 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL D 64 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU D 82 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TYR D 67 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR D 84 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 204 through 207 removed outlier: 3.509A pdb=" N ARG D 205 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 257 through 259 removed outlier: 3.842A pdb=" N GLU D 324 " --> pdb=" O GLU D 311 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 275 through 277 removed outlier: 3.657A pdb=" N VAL D 427 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 564 through 567 Processing sheet with id= V, first strand: chain 'D' and resid 768 through 771 removed outlier: 6.929A pdb=" N LEU D 738 " --> pdb=" O HIS D 769 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N HIS D 771 " --> pdb=" O LEU D 738 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE D 740 " --> pdb=" O HIS D 771 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N ASN D 606 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 13.206A pdb=" N ARG D 644 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 1047 through 1051 removed outlier: 6.927A pdb=" N PHE D1077 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL D1065 " --> pdb=" O GLN D1075 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN D1075 " --> pdb=" O VAL D1065 " (cutoff:3.500A) 915 hydrogen bonds defined for protein. 2619 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.24 Time building geometry restraints manager: 11.28 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: 6340 1.33 - 1.45: 5556 1.45 - 1.57: 15588 1.57 - 1.70: 20 1.70 - 1.82: 264 Bond restraints: 27768 Sorted by residual: bond pdb=" N ILE C 516 " pdb=" CA ILE C 516 " ideal model delta sigma weight residual 1.458 1.493 -0.036 7.70e-03 1.69e+04 2.15e+01 bond pdb=" N ILE D 516 " pdb=" CA ILE D 516 " ideal model delta sigma weight residual 1.460 1.493 -0.034 7.50e-03 1.78e+04 2.05e+01 bond pdb=" N ILE D 86 " pdb=" CA ILE D 86 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.11e-02 8.12e+03 1.31e+01 bond pdb=" N VAL D 826 " pdb=" CA VAL D 826 " ideal model delta sigma weight residual 1.462 1.495 -0.034 1.01e-02 9.80e+03 1.10e+01 bond pdb=" N VAL C 164 " pdb=" CA VAL C 164 " ideal model delta sigma weight residual 1.461 1.501 -0.039 1.23e-02 6.61e+03 1.03e+01 ... (remaining 27763 not shown) Histogram of bond angle deviations from ideal: 97.68 - 106.11: 947 106.11 - 114.54: 16274 114.54 - 122.97: 18382 122.97 - 131.40: 2047 131.40 - 139.84: 27 Bond angle restraints: 37677 Sorted by residual: angle pdb=" C3B ACO C2001 " pdb=" O3B ACO C2001 " pdb=" P3B ACO C2001 " ideal model delta sigma weight residual 121.12 110.00 11.12 1.00e+00 1.00e+00 1.24e+02 angle pdb=" C3B ACO D2001 " pdb=" O3B ACO D2001 " pdb=" P3B ACO D2001 " ideal model delta sigma weight residual 121.12 110.04 11.08 1.00e+00 1.00e+00 1.23e+02 angle pdb=" PB ATP C2000 " pdb=" O3B ATP C2000 " pdb=" PG ATP C2000 " ideal model delta sigma weight residual 139.87 132.70 7.17 1.00e+00 1.00e+00 5.14e+01 angle pdb=" N VAL C 649 " pdb=" CA VAL C 649 " pdb=" C VAL C 649 " ideal model delta sigma weight residual 113.71 108.47 5.24 9.50e-01 1.11e+00 3.04e+01 angle pdb=" C ARG C 202 " pdb=" CA ARG C 202 " pdb=" CB ARG C 202 " ideal model delta sigma weight residual 116.63 110.97 5.66 1.16e+00 7.43e-01 2.38e+01 ... (remaining 37672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15067 17.95 - 35.89: 1302 35.89 - 53.84: 253 53.84 - 71.78: 74 71.78 - 89.72: 27 Dihedral angle restraints: 16723 sinusoidal: 6702 harmonic: 10021 Sorted by residual: dihedral pdb=" CB CYS B 752 " pdb=" SG CYS B 752 " pdb=" SG CYS B 786 " pdb=" CB CYS B 786 " ideal model delta sinusoidal sigma weight residual 93.00 179.39 -86.39 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS A 752 " pdb=" SG CYS A 752 " pdb=" SG CYS A 786 " pdb=" CB CYS A 786 " ideal model delta sinusoidal sigma weight residual 93.00 169.54 -76.54 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS D 752 " pdb=" SG CYS D 752 " pdb=" SG CYS D 786 " pdb=" CB CYS D 786 " ideal model delta sinusoidal sigma weight residual 93.00 141.06 -48.06 1 1.00e+01 1.00e-02 3.18e+01 ... (remaining 16720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3655 0.074 - 0.148: 478 0.148 - 0.221: 29 0.221 - 0.295: 1 0.295 - 0.369: 3 Chirality restraints: 4166 Sorted by residual: chirality pdb=" CB VAL C 164 " pdb=" CA VAL C 164 " pdb=" CG1 VAL C 164 " pdb=" CG2 VAL C 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA VAL C 164 " pdb=" N VAL C 164 " pdb=" C VAL C 164 " pdb=" CB VAL C 164 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ASN C 495 " pdb=" N ASN C 495 " pdb=" C ASN C 495 " pdb=" CB ASN C 495 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 4163 not shown) Planarity restraints: 4955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO D2001 " -0.099 2.00e-02 2.50e+03 8.17e-02 8.35e+01 pdb=" C5P ACO D2001 " 0.027 2.00e-02 2.50e+03 pdb=" C6P ACO D2001 " -0.074 2.00e-02 2.50e+03 pdb=" N4P ACO D2001 " 0.130 2.00e-02 2.50e+03 pdb=" O5P ACO D2001 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO C2001 " 0.099 2.00e-02 2.50e+03 8.16e-02 8.33e+01 pdb=" C5P ACO C2001 " -0.027 2.00e-02 2.50e+03 pdb=" C6P ACO C2001 " 0.074 2.00e-02 2.50e+03 pdb=" N4P ACO C2001 " -0.130 2.00e-02 2.50e+03 pdb=" O5P ACO C2001 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 199 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C GLY C 199 " 0.073 2.00e-02 2.50e+03 pdb=" O GLY C 199 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY C 200 " -0.024 2.00e-02 2.50e+03 ... (remaining 4952 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 1 1.81 - 2.58: 262 2.58 - 3.36: 35471 3.36 - 4.13: 63751 4.13 - 4.90: 113288 Nonbonded interactions: 212773 Sorted by model distance: nonbonded pdb=" CD2 LEU B1063 " pdb=" OE2 GLU B1079 " model vdw 1.040 3.460 nonbonded pdb=" CA PRO C 524 " pdb=" NH2 ARG C1036 " model vdw 1.846 3.550 nonbonded pdb=" CG LEU B1063 " pdb=" OE2 GLU B1079 " model vdw 1.859 3.470 nonbonded pdb=" O GLY C 199 " pdb=" O3A ATP C2000 " model vdw 1.948 3.040 nonbonded pdb=" OD1 ASP D 112 " pdb=" NH1 ARG D 137 " model vdw 1.956 2.520 ... (remaining 212768 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 33 through 1178) selection = (chain 'D' and resid 33 through 1178) } 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 152 5.16 5 C 17172 2.51 5 N 4735 2.21 5 O 5089 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 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.710 Check model and map are aligned: 0.420 Process input model: 68.560 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.220 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.004 0.044 27768 Z= 0.285 Angle : 0.743 12.475 37677 Z= 0.451 Chirality : 0.048 0.369 4166 Planarity : 0.005 0.082 4955 Dihedral : 14.488 89.725 10281 Min Nonbonded Distance : 1.040 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.54 % Favored : 93.40 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3485 helix: 1.05 (0.14), residues: 1419 sheet: -0.29 (0.23), residues: 501 loop : -1.63 (0.15), residues: 1565 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 376 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 4 residues processed: 408 average time/residue: 0.4588 time to fit residues: 287.1298 Evaluate side-chains 240 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 236 time to evaluate : 3.178 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2556 time to fit residues: 6.3020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 316 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1073 GLN B 858 ASN ** B 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN C 498 GLN ** C 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 GLN C1040 GLN ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 ASN ** D 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1075 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 27768 Z= 0.256 Angle : 0.636 11.187 37677 Z= 0.320 Chirality : 0.044 0.271 4166 Planarity : 0.005 0.063 4955 Dihedral : 4.853 58.454 3815 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.69 % Favored : 93.29 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3485 helix: 0.99 (0.14), residues: 1454 sheet: -0.14 (0.22), residues: 535 loop : -1.64 (0.15), residues: 1496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 248 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 25 residues processed: 279 average time/residue: 0.3910 time to fit residues: 175.8626 Evaluate side-chains 245 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 3.121 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2428 time to fit residues: 15.6969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 0.0770 chunk 98 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 316 optimal weight: 10.0000 chunk 342 optimal weight: 4.9990 chunk 281 optimal weight: 5.9990 chunk 313 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 253 optimal weight: 5.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 HIS A 924 ASN B 585 HIS ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 27768 Z= 0.399 Angle : 0.720 11.702 37677 Z= 0.368 Chirality : 0.045 0.236 4166 Planarity : 0.005 0.043 4955 Dihedral : 5.214 59.091 3815 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.80 % Favored : 92.17 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3485 helix: 0.62 (0.14), residues: 1442 sheet: -0.39 (0.22), residues: 524 loop : -1.71 (0.15), residues: 1519 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 213 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 252 average time/residue: 0.4108 time to fit residues: 166.8261 Evaluate side-chains 212 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 193 time to evaluate : 3.157 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2582 time to fit residues: 13.4459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 9.9990 chunk 238 optimal weight: 0.7980 chunk 164 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 212 optimal weight: 20.0000 chunk 317 optimal weight: 4.9990 chunk 336 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN C 681 ASN C 858 ASN ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 HIS ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 27768 Z= 0.276 Angle : 0.637 12.207 37677 Z= 0.319 Chirality : 0.043 0.157 4166 Planarity : 0.004 0.049 4955 Dihedral : 5.017 59.074 3815 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.83 % Favored : 93.14 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3485 helix: 0.73 (0.14), residues: 1440 sheet: -0.34 (0.23), residues: 525 loop : -1.66 (0.15), residues: 1520 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 211 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 239 average time/residue: 0.4052 time to fit residues: 156.6021 Evaluate side-chains 214 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 196 time to evaluate : 2.897 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2403 time to fit residues: 12.2511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 250 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 287 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 301 optimal weight: 0.0370 chunk 84 optimal weight: 6.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 27768 Z= 0.253 Angle : 0.626 9.953 37677 Z= 0.311 Chirality : 0.043 0.193 4166 Planarity : 0.004 0.047 4955 Dihedral : 4.898 55.185 3815 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.55 % Favored : 92.42 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3485 helix: 0.77 (0.14), residues: 1438 sheet: -0.30 (0.23), residues: 525 loop : -1.65 (0.15), residues: 1522 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 205 time to evaluate : 3.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 22 residues processed: 236 average time/residue: 0.4029 time to fit residues: 154.4353 Evaluate side-chains 214 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 3.289 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3007 time to fit residues: 16.4450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 0.7980 chunk 302 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 336 optimal weight: 4.9990 chunk 279 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 GLN C1075 GLN D 44 ASN D 436 HIS ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 27768 Z= 0.206 Angle : 0.603 10.340 37677 Z= 0.298 Chirality : 0.042 0.197 4166 Planarity : 0.004 0.046 4955 Dihedral : 4.757 50.517 3815 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3485 helix: 0.89 (0.14), residues: 1438 sheet: -0.26 (0.23), residues: 525 loop : -1.60 (0.15), residues: 1522 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 208 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 12 residues processed: 236 average time/residue: 0.3929 time to fit residues: 150.4003 Evaluate side-chains 211 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 199 time to evaluate : 3.258 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2606 time to fit residues: 10.2779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 4.9990 chunk 37 optimal weight: 0.0170 chunk 191 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 283 optimal weight: 0.0270 chunk 188 optimal weight: 8.9990 chunk 335 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 879 HIS D 956 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 27768 Z= 0.176 Angle : 0.613 11.086 37677 Z= 0.297 Chirality : 0.042 0.215 4166 Planarity : 0.004 0.047 4955 Dihedral : 4.646 48.605 3815 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3485 helix: 0.98 (0.14), residues: 1429 sheet: -0.17 (0.23), residues: 519 loop : -1.58 (0.15), residues: 1537 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 207 time to evaluate : 3.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 223 average time/residue: 0.4014 time to fit residues: 145.0734 Evaluate side-chains 203 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 196 time to evaluate : 3.119 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2618 time to fit residues: 7.6801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 3.9990 chunk 133 optimal weight: 0.0570 chunk 200 optimal weight: 3.9990 chunk 101 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 213 optimal weight: 0.5980 chunk 228 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 263 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 ASN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 27768 Z= 0.154 Angle : 0.612 11.621 37677 Z= 0.294 Chirality : 0.042 0.218 4166 Planarity : 0.004 0.108 4955 Dihedral : 4.526 48.470 3815 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3485 helix: 0.98 (0.14), residues: 1439 sheet: -0.08 (0.23), residues: 521 loop : -1.52 (0.15), residues: 1525 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 212 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 225 average time/residue: 0.4067 time to fit residues: 147.3304 Evaluate side-chains 206 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 201 time to evaluate : 3.342 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2743 time to fit residues: 7.0658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 4.9990 chunk 321 optimal weight: 0.0980 chunk 293 optimal weight: 1.9990 chunk 312 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 245 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 282 optimal weight: 0.0970 chunk 295 optimal weight: 8.9990 chunk 311 optimal weight: 0.9980 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 27768 Z= 0.193 Angle : 0.624 12.076 37677 Z= 0.301 Chirality : 0.042 0.239 4166 Planarity : 0.004 0.078 4955 Dihedral : 4.535 48.209 3815 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3485 helix: 1.02 (0.14), residues: 1440 sheet: -0.14 (0.23), residues: 519 loop : -1.54 (0.15), residues: 1526 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 202 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 211 average time/residue: 0.4154 time to fit residues: 142.4989 Evaluate side-chains 198 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 3.429 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2775 time to fit residues: 5.7269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 9.9990 chunk 330 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 229 optimal weight: 0.0980 chunk 346 optimal weight: 10.0000 chunk 319 optimal weight: 0.5980 chunk 276 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 213 optimal weight: 0.0070 chunk 169 optimal weight: 0.0570 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 27768 Z= 0.156 Angle : 0.637 12.437 37677 Z= 0.303 Chirality : 0.042 0.239 4166 Planarity : 0.004 0.048 4955 Dihedral : 4.459 50.509 3815 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3485 helix: 0.97 (0.14), residues: 1444 sheet: 0.03 (0.24), residues: 519 loop : -1.50 (0.15), residues: 1522 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 217 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 221 average time/residue: 0.3984 time to fit residues: 144.2638 Evaluate side-chains 202 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 3.191 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3022 time to fit residues: 4.8879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 0.0020 chunk 294 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 283 optimal weight: 0.0670 chunk 35 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.4726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.080891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.063358 restraints weight = 123561.602| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 6.00 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 27768 Z= 0.155 Angle : 0.622 12.071 37677 Z= 0.296 Chirality : 0.042 0.249 4166 Planarity : 0.004 0.047 4955 Dihedral : 4.340 51.440 3815 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3485 helix: 1.05 (0.14), residues: 1432 sheet: 0.16 (0.24), residues: 511 loop : -1.52 (0.15), residues: 1542 =============================================================================== Job complete usr+sys time: 5030.72 seconds wall clock time: 93 minutes 28.17 seconds (5608.17 seconds total)