Starting phenix.real_space_refine on Thu Dec 14 04:10:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wte_32780/12_2023/7wte_32780_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wte_32780/12_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_32780/12_2023/7wte_32780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wte_32780/12_2023/7wte_32780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wte_32780/12_2023/7wte_32780_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wte_32780/12_2023/7wte_32780_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 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. 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 14.61, per 1000 atoms: 0.54 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: 11.35 Conformation dependent library (CDL) restraints added in 5.1 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: 7.28 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: 10.07 Time building geometry restraints manager: 12.00 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: 15106 17.95 - 35.89: 1350 35.89 - 53.84: 275 53.84 - 71.78: 107 71.78 - 89.72: 29 Dihedral angle restraints: 16867 sinusoidal: 6846 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 16864 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 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.330 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 73.710 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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 : 15.109 89.725 10425 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 % Allowed : 1.08 % Favored : 96.97 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 607 HIS 0.009 0.001 HIS B 875 PHE 0.014 0.001 PHE C 920 TYR 0.023 0.001 TYR D 304 ARG 0.009 0.001 ARG D1070 *********************** 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 : 2.938 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: 0.4334 time to fit residues: 270.4945 Evaluate side-chains 240 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 236 time to evaluate : 3.150 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2592 time to fit residues: 6.0861 ------------------------------------------------------------------------------- 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: 0.7792 moved from start: 0.1547 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= 0.253 Angle : 0.635 10.909 37677 Z= 0.321 Chirality : 0.044 0.201 4166 Planarity : 0.005 0.057 4955 Dihedral : 8.005 64.480 3959 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.63 % Favored : 93.34 % Rotamer: Outliers : 1.46 % Allowed : 10.00 % Favored : 88.54 % 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: -0.41 (0.14), residues: 3485 helix: 1.03 (0.14), residues: 1442 sheet: -0.14 (0.22), residues: 535 loop : -1.64 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 607 HIS 0.015 0.001 HIS B 879 PHE 0.032 0.002 PHE C 387 TYR 0.020 0.001 TYR D 261 ARG 0.011 0.001 ARG D 406 *********************** 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 291 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 249 time to evaluate : 3.242 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: 42 outliers final: 25 residues processed: 280 average time/residue: 0.3971 time to fit residues: 180.1596 Evaluate side-chains 245 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 3.585 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2628 time to fit residues: 16.9431 ------------------------------------------------------------------------------- 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: 6.9990 chunk 98 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 316 optimal weight: 9.9990 chunk 342 optimal weight: 3.9990 chunk 281 optimal weight: 5.9990 chunk 313 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 44 ASN ** 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 D 44 ASN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 27768 Z= 0.522 Angle : 0.818 11.102 37677 Z= 0.425 Chirality : 0.048 0.204 4166 Planarity : 0.006 0.052 4955 Dihedral : 7.827 58.510 3959 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.32 % Favored : 91.65 % Rotamer: Outliers : 1.95 % Allowed : 14.07 % Favored : 83.98 % 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: -1.20 (0.14), residues: 3485 helix: 0.20 (0.13), residues: 1443 sheet: -0.59 (0.22), residues: 525 loop : -1.84 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 607 HIS 0.015 0.002 HIS C 875 PHE 0.022 0.003 PHE C 234 TYR 0.024 0.002 TYR D 261 ARG 0.011 0.001 ARG A1070 *********************** 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 271 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 215 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 28 residues processed: 261 average time/residue: 0.4102 time to fit residues: 173.3367 Evaluate side-chains 225 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 3.451 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2554 time to fit residues: 18.5639 ------------------------------------------------------------------------------- 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: 4.9990 chunk 238 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 212 optimal weight: 50.0000 chunk 317 optimal weight: 0.9980 chunk 336 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 301 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 301 GLN C 348 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 44 ASN D 436 HIS ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27768 Z= 0.219 Angle : 0.625 9.748 37677 Z= 0.312 Chirality : 0.043 0.154 4166 Planarity : 0.004 0.049 4955 Dihedral : 7.353 58.630 3959 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.54 % Favored : 93.43 % Rotamer: Outliers : 1.29 % Allowed : 15.57 % Favored : 83.14 % 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: -0.72 (0.14), residues: 3485 helix: 0.67 (0.14), residues: 1446 sheet: -0.33 (0.23), residues: 520 loop : -1.66 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 838 HIS 0.007 0.001 HIS B 574 PHE 0.019 0.001 PHE D 387 TYR 0.020 0.001 TYR D 261 ARG 0.009 0.000 ARG C1070 *********************** 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 255 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 218 time to evaluate : 3.389 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: 37 outliers final: 20 residues processed: 248 average time/residue: 0.3862 time to fit residues: 156.1344 Evaluate side-chains 220 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 3.191 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2466 time to fit residues: 13.3215 ------------------------------------------------------------------------------- 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: 2.9990 chunk 190 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 250 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 301 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 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 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 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 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** D 574 HIS ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 956 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27768 Z= 0.282 Angle : 0.637 9.825 37677 Z= 0.319 Chirality : 0.043 0.159 4166 Planarity : 0.004 0.046 4955 Dihedral : 7.119 58.810 3959 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.92 % Favored : 92.05 % Rotamer: Outliers : 1.81 % Allowed : 16.86 % Favored : 81.33 % 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: -0.73 (0.14), residues: 3485 helix: 0.70 (0.14), residues: 1437 sheet: -0.42 (0.23), residues: 529 loop : -1.68 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 838 HIS 0.010 0.001 HIS C 259 PHE 0.031 0.002 PHE A 887 TYR 0.018 0.001 TYR D 261 ARG 0.006 0.000 ARG C 377 *********************** 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 259 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 207 time to evaluate : 3.075 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: 52 outliers final: 24 residues processed: 247 average time/residue: 0.3790 time to fit residues: 155.1093 Evaluate side-chains 216 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 192 time to evaluate : 3.015 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2644 time to fit residues: 15.7509 ------------------------------------------------------------------------------- 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: 0.9990 chunk 302 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 336 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 GLN C1075 GLN D 436 HIS D 574 HIS ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 879 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27768 Z= 0.249 Angle : 0.623 10.432 37677 Z= 0.311 Chirality : 0.043 0.157 4166 Planarity : 0.004 0.062 4955 Dihedral : 6.931 61.134 3959 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.86 % Favored : 93.11 % Rotamer: Outliers : 1.29 % Allowed : 17.38 % Favored : 81.33 % 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: -0.69 (0.14), residues: 3485 helix: 0.72 (0.14), residues: 1447 sheet: -0.43 (0.23), residues: 528 loop : -1.63 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 838 HIS 0.011 0.001 HIS C 259 PHE 0.017 0.001 PHE C 183 TYR 0.017 0.001 TYR D 261 ARG 0.010 0.000 ARG A1070 *********************** 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 240 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 3.323 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: 37 outliers final: 16 residues processed: 235 average time/residue: 0.3890 time to fit residues: 149.0204 Evaluate side-chains 209 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 3.252 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2892 time to fit residues: 13.6495 ------------------------------------------------------------------------------- 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: 7.9990 chunk 37 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 245 optimal weight: 0.7980 chunk 190 optimal weight: 10.0000 chunk 283 optimal weight: 0.0570 chunk 188 optimal weight: 8.9990 chunk 335 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 overall best weight: 2.9704 ------------------------------------------------------------------------------- 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 559 ASN 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 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7957 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27768 Z= 0.277 Angle : 0.651 10.330 37677 Z= 0.323 Chirality : 0.043 0.170 4166 Planarity : 0.004 0.046 4955 Dihedral : 6.836 64.378 3959 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.06 % Favored : 91.91 % Rotamer: Outliers : 1.04 % Allowed : 18.70 % Favored : 80.25 % 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: -0.70 (0.14), residues: 3485 helix: 0.70 (0.14), residues: 1444 sheet: -0.43 (0.23), residues: 527 loop : -1.63 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 838 HIS 0.010 0.001 HIS C 259 PHE 0.015 0.001 PHE D 387 TYR 0.016 0.001 TYR D 261 ARG 0.014 0.000 ARG A1070 *********************** 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 225 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 195 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 216 average time/residue: 0.4419 time to fit residues: 156.2938 Evaluate side-chains 203 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 187 time to evaluate : 3.610 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2705 time to fit residues: 12.4628 ------------------------------------------------------------------------------- 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: 0.0980 chunk 133 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 213 optimal weight: 0.3980 chunk 228 optimal weight: 0.0050 chunk 165 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 overall best weight: 0.2994 ------------------------------------------------------------------------------- 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 ** C 375 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: 0.7877 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 27768 Z= 0.157 Angle : 0.624 11.359 37677 Z= 0.302 Chirality : 0.042 0.170 4166 Planarity : 0.004 0.049 4955 Dihedral : 6.551 68.707 3959 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.56 % Allowed : 18.95 % Favored : 80.49 % 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: -0.50 (0.14), residues: 3485 helix: 0.88 (0.14), residues: 1438 sheet: -0.21 (0.23), residues: 526 loop : -1.57 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 838 HIS 0.012 0.001 HIS C 259 PHE 0.020 0.001 PHE C 387 TYR 0.015 0.001 TYR D 261 ARG 0.004 0.000 ARG C1070 *********************** 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 232 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 216 time to evaluate : 3.780 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: 16 outliers final: 6 residues processed: 229 average time/residue: 0.4102 time to fit residues: 154.3081 Evaluate side-chains 202 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 196 time to evaluate : 3.531 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2770 time to fit residues: 7.2676 ------------------------------------------------------------------------------- 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: 20.0000 chunk 321 optimal weight: 0.6980 chunk 293 optimal weight: 2.9990 chunk 312 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 245 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 282 optimal weight: 0.2980 chunk 295 optimal weight: 0.0370 chunk 311 optimal weight: 2.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 HIS ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 574 HIS ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3545 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= 0.187 Angle : 0.640 11.540 37677 Z= 0.308 Chirality : 0.042 0.176 4166 Planarity : 0.004 0.075 4955 Dihedral : 6.430 69.751 3959 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.38 % Allowed : 19.75 % Favored : 79.87 % 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: -0.45 (0.14), residues: 3485 helix: 0.91 (0.14), residues: 1441 sheet: -0.22 (0.23), residues: 523 loop : -1.53 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 838 HIS 0.010 0.001 HIS C 259 PHE 0.013 0.001 PHE B 920 TYR 0.013 0.001 TYR D 261 ARG 0.015 0.000 ARG A1070 *********************** 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 210 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 3.258 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: 11 outliers final: 1 residues processed: 208 average time/residue: 0.4084 time to fit residues: 138.4516 Evaluate side-chains 197 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 3.261 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.9200 time to fit residues: 5.7578 ------------------------------------------------------------------------------- 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: 0.0980 chunk 330 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 346 optimal weight: 4.9990 chunk 319 optimal weight: 0.0370 chunk 276 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 864 ASN ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3609 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= 0.171 Angle : 0.644 11.842 37677 Z= 0.307 Chirality : 0.042 0.226 4166 Planarity : 0.004 0.055 4955 Dihedral : 6.350 69.207 3959 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.14 % Allowed : 20.06 % Favored : 79.80 % 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: 0.92 (0.14), residues: 1441 sheet: -0.17 (0.23), residues: 522 loop : -1.54 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 838 HIS 0.010 0.001 HIS C 259 PHE 0.013 0.001 PHE B 920 TYR 0.013 0.001 TYR D 261 ARG 0.012 0.000 ARG C 219 ********************** 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 204 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 200 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 203 average time/residue: 0.4282 time to fit residues: 143.2683 Evaluate side-chains 197 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 3.347 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3030 time to fit residues: 5.1451 ------------------------------------------------------------------------------- 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: 0.8980 chunk 294 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 276 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 283 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 875 HIS ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.079600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.061848 restraints weight = 124921.538| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 6.12 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27768 Z= 0.161 Angle : 0.641 12.252 37677 Z= 0.304 Chirality : 0.042 0.197 4166 Planarity : 0.004 0.048 4955 Dihedral : 6.201 69.367 3959 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.14 % Allowed : 20.10 % Favored : 79.76 % 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: -0.41 (0.14), residues: 3485 helix: 0.94 (0.14), residues: 1443 sheet: -0.10 (0.24), residues: 520 loop : -1.54 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 838 HIS 0.010 0.001 HIS C 259 PHE 0.014 0.001 PHE B 920 TYR 0.017 0.001 TYR A 682 ARG 0.021 0.000 ARG A1070 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5406.27 seconds wall clock time: 99 minutes 34.86 seconds (5974.86 seconds total)