Starting phenix.real_space_refine on Tue Apr 9 06:06:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxa_14196/04_2024/7qxa_14196_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxa_14196/04_2024/7qxa_14196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxa_14196/04_2024/7qxa_14196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxa_14196/04_2024/7qxa_14196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxa_14196/04_2024/7qxa_14196_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxa_14196/04_2024/7qxa_14196_neut.pdb" } resolution = 3.2 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= 0.003 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 265 5.49 5 S 42 5.16 5 C 8869 2.51 5 N 2831 2.21 5 O 3569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 6": "NH1" <-> "NH2" Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 11": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A ARG 486": "NH1" <-> "NH2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 515": "NH1" <-> "NH2" Residue "A ARG 521": "NH1" <-> "NH2" Residue "A ARG 522": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 613": "NH1" <-> "NH2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A ARG 643": "NH1" <-> "NH2" Residue "A PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 688": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A ARG 743": "NH1" <-> "NH2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ARG 774": "NH1" <-> "NH2" Residue "A ARG 787": "NH1" <-> "NH2" Residue "A ARG 811": "NH1" <-> "NH2" Residue "A PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 821": "NH1" <-> "NH2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A ARG 865": "NH1" <-> "NH2" Residue "A PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 885": "NH1" <-> "NH2" Residue "A ARG 889": "NH1" <-> "NH2" Residue "A ARG 901": "NH1" <-> "NH2" Residue "A ARG 938": "NH1" <-> "NH2" Residue "A ARG 951": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 962": "NH1" <-> "NH2" Residue "A ARG 968": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 972": "NH1" <-> "NH2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "A ARG 1011": "NH1" <-> "NH2" Residue "A PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1034": "NH1" <-> "NH2" Residue "A ARG 1084": "NH1" <-> "NH2" Residue "A ARG 1086": "NH1" <-> "NH2" Residue "A ARG 1097": "NH1" <-> "NH2" Residue "A ARG 1105": "NH1" <-> "NH2" Residue "A PHE 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 36": "NH1" <-> "NH2" Residue "L ARG 43": "NH1" <-> "NH2" Residue "L ARG 72": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 82": "NH1" <-> "NH2" Residue "L ARG 89": "NH1" <-> "NH2" Residue "M ARG 73": "NH1" <-> "NH2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "M ARG 87": "NH1" <-> "NH2" Residue "M ARG 93": "NH1" <-> "NH2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "O ARG 92": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "O ARG 113": "NH1" <-> "NH2" Residue "O ARG 154": "NH1" <-> "NH2" Residue "O ARG 159": "NH1" <-> "NH2" Residue "O ARG 175": "NH1" <-> "NH2" Residue "O ARG 180": "NH1" <-> "NH2" Residue "O ARG 208": "NH1" <-> "NH2" Residue "O ARG 218": "NH1" <-> "NH2" Residue "O ARG 220": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15576 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7649 Classifications: {'peptide': 954} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 55, 'TRANS': 895} Chain breaks: 3 Chain: "B" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 5371 Classifications: {'RNA': 253} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 19, 'rna3p_pur': 99, 'rna3p_pyr': 118} Link IDs: {'rna2p': 36, 'rna3p': 216} Chain breaks: 3 Chain: "L" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 632 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "M" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "N" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 254 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "O" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain breaks: 3 Time building chain proxies: 9.30, per 1000 atoms: 0.60 Number of scatterers: 15576 At special positions: 0 Unit cell: (166.77, 123.17, 146.06, 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 42 16.00 P 265 15.00 O 3569 8.00 N 2831 7.00 C 8869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 54.3% alpha, 12.7% beta 51 base pairs and 131 stacking pairs defined. Time for finding SS restraints: 5.80 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 removed outlier: 3.910A pdb=" N ARG A 11 " --> pdb=" O CYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.582A pdb=" N VAL A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 92 removed outlier: 3.583A pdb=" N VAL A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.863A pdb=" N GLY A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.799A pdb=" N ARG A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.725A pdb=" N LEU A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 389 through 402 removed outlier: 3.657A pdb=" N PHE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.503A pdb=" N LEU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 454 removed outlier: 3.537A pdb=" N ARG A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.938A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.691A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 497 removed outlier: 3.545A pdb=" N LYS A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 496 " --> pdb=" O LYS A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.679A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 551 removed outlier: 3.542A pdb=" N LYS A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.655A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 597 removed outlier: 3.741A pdb=" N LYS A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.681A pdb=" N GLU A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 672 removed outlier: 4.112A pdb=" N LYS A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 Processing helix chain 'A' and resid 682 through 698 removed outlier: 3.869A pdb=" N THR A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 734 removed outlier: 3.659A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 733 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 769 removed outlier: 3.570A pdb=" N LEU A 769 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 Processing helix chain 'A' and resid 802 through 814 Processing helix chain 'A' and resid 837 through 854 removed outlier: 3.669A pdb=" N CYS A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 843 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 859 Processing helix chain 'A' and resid 876 through 890 removed outlier: 3.675A pdb=" N ALA A 880 " --> pdb=" O HIS A 876 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 890 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 950 removed outlier: 3.646A pdb=" N TYR A 949 " --> pdb=" O TYR A 946 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 950 " --> pdb=" O SER A 947 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 946 through 950' Processing helix chain 'A' and resid 965 through 982 removed outlier: 3.588A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 993 through 1017 removed outlier: 3.604A pdb=" N LEU A1007 " --> pdb=" O LYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1028 removed outlier: 3.554A pdb=" N LYS A1027 " --> pdb=" O GLN A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1051 removed outlier: 3.588A pdb=" N ASP A1038 " --> pdb=" O ARG A1034 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS A1043 " --> pdb=" O THR A1039 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1085 removed outlier: 3.897A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS A1075 " --> pdb=" O GLN A1071 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.579A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Proline residue: A1091 - end of helix removed outlier: 4.073A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A1102 " --> pdb=" O THR A1098 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A1106 " --> pdb=" O GLN A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1119 removed outlier: 3.894A pdb=" N THR A1113 " --> pdb=" O GLY A1109 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 38 removed outlier: 4.389A pdb=" N LEU L 34 " --> pdb=" O ARG L 30 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU L 35 " --> pdb=" O VAL L 31 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 73 removed outlier: 4.489A pdb=" N VAL L 50 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR L 51 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 91 removed outlier: 3.964A pdb=" N LEU L 84 " --> pdb=" O ILE L 80 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG L 89 " --> pdb=" O GLN L 85 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 99 removed outlier: 3.639A pdb=" N ASN L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS L 96 " --> pdb=" O GLU L 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 50 removed outlier: 3.662A pdb=" N VAL M 45 " --> pdb=" O TYR M 41 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS M 47 " --> pdb=" O TYR M 43 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL M 49 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 86 removed outlier: 3.995A pdb=" N SER M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS M 83 " --> pdb=" O SER M 79 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR M 84 " --> pdb=" O ARG M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 103 removed outlier: 3.769A pdb=" N ILE M 95 " --> pdb=" O THR M 91 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN M 96 " --> pdb=" O SER M 92 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR M 97 " --> pdb=" O ARG M 93 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU M 103 " --> pdb=" O VAL M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.747A pdb=" N SER M 113 " --> pdb=" O LYS M 109 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU M 114 " --> pdb=" O HIS M 110 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY M 115 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR M 120 " --> pdb=" O THR M 116 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER M 125 " --> pdb=" O LYS M 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 104 removed outlier: 3.837A pdb=" N ILE O 103 " --> pdb=" O ILE O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 164 removed outlier: 3.623A pdb=" N LEU O 162 " --> pdb=" O THR O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 238 removed outlier: 3.527A pdb=" N LYS O 232 " --> pdb=" O LEU O 228 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS O 233 " --> pdb=" O ASP O 229 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR O 235 " --> pdb=" O GLN O 231 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP O 236 " --> pdb=" O LYS O 232 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS O 237 " --> pdb=" O LYS O 233 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU O 238 " --> pdb=" O LEU O 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.778A pdb=" N ALA A 157 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 11.317A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.778A pdb=" N ALA A 157 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 11.317A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 739 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA6, first strand: chain 'A' and resid 599 through 600 removed outlier: 7.356A pdb=" N LEU A 617 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ARG A 819 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 679 through 680 removed outlier: 3.720A pdb=" N LEU A 866 " --> pdb=" O ASP A 869 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 869 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 711 " --> pdb=" O PHE A 870 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 709 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 905 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 927 through 930 Processing sheet with id=AA9, first strand: chain 'O' and resid 181 through 184 removed outlier: 7.223A pdb=" N LEU O 145 " --> pdb=" O LEU O 118 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL O 120 " --> pdb=" O THR O 143 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR O 143 " --> pdb=" O VAL O 120 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N LEU O 204 " --> pdb=" O SER O 152 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ARG O 154 " --> pdb=" O LEU O 204 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL O 206 " --> pdb=" O ARG O 154 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU O 156 " --> pdb=" O VAL O 206 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 135 hydrogen bonds 258 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 131 stacking parallelities Total time for adding SS restraints: 8.27 Time building geometry restraints manager: 7.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2427 1.33 - 1.46: 6059 1.46 - 1.59: 7519 1.59 - 1.73: 381 1.73 - 1.86: 55 Bond restraints: 16441 Sorted by residual: bond pdb=" O3' A B 176 " pdb=" P U B 177 " ideal model delta sigma weight residual 1.607 1.697 -0.090 1.50e-02 4.44e+03 3.56e+01 bond pdb=" CA ILE A 624 " pdb=" C ILE A 624 " ideal model delta sigma weight residual 1.524 1.585 -0.060 1.05e-02 9.07e+03 3.31e+01 bond pdb=" C SER A 513 " pdb=" O SER A 513 " ideal model delta sigma weight residual 1.234 1.303 -0.069 1.23e-02 6.61e+03 3.13e+01 bond pdb=" CA PHE A1031 " pdb=" C PHE A1031 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.32e-02 5.74e+03 1.87e+01 bond pdb=" CA SER A 513 " pdb=" C SER A 513 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.30e-02 5.92e+03 1.72e+01 ... (remaining 16436 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.42: 1426 105.42 - 112.62: 8343 112.62 - 119.82: 6422 119.82 - 127.02: 6667 127.02 - 134.21: 671 Bond angle restraints: 23529 Sorted by residual: angle pdb=" O3' C B 72 " pdb=" C3' C B 72 " pdb=" C2' C B 72 " ideal model delta sigma weight residual 109.50 118.94 -9.44 1.50e+00 4.44e-01 3.96e+01 angle pdb=" O3' G B 44 " pdb=" C3' G B 44 " pdb=" C2' G B 44 " ideal model delta sigma weight residual 113.70 122.65 -8.95 1.50e+00 4.44e-01 3.56e+01 angle pdb=" C4' C B 74 " pdb=" C3' C B 74 " pdb=" O3' C B 74 " ideal model delta sigma weight residual 109.40 118.02 -8.62 1.50e+00 4.44e-01 3.31e+01 angle pdb=" N SER A 838 " pdb=" CA SER A 838 " pdb=" C SER A 838 " ideal model delta sigma weight residual 111.33 117.93 -6.60 1.21e+00 6.83e-01 2.98e+01 angle pdb=" O3' A B 174 " pdb=" C3' A B 174 " pdb=" C2' A B 174 " ideal model delta sigma weight residual 113.70 121.73 -8.03 1.50e+00 4.44e-01 2.87e+01 ... (remaining 23524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 9513 35.95 - 71.89: 700 71.89 - 107.84: 107 107.84 - 143.78: 8 143.78 - 179.73: 10 Dihedral angle restraints: 10338 sinusoidal: 6717 harmonic: 3621 Sorted by residual: dihedral pdb=" C5' C B 74 " pdb=" C4' C B 74 " pdb=" C3' C B 74 " pdb=" O3' C B 74 " ideal model delta sinusoidal sigma weight residual 147.00 74.89 72.11 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C4' C B 74 " pdb=" C3' C B 74 " pdb=" C2' C B 74 " pdb=" C1' C B 74 " ideal model delta sinusoidal sigma weight residual -35.00 33.16 -68.16 1 8.00e+00 1.56e-02 9.42e+01 dihedral pdb=" C5' A B 176 " pdb=" C4' A B 176 " pdb=" C3' A B 176 " pdb=" O3' A B 176 " ideal model delta sinusoidal sigma weight residual 147.00 79.66 67.34 1 8.00e+00 1.56e-02 9.22e+01 ... (remaining 10335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2208 0.101 - 0.203: 546 0.203 - 0.304: 106 0.304 - 0.405: 6 0.405 - 0.506: 4 Chirality restraints: 2870 Sorted by residual: chirality pdb=" C3' C B 72 " pdb=" C4' C B 72 " pdb=" O3' C B 72 " pdb=" C2' C B 72 " both_signs ideal model delta sigma weight residual False -2.74 -2.24 -0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" C3' G B 300 " pdb=" C4' G B 300 " pdb=" O3' G B 300 " pdb=" C2' G B 300 " both_signs ideal model delta sigma weight residual False -2.74 -2.24 -0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" C3' U B 42 " pdb=" C4' U B 42 " pdb=" O3' U B 42 " pdb=" C2' U B 42 " both_signs ideal model delta sigma weight residual False -2.74 -2.26 -0.49 2.00e-01 2.50e+01 5.90e+00 ... (remaining 2867 not shown) Planarity restraints: 2018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 177 " -0.104 2.00e-02 2.50e+03 5.14e-02 5.95e+01 pdb=" N1 U B 177 " 0.057 2.00e-02 2.50e+03 pdb=" C2 U B 177 " 0.041 2.00e-02 2.50e+03 pdb=" O2 U B 177 " 0.037 2.00e-02 2.50e+03 pdb=" N3 U B 177 " -0.047 2.00e-02 2.50e+03 pdb=" C4 U B 177 " -0.040 2.00e-02 2.50e+03 pdb=" O4 U B 177 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U B 177 " 0.011 2.00e-02 2.50e+03 pdb=" C6 U B 177 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 307 " -0.068 2.00e-02 2.50e+03 3.50e-02 2.75e+01 pdb=" N1 U B 307 " 0.061 2.00e-02 2.50e+03 pdb=" C2 U B 307 " 0.014 2.00e-02 2.50e+03 pdb=" O2 U B 307 " 0.010 2.00e-02 2.50e+03 pdb=" N3 U B 307 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U B 307 " -0.040 2.00e-02 2.50e+03 pdb=" O4 U B 307 " -0.012 2.00e-02 2.50e+03 pdb=" C5 U B 307 " 0.021 2.00e-02 2.50e+03 pdb=" C6 U B 307 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 30 " -0.036 2.00e-02 2.50e+03 2.63e-02 2.08e+01 pdb=" N9 DG N 30 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG N 30 " 0.021 2.00e-02 2.50e+03 pdb=" N7 DG N 30 " 0.030 2.00e-02 2.50e+03 pdb=" C5 DG N 30 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG N 30 " -0.023 2.00e-02 2.50e+03 pdb=" O6 DG N 30 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DG N 30 " -0.032 2.00e-02 2.50e+03 pdb=" C2 DG N 30 " -0.003 2.00e-02 2.50e+03 pdb=" N2 DG N 30 " 0.054 2.00e-02 2.50e+03 pdb=" N3 DG N 30 " -0.019 2.00e-02 2.50e+03 pdb=" C4 DG N 30 " -0.015 2.00e-02 2.50e+03 ... (remaining 2015 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1975 2.78 - 3.31: 13932 3.31 - 3.84: 25459 3.84 - 4.37: 30664 4.37 - 4.90: 47163 Nonbonded interactions: 119193 Sorted by model distance: nonbonded pdb=" OP1 C B 320 " pdb=" OH TYR M 41 " model vdw 2.254 2.440 nonbonded pdb=" NH2 ARG A 535 " pdb=" O2' A B 302 " model vdw 2.276 2.520 nonbonded pdb=" O4' U B 316 " pdb=" O2 U B 316 " model vdw 2.303 3.040 nonbonded pdb=" O TRP A 510 " pdb=" O2' C B 313 " model vdw 2.304 2.440 nonbonded pdb=" O4' U B 194 " pdb=" O2 U B 194 " model vdw 2.366 3.040 ... (remaining 119188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.940 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: 5.530 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 50.450 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 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 : 0.010 0.090 16441 Z= 0.628 Angle : 1.183 9.445 23529 Z= 0.779 Chirality : 0.092 0.506 2870 Planarity : 0.006 0.051 2018 Dihedral : 22.115 179.730 7992 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.03 % Favored : 93.56 % Rotamer: Outliers : 0.28 % Allowed : 2.05 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -3.16 (0.19), residues: 1227 helix: -2.02 (0.17), residues: 538 sheet: -2.06 (0.43), residues: 96 loop : -2.10 (0.22), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP A 547 HIS 0.014 0.003 HIS A1013 PHE 0.030 0.005 PHE A 870 TYR 0.043 0.006 TYR A 949 ARG 0.014 0.001 ARG A 669 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8261 (mp0) REVERT: A 86 GLN cc_start: 0.7885 (tt0) cc_final: 0.7432 (tp-100) REVERT: A 95 ASN cc_start: 0.7957 (t0) cc_final: 0.7515 (t0) REVERT: A 99 PHE cc_start: 0.6908 (m-10) cc_final: 0.6657 (m-80) REVERT: A 142 ARG cc_start: 0.7195 (mtp180) cc_final: 0.6457 (tpt90) REVERT: A 159 PHE cc_start: 0.7091 (m-80) cc_final: 0.6633 (m-80) REVERT: A 603 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8410 (tm-30) REVERT: A 636 MET cc_start: 0.8316 (mmt) cc_final: 0.8096 (mmt) REVERT: A 743 ARG cc_start: 0.6819 (mtt90) cc_final: 0.6568 (mtp85) REVERT: A 756 ARG cc_start: 0.6205 (mtp-110) cc_final: 0.5476 (mmt180) REVERT: A 800 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6871 (mm-30) REVERT: A 899 ASN cc_start: 0.8230 (t0) cc_final: 0.7853 (t0) REVERT: A 922 MET cc_start: 0.7350 (mmm) cc_final: 0.7139 (mtp) REVERT: L 69 ASN cc_start: 0.6793 (t0) cc_final: 0.6586 (m-40) REVERT: M 63 MET cc_start: 0.7274 (mtt) cc_final: 0.6764 (mmp) REVERT: M 117 LYS cc_start: 0.6361 (mttt) cc_final: 0.6006 (mtpt) REVERT: O 165 SER cc_start: 0.4853 (t) cc_final: 0.4564 (m) REVERT: O 170 LYS cc_start: 0.7804 (ptpt) cc_final: 0.7049 (tppt) REVERT: O 175 ARG cc_start: 0.7238 (mtt-85) cc_final: 0.6620 (mtt180) REVERT: O 205 GLN cc_start: 0.8061 (tt0) cc_final: 0.7779 (pp30) REVERT: O 209 PHE cc_start: 0.7767 (p90) cc_final: 0.7345 (p90) REVERT: O 219 LEU cc_start: 0.7588 (mt) cc_final: 0.7382 (tp) outliers start: 3 outliers final: 0 residues processed: 160 average time/residue: 0.3987 time to fit residues: 86.2801 Evaluate side-chains 92 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 136 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN A 460 GLN A 794 GLN A1000 ASN A1013 HIS L 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16441 Z= 0.169 Angle : 0.641 8.521 23529 Z= 0.332 Chirality : 0.039 0.269 2870 Planarity : 0.005 0.048 2018 Dihedral : 23.650 174.132 5573 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 0.56 % Allowed : 7.45 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.28 (0.22), residues: 1227 helix: 0.02 (0.20), residues: 580 sheet: -1.63 (0.42), residues: 122 loop : -1.58 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 547 HIS 0.005 0.001 HIS A 546 PHE 0.012 0.002 PHE A 331 TYR 0.011 0.002 TYR A 176 ARG 0.005 0.001 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.7233 (mtt-85) cc_final: 0.6780 (ptm160) REVERT: A 95 ASN cc_start: 0.8085 (t0) cc_final: 0.7670 (t0) REVERT: A 139 LEU cc_start: 0.5476 (tp) cc_final: 0.4965 (mp) REVERT: A 603 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8228 (mm-30) REVERT: A 889 ARG cc_start: 0.8911 (ttt-90) cc_final: 0.8457 (ptp-170) REVERT: A 899 ASN cc_start: 0.8011 (t0) cc_final: 0.7588 (t0) REVERT: A 922 MET cc_start: 0.7044 (mmm) cc_final: 0.6817 (mtp) REVERT: L 32 ARG cc_start: 0.6122 (mtp180) cc_final: 0.5592 (ttt-90) REVERT: L 64 LEU cc_start: 0.5036 (tp) cc_final: 0.4542 (tp) REVERT: L 69 ASN cc_start: 0.6822 (t0) cc_final: 0.6586 (m-40) REVERT: L 86 LEU cc_start: 0.7490 (mt) cc_final: 0.7257 (tp) REVERT: M 63 MET cc_start: 0.6962 (mtt) cc_final: 0.6628 (mmp) REVERT: O 119 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7694 (mm-30) REVERT: O 165 SER cc_start: 0.4551 (t) cc_final: 0.3739 (m) REVERT: O 170 LYS cc_start: 0.7656 (ptpt) cc_final: 0.7004 (mmmt) REVERT: O 175 ARG cc_start: 0.6922 (mtt-85) cc_final: 0.6381 (mtt180) REVERT: O 205 GLN cc_start: 0.8074 (tt0) cc_final: 0.7811 (pp30) outliers start: 6 outliers final: 3 residues processed: 119 average time/residue: 0.3608 time to fit residues: 60.1158 Evaluate side-chains 100 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain O residue 147 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 136 optimal weight: 0.0470 chunk 147 optimal weight: 5.9990 chunk 121 optimal weight: 30.0000 chunk 135 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16441 Z= 0.143 Angle : 0.550 8.363 23529 Z= 0.283 Chirality : 0.035 0.208 2870 Planarity : 0.004 0.057 2018 Dihedral : 23.418 171.045 5573 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 0.74 % Allowed : 8.85 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.20 (0.23), residues: 1227 helix: 1.04 (0.21), residues: 577 sheet: -1.17 (0.44), residues: 122 loop : -1.17 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 547 HIS 0.004 0.001 HIS A 983 PHE 0.017 0.001 PHE A 71 TYR 0.009 0.001 TYR A 638 ARG 0.006 0.000 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8295 (mm-30) REVERT: A 91 ARG cc_start: 0.7292 (mtt-85) cc_final: 0.6855 (ptm160) REVERT: A 95 ASN cc_start: 0.8115 (t0) cc_final: 0.7803 (t0) REVERT: A 372 MET cc_start: 0.1607 (tpp) cc_final: 0.1069 (tmm) REVERT: A 603 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7996 (mm-30) REVERT: A 889 ARG cc_start: 0.8934 (ttt-90) cc_final: 0.8452 (ptp-170) REVERT: A 903 THR cc_start: 0.8934 (m) cc_final: 0.8715 (p) REVERT: L 32 ARG cc_start: 0.5984 (mtp180) cc_final: 0.5460 (ttt-90) REVERT: L 64 LEU cc_start: 0.4862 (tp) cc_final: 0.4406 (tp) REVERT: L 69 ASN cc_start: 0.6673 (t0) cc_final: 0.6450 (m-40) REVERT: L 74 ASN cc_start: 0.6852 (OUTLIER) cc_final: 0.6624 (t0) REVERT: L 86 LEU cc_start: 0.7474 (mt) cc_final: 0.7250 (tp) REVERT: M 63 MET cc_start: 0.6917 (mtt) cc_final: 0.6608 (mmp) REVERT: M 117 LYS cc_start: 0.5651 (mttp) cc_final: 0.5329 (mtpt) REVERT: O 165 SER cc_start: 0.3665 (t) cc_final: 0.3352 (m) REVERT: O 170 LYS cc_start: 0.7583 (ptpt) cc_final: 0.6894 (mmmt) REVERT: O 187 CYS cc_start: 0.6786 (p) cc_final: 0.6158 (p) REVERT: O 205 GLN cc_start: 0.8055 (tt0) cc_final: 0.7825 (pp30) outliers start: 8 outliers final: 4 residues processed: 104 average time/residue: 0.3435 time to fit residues: 50.9226 Evaluate side-chains 98 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 74 ASN Chi-restraints excluded: chain O residue 174 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 91 optimal weight: 0.0070 chunk 136 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 ASN A1051 ASN A1075 HIS ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16441 Z= 0.301 Angle : 0.666 9.331 23529 Z= 0.341 Chirality : 0.039 0.236 2870 Planarity : 0.005 0.061 2018 Dihedral : 23.559 175.955 5573 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.44 % Rotamer: Outliers : 2.33 % Allowed : 8.57 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.42 (0.23), residues: 1227 helix: 0.67 (0.21), residues: 584 sheet: -1.08 (0.43), residues: 133 loop : -1.10 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 547 HIS 0.009 0.002 HIS A1013 PHE 0.018 0.002 PHE A 331 TYR 0.016 0.002 TYR A 638 ARG 0.010 0.001 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 80 time to evaluate : 1.422 Fit side-chains REVERT: A 79 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8486 (mm-30) REVERT: A 91 ARG cc_start: 0.7453 (mtt-85) cc_final: 0.7236 (ptm160) REVERT: A 95 ASN cc_start: 0.8200 (t0) cc_final: 0.7925 (t0) REVERT: A 603 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8357 (mm-30) REVERT: A 889 ARG cc_start: 0.8929 (ttt-90) cc_final: 0.8444 (ptp-170) REVERT: A 1017 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8024 (mp) REVERT: L 32 ARG cc_start: 0.6111 (mtp180) cc_final: 0.5430 (ttt-90) REVERT: L 86 LEU cc_start: 0.7394 (mt) cc_final: 0.7163 (tp) REVERT: M 117 LYS cc_start: 0.5546 (mttp) cc_final: 0.5272 (mtmm) outliers start: 25 outliers final: 17 residues processed: 94 average time/residue: 0.3225 time to fit residues: 43.9320 Evaluate side-chains 92 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 189 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 10.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 GLN M 50 HIS O 116 GLN O 205 GLN O 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16441 Z= 0.358 Angle : 0.712 12.352 23529 Z= 0.360 Chirality : 0.040 0.236 2870 Planarity : 0.006 0.065 2018 Dihedral : 23.729 179.304 5573 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.65 % Favored : 95.19 % Rotamer: Outliers : 2.14 % Allowed : 10.52 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.77 (0.23), residues: 1227 helix: 0.21 (0.20), residues: 602 sheet: -0.74 (0.44), residues: 131 loop : -1.25 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 137 HIS 0.008 0.002 HIS A1013 PHE 0.030 0.003 PHE A 159 TYR 0.020 0.002 TYR A 122 ARG 0.006 0.001 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: A 91 ARG cc_start: 0.7513 (mtt-85) cc_final: 0.7289 (ptm160) REVERT: A 95 ASN cc_start: 0.8315 (t0) cc_final: 0.8064 (t0) REVERT: A 889 ARG cc_start: 0.8899 (ttt-90) cc_final: 0.8468 (ptp-170) REVERT: A 899 ASN cc_start: 0.8116 (t0) cc_final: 0.7641 (t0) REVERT: A 1017 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7975 (mp) REVERT: L 26 PHE cc_start: 0.6090 (m-80) cc_final: 0.5819 (m-80) REVERT: L 32 ARG cc_start: 0.5434 (mtp180) cc_final: 0.4953 (ttt-90) REVERT: L 86 LEU cc_start: 0.7424 (mt) cc_final: 0.7172 (tp) REVERT: M 117 LYS cc_start: 0.5764 (mttp) cc_final: 0.5450 (mtmm) outliers start: 23 outliers final: 17 residues processed: 97 average time/residue: 0.3385 time to fit residues: 46.5289 Evaluate side-chains 88 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 205 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN O 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16441 Z= 0.165 Angle : 0.575 9.893 23529 Z= 0.291 Chirality : 0.035 0.251 2870 Planarity : 0.004 0.066 2018 Dihedral : 23.525 176.859 5573 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.83 % Favored : 96.01 % Rotamer: Outliers : 1.49 % Allowed : 12.20 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.10 (0.24), residues: 1227 helix: 0.77 (0.21), residues: 613 sheet: -0.45 (0.48), residues: 123 loop : -0.95 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 547 HIS 0.003 0.001 HIS A 983 PHE 0.015 0.001 PHE A 331 TYR 0.009 0.001 TYR A 122 ARG 0.009 0.000 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 1.264 Fit side-chains REVERT: A 91 ARG cc_start: 0.7501 (mtt-85) cc_final: 0.7211 (ptm160) REVERT: A 95 ASN cc_start: 0.8246 (t0) cc_final: 0.7976 (t0) REVERT: A 139 LEU cc_start: 0.6950 (mp) cc_final: 0.6688 (tp) REVERT: A 889 ARG cc_start: 0.8885 (ttt-90) cc_final: 0.8449 (ptp-170) REVERT: A 903 THR cc_start: 0.8955 (m) cc_final: 0.8612 (p) REVERT: A 1017 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7878 (mp) REVERT: L 26 PHE cc_start: 0.5995 (m-80) cc_final: 0.5689 (m-80) REVERT: L 32 ARG cc_start: 0.5307 (mtp180) cc_final: 0.4742 (ttt-90) REVERT: L 74 ASN cc_start: 0.7219 (OUTLIER) cc_final: 0.6999 (t0) REVERT: L 86 LEU cc_start: 0.7204 (mt) cc_final: 0.6969 (tp) REVERT: M 117 LYS cc_start: 0.5616 (mttp) cc_final: 0.5282 (mtmm) REVERT: O 205 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7261 (pm20) outliers start: 16 outliers final: 11 residues processed: 89 average time/residue: 0.3422 time to fit residues: 43.7938 Evaluate side-chains 90 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 74 ASN Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 205 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 205 GLN O 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16441 Z= 0.216 Angle : 0.596 10.878 23529 Z= 0.300 Chirality : 0.035 0.208 2870 Planarity : 0.005 0.066 2018 Dihedral : 23.495 177.538 5573 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.44 % Rotamer: Outliers : 1.86 % Allowed : 12.01 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.06 (0.24), residues: 1227 helix: 0.81 (0.21), residues: 612 sheet: -0.57 (0.45), residues: 135 loop : -0.89 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 547 HIS 0.004 0.001 HIS A1013 PHE 0.017 0.002 PHE A 331 TYR 0.011 0.001 TYR A 122 ARG 0.011 0.000 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: A 91 ARG cc_start: 0.7543 (mtt-85) cc_final: 0.7182 (ptm160) REVERT: A 95 ASN cc_start: 0.8203 (t0) cc_final: 0.7927 (t0) REVERT: A 139 LEU cc_start: 0.7139 (mp) cc_final: 0.6923 (tp) REVERT: A 889 ARG cc_start: 0.8898 (ttt-90) cc_final: 0.8477 (ptp-170) REVERT: A 899 ASN cc_start: 0.8178 (t0) cc_final: 0.7699 (t0) REVERT: A 903 THR cc_start: 0.8920 (m) cc_final: 0.8558 (p) REVERT: A 1017 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8010 (mp) REVERT: L 26 PHE cc_start: 0.6284 (m-80) cc_final: 0.6016 (m-80) REVERT: L 32 ARG cc_start: 0.5323 (mtp180) cc_final: 0.4736 (ttt-90) REVERT: L 86 LEU cc_start: 0.7202 (mt) cc_final: 0.6965 (tp) REVERT: M 117 LYS cc_start: 0.5764 (mttp) cc_final: 0.5444 (mtmm) REVERT: O 154 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6914 (ptt90) outliers start: 20 outliers final: 17 residues processed: 90 average time/residue: 0.3369 time to fit residues: 43.8503 Evaluate side-chains 95 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain O residue 154 ARG Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 205 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 98 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 138 optimal weight: 0.0870 chunk 126 optimal weight: 6.9990 overall best weight: 2.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 85 ASN O 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16441 Z= 0.276 Angle : 0.641 14.710 23529 Z= 0.320 Chirality : 0.037 0.216 2870 Planarity : 0.005 0.065 2018 Dihedral : 23.551 178.390 5573 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.81 % Favored : 95.11 % Rotamer: Outliers : 2.05 % Allowed : 12.20 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.18 (0.24), residues: 1227 helix: 0.71 (0.21), residues: 606 sheet: -0.54 (0.45), residues: 133 loop : -0.97 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 547 HIS 0.004 0.001 HIS A1013 PHE 0.019 0.002 PHE A 331 TYR 0.012 0.002 TYR A 122 ARG 0.010 0.000 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 1.434 Fit side-chains revert: symmetry clash REVERT: A 91 ARG cc_start: 0.7548 (mtt-85) cc_final: 0.7177 (ptm160) REVERT: A 95 ASN cc_start: 0.8235 (t0) cc_final: 0.7956 (t0) REVERT: A 139 LEU cc_start: 0.7111 (mp) cc_final: 0.6860 (tp) REVERT: A 889 ARG cc_start: 0.8900 (ttt-90) cc_final: 0.8467 (ptp-170) REVERT: A 899 ASN cc_start: 0.8105 (t0) cc_final: 0.7662 (t0) REVERT: A 903 THR cc_start: 0.8886 (m) cc_final: 0.8497 (p) REVERT: L 26 PHE cc_start: 0.6020 (m-80) cc_final: 0.5532 (m-80) REVERT: L 32 ARG cc_start: 0.5307 (mtp180) cc_final: 0.4707 (ttt-90) REVERT: L 86 LEU cc_start: 0.7212 (mt) cc_final: 0.6953 (tp) REVERT: M 117 LYS cc_start: 0.5705 (mttp) cc_final: 0.5379 (mtmm) REVERT: O 154 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6952 (ptt90) outliers start: 22 outliers final: 19 residues processed: 93 average time/residue: 0.3419 time to fit residues: 45.6450 Evaluate side-chains 94 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain O residue 154 ARG Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 GLN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16441 Z= 0.163 Angle : 0.565 13.383 23529 Z= 0.281 Chirality : 0.034 0.201 2870 Planarity : 0.004 0.064 2018 Dihedral : 23.444 176.839 5573 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.99 % Favored : 95.84 % Rotamer: Outliers : 1.49 % Allowed : 12.94 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.17 (0.24), residues: 1227 helix: 1.01 (0.22), residues: 612 sheet: -0.37 (0.45), residues: 130 loop : -0.83 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 547 HIS 0.004 0.001 HIS A 983 PHE 0.015 0.001 PHE A 331 TYR 0.009 0.001 TYR A 122 ARG 0.011 0.000 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 1.666 Fit side-chains revert: symmetry clash REVERT: A 91 ARG cc_start: 0.7515 (mtt-85) cc_final: 0.7180 (ptm160) REVERT: A 95 ASN cc_start: 0.8137 (t0) cc_final: 0.7872 (t0) REVERT: A 139 LEU cc_start: 0.7114 (mp) cc_final: 0.6888 (tp) REVERT: A 889 ARG cc_start: 0.8907 (ttt-90) cc_final: 0.8474 (ptp-170) REVERT: A 899 ASN cc_start: 0.8168 (t0) cc_final: 0.7687 (t0) REVERT: A 903 THR cc_start: 0.8947 (m) cc_final: 0.8598 (p) REVERT: L 26 PHE cc_start: 0.6074 (m-80) cc_final: 0.5866 (m-80) REVERT: L 32 ARG cc_start: 0.5261 (mtp180) cc_final: 0.4700 (ttt-90) REVERT: L 86 LEU cc_start: 0.7184 (mt) cc_final: 0.6954 (tt) REVERT: M 117 LYS cc_start: 0.5856 (mttp) cc_final: 0.5512 (mtmm) REVERT: O 154 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7069 (ptt90) outliers start: 16 outliers final: 13 residues processed: 93 average time/residue: 0.3416 time to fit residues: 46.3683 Evaluate side-chains 92 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain O residue 154 ARG Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 6.9990 chunk 99 optimal weight: 10.9990 chunk 149 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16441 Z= 0.213 Angle : 0.590 12.889 23529 Z= 0.294 Chirality : 0.035 0.204 2870 Planarity : 0.004 0.063 2018 Dihedral : 23.471 177.142 5573 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.27 % Rotamer: Outliers : 1.58 % Allowed : 12.57 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.11 (0.24), residues: 1227 helix: 0.94 (0.21), residues: 609 sheet: -0.26 (0.45), residues: 135 loop : -0.87 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 547 HIS 0.004 0.001 HIS A 983 PHE 0.016 0.002 PHE A 331 TYR 0.010 0.001 TYR A 122 ARG 0.011 0.000 ARG L 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 91 ARG cc_start: 0.7485 (mtt-85) cc_final: 0.7158 (ptm160) REVERT: A 95 ASN cc_start: 0.8171 (t0) cc_final: 0.7912 (t0) REVERT: A 139 LEU cc_start: 0.7139 (mp) cc_final: 0.6877 (tp) REVERT: A 889 ARG cc_start: 0.8923 (ttt-90) cc_final: 0.8496 (ptp-170) REVERT: A 899 ASN cc_start: 0.8184 (t0) cc_final: 0.7702 (t0) REVERT: A 903 THR cc_start: 0.8915 (m) cc_final: 0.8552 (p) REVERT: A 970 MET cc_start: 0.7170 (ttm) cc_final: 0.6877 (ttt) REVERT: L 32 ARG cc_start: 0.5295 (mtp180) cc_final: 0.4701 (ttt-90) REVERT: M 117 LYS cc_start: 0.5847 (mttp) cc_final: 0.5506 (mtmm) REVERT: O 154 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7090 (ptt90) REVERT: O 170 LYS cc_start: 0.7347 (ptpt) cc_final: 0.6739 (tppt) outliers start: 17 outliers final: 15 residues processed: 91 average time/residue: 0.3392 time to fit residues: 44.8511 Evaluate side-chains 96 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain O residue 154 ARG Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 119 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.141059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.092022 restraints weight = 37121.595| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.38 r_work: 0.3258 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16441 Z= 0.368 Angle : 0.702 12.836 23529 Z= 0.351 Chirality : 0.039 0.231 2870 Planarity : 0.005 0.063 2018 Dihedral : 23.701 179.536 5573 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.70 % Favored : 94.21 % Rotamer: Outliers : 1.86 % Allowed : 12.57 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.39 (0.24), residues: 1227 helix: 0.46 (0.21), residues: 606 sheet: -0.26 (0.45), residues: 133 loop : -1.09 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 690 HIS 0.006 0.001 HIS A1013 PHE 0.020 0.002 PHE A 331 TYR 0.015 0.002 TYR A 122 ARG 0.010 0.001 ARG L 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3037.62 seconds wall clock time: 56 minutes 12.90 seconds (3372.90 seconds total)