Starting phenix.real_space_refine on Sat Mar 16 03:08:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trf_26088/03_2024/7trf_26088.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trf_26088/03_2024/7trf_26088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trf_26088/03_2024/7trf_26088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trf_26088/03_2024/7trf_26088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trf_26088/03_2024/7trf_26088.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trf_26088/03_2024/7trf_26088.pdb" } resolution = 3.7 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 224 5.49 5 S 38 5.16 5 C 7774 2.51 5 N 2469 2.21 5 O 3076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 77": "OE1" <-> "OE2" Residue "E PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "A TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ASP 701": "OD1" <-> "OD2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "A ARG 743": "NH1" <-> "NH2" Residue "A TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 787": "NH1" <-> "NH2" Residue "A ASP 807": "OD1" <-> "OD2" Residue "A TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 848": "OD1" <-> "OD2" Residue "A GLU 850": "OE1" <-> "OE2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A ARG 865": "NH1" <-> "NH2" Residue "A TYR 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 901": "NH1" <-> "NH2" Residue "A GLU 910": "OE1" <-> "OE2" Residue "A GLU 912": "OE1" <-> "OE2" Residue "A PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A ARG 938": "NH1" <-> "NH2" Residue "A ARG 951": "NH1" <-> "NH2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "A PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1097": "NH1" <-> "NH2" Residue "A ARG 1105": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13581 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" 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: "E" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 642 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "B" Number of atoms: 4605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 4605 Classifications: {'RNA': 217} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 21, 'rna3p_pur': 85, 'rna3p_pyr': 96} Link IDs: {'rna2p': 36, 'rna3p': 180} Chain breaks: 2 Chain: "A" Number of atoms: 7488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 934, 7488 Classifications: {'peptide': 934} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 877} Chain breaks: 4 Chain: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 8.10, per 1000 atoms: 0.60 Number of scatterers: 13581 At special positions: 0 Unit cell: (117.7, 122.1, 121, 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 38 16.00 P 224 15.00 O 3076 8.00 N 2469 7.00 C 7774 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: 6.41 Conformation dependent library (CDL) restraints added in 1.7 seconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 59.4% alpha, 13.0% beta 64 base pairs and 97 stacking pairs defined. Time for finding SS restraints: 5.45 Creating SS restraints... Processing helix chain 'F' and resid 38 through 50 removed outlier: 3.800A pdb=" N TYR F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN F 48 " --> pdb=" O LYS F 44 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL F 49 " --> pdb=" O VAL F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 86 removed outlier: 4.107A pdb=" N SER F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE F 66 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL F 67 " --> pdb=" O MET F 63 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE F 70 " --> pdb=" O PHE F 66 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 103 removed outlier: 4.193A pdb=" N ILE F 95 " --> pdb=" O THR F 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 124 removed outlier: 3.548A pdb=" N LYS F 109 " --> pdb=" O GLY F 105 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 23 Processing helix chain 'E' and resid 27 through 38 removed outlier: 3.854A pdb=" N GLY E 38 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 74 removed outlier: 4.561A pdb=" N VAL E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 64 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP E 73 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 91 removed outlier: 3.810A pdb=" N ALA E 87 " --> pdb=" O HIS E 83 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 98 removed outlier: 3.596A pdb=" N LEU E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 76 through 92 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 146 through 156 Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.839A pdb=" N LEU A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 removed outlier: 4.000A pdb=" N LEU A 332 " --> pdb=" O LYS A 329 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.574A pdb=" N ALA A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 389 through 401 removed outlier: 4.037A pdb=" N PHE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.782A pdb=" N LEU A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 454 removed outlier: 3.781A pdb=" N GLN A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.717A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.506A pdb=" N GLU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.654A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 560 removed outlier: 3.764A pdb=" N HIS A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 4.388A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.515A pdb=" N GLU A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 672 removed outlier: 3.532A pdb=" N SER A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.652A pdb=" N LEU A 676 " --> pdb=" O PRO A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 698 removed outlier: 3.762A pdb=" N ILE A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 Processing helix chain 'A' and resid 765 through 769 removed outlier: 4.005A pdb=" N LEU A 769 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 removed outlier: 3.583A pdb=" N PHE A 776 " --> pdb=" O TYR A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 815 Processing helix chain 'A' and resid 837 through 854 Processing helix chain 'A' and resid 876 through 890 Processing helix chain 'A' and resid 946 through 950 removed outlier: 3.788A pdb=" N ALA A 950 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 958 removed outlier: 4.052A pdb=" N LEU A 958 " --> pdb=" O ARG A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 982 Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 993 through 1017 Processing helix chain 'A' and resid 1024 through 1027 Processing helix chain 'A' and resid 1028 through 1051 removed outlier: 4.120A pdb=" N PHE A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A1051 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1082 removed outlier: 4.323A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TRP A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.651A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Proline residue: A1091 - end of helix removed outlier: 4.508A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A1106 " --> pdb=" O GLN A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1119 removed outlier: 3.712A pdb=" N ALA A1119 " --> pdb=" O LEU A1115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 89 through 90 removed outlier: 3.756A pdb=" N ILE F 90 " --> pdb=" O ARG E 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 removed outlier: 6.418A pdb=" N LEU A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 160 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 168 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 14.579A pdb=" N CYS A 171 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 744 " --> pdb=" O LYS A 760 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 23 removed outlier: 6.418A pdb=" N LEU A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 160 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 168 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 14.579A pdb=" N CYS A 171 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA6, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA7, first strand: chain 'A' and resid 598 through 600 removed outlier: 6.601A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 862 through 865 removed outlier: 3.640A pdb=" N VAL A 904 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP A 712 " --> pdb=" O LYS A 902 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS A 902 " --> pdb=" O ASP A 712 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 927 through 930 467 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 173 hydrogen bonds 330 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 97 stacking parallelities Total time for adding SS restraints: 6.61 Time building geometry restraints manager: 6.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3548 1.34 - 1.46: 4450 1.46 - 1.58: 5835 1.58 - 1.71: 444 1.71 - 1.83: 51 Bond restraints: 14328 Sorted by residual: bond pdb=" C LYS A 973 " pdb=" N LEU A 974 " ideal model delta sigma weight residual 1.334 1.384 -0.049 1.27e-02 6.20e+03 1.50e+01 bond pdb=" CA ILE E 79 " pdb=" CB ILE E 79 " ideal model delta sigma weight residual 1.540 1.575 -0.035 1.10e-02 8.26e+03 1.04e+01 bond pdb=" N VAL E 31 " pdb=" CA VAL E 31 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.19e-02 7.06e+03 9.83e+00 bond pdb=" N ILE E 79 " pdb=" CA ILE E 79 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.32e-02 5.74e+03 9.48e+00 bond pdb=" N VAL A 697 " pdb=" CA VAL A 697 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.98e+00 ... (remaining 14323 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.24: 1471 106.24 - 113.19: 7976 113.19 - 120.13: 5381 120.13 - 127.07: 5101 127.07 - 134.02: 547 Bond angle restraints: 20476 Sorted by residual: angle pdb=" O LYS A 973 " pdb=" C LYS A 973 " pdb=" N LEU A 974 " ideal model delta sigma weight residual 122.07 117.21 4.86 1.03e+00 9.43e-01 2.23e+01 angle pdb=" N VAL A 596 " pdb=" CA VAL A 596 " pdb=" C VAL A 596 " ideal model delta sigma weight residual 112.43 108.64 3.79 9.20e-01 1.18e+00 1.70e+01 angle pdb=" C ILE E 80 " pdb=" N PRO E 81 " pdb=" CA PRO E 81 " ideal model delta sigma weight residual 119.84 124.98 -5.14 1.25e+00 6.40e-01 1.69e+01 angle pdb=" CA LYS A 973 " pdb=" C LYS A 973 " pdb=" N LEU A 974 " ideal model delta sigma weight residual 117.07 121.61 -4.54 1.14e+00 7.69e-01 1.59e+01 angle pdb=" C LYS A 973 " pdb=" N LEU A 974 " pdb=" CA LEU A 974 " ideal model delta sigma weight residual 120.44 125.58 -5.14 1.30e+00 5.92e-01 1.56e+01 ... (remaining 20471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 8266 35.84 - 71.69: 627 71.69 - 107.53: 95 107.53 - 143.38: 5 143.38 - 179.22: 3 Dihedral angle restraints: 8996 sinusoidal: 5775 harmonic: 3221 Sorted by residual: dihedral pdb=" O4' U B 43 " pdb=" C1' U B 43 " pdb=" N1 U B 43 " pdb=" C2 U B 43 " ideal model delta sinusoidal sigma weight residual 232.00 52.78 179.22 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 133 " pdb=" C1' U B 133 " pdb=" N1 U B 133 " pdb=" C2 U B 133 " ideal model delta sinusoidal sigma weight residual -128.00 48.72 -176.72 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 291 " pdb=" C1' U B 291 " pdb=" N1 U B 291 " pdb=" C2 U B 291 " ideal model delta sinusoidal sigma weight residual -128.00 40.43 -168.43 1 1.70e+01 3.46e-03 6.58e+01 ... (remaining 8993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2401 0.113 - 0.227: 86 0.227 - 0.340: 8 0.340 - 0.454: 0 0.454 - 0.567: 1 Chirality restraints: 2496 Sorted by residual: chirality pdb=" P G B 251 " pdb=" OP1 G B 251 " pdb=" OP2 G B 251 " pdb=" O5' G B 251 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.05e+00 chirality pdb=" CA MET F 63 " pdb=" N MET F 63 " pdb=" C MET F 63 " pdb=" CB MET F 63 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" P G B 319 " pdb=" OP1 G B 319 " pdb=" OP2 G B 319 " pdb=" O5' G B 319 " both_signs ideal model delta sigma weight residual True 2.41 -2.65 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2493 not shown) Planarity restraints: 1776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 26 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" C PHE E 26 " -0.052 2.00e-02 2.50e+03 pdb=" O PHE E 26 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO E 27 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 312 " -0.000 2.00e-02 2.50e+03 1.70e-02 6.49e+00 pdb=" N1 U B 312 " 0.015 2.00e-02 2.50e+03 pdb=" C2 U B 312 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U B 312 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U B 312 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U B 312 " -0.016 2.00e-02 2.50e+03 pdb=" O4 U B 312 " 0.000 2.00e-02 2.50e+03 pdb=" C5 U B 312 " 0.032 2.00e-02 2.50e+03 pdb=" C6 U B 312 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 43 " 0.023 2.00e-02 2.50e+03 1.70e-02 5.76e+00 pdb=" CG TYR F 43 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR F 43 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR F 43 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR F 43 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR F 43 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR F 43 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR F 43 " -0.002 2.00e-02 2.50e+03 ... (remaining 1773 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1519 2.75 - 3.28: 12437 3.28 - 3.82: 23235 3.82 - 4.36: 26628 4.36 - 4.90: 41800 Nonbonded interactions: 105619 Sorted by model distance: nonbonded pdb=" O LEU A1079 " pdb=" OG1 THR A1083 " model vdw 2.206 2.440 nonbonded pdb=" NE ARG E 78 " pdb=" O6 G B 315 " model vdw 2.221 2.520 nonbonded pdb=" O2' G B 71 " pdb=" OP1 C B 72 " model vdw 2.241 2.440 nonbonded pdb=" O TYR F 38 " pdb=" N VAL F 40 " model vdw 2.245 2.520 nonbonded pdb=" OG SER A 619 " pdb=" O ASN A 635 " model vdw 2.261 2.440 ... (remaining 105614 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.300 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 45.370 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 : 0.005 0.049 14328 Z= 0.329 Angle : 0.743 7.614 20476 Z= 0.460 Chirality : 0.049 0.567 2496 Planarity : 0.004 0.041 1776 Dihedral : 21.473 179.219 6910 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.58 % Favored : 95.33 % Rotamer: Outliers : 0.10 % Allowed : 1.26 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -0.55 (0.26), residues: 1092 helix: 0.47 (0.23), residues: 546 sheet: -0.29 (0.51), residues: 93 loop : -1.38 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 581 HIS 0.012 0.002 HIS F 50 PHE 0.030 0.002 PHE F 66 TYR 0.024 0.002 TYR F 43 ARG 0.006 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.286 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: F 63 MET cc_start: 0.9253 (ptt) cc_final: 0.9053 (mmt) REVERT: E 37 LYS cc_start: 0.5136 (tptp) cc_final: 0.4891 (mptt) REVERT: E 62 GLU cc_start: 0.9252 (tp30) cc_final: 0.8818 (mm-30) REVERT: E 80 ILE cc_start: 0.6512 (tt) cc_final: 0.6149 (tp) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.3003 time to fit residues: 58.5454 Evaluate side-chains 86 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 0.0050 chunk 102 optimal weight: 0.9980 chunk 39 optimal weight: 0.0870 chunk 62 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.6174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 384 GLN A 827 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14328 Z= 0.150 Angle : 0.573 9.235 20476 Z= 0.286 Chirality : 0.033 0.160 2496 Planarity : 0.004 0.036 1776 Dihedral : 23.023 179.015 4769 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.26 % Allowed : 7.14 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.16 (0.26), residues: 1092 helix: 1.07 (0.23), residues: 569 sheet: 0.04 (0.52), residues: 86 loop : -1.16 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 459 HIS 0.008 0.001 HIS E 32 PHE 0.019 0.001 PHE A 27 TYR 0.017 0.001 TYR F 43 ARG 0.016 0.000 ARG E 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 ARG cc_start: 0.7256 (mtm110) cc_final: 0.6821 (ptt-90) REVERT: E 26 PHE cc_start: 0.8739 (m-80) cc_final: 0.8474 (m-10) REVERT: E 76 LYS cc_start: 0.8665 (mmtt) cc_final: 0.8114 (mmmt) REVERT: A 813 MET cc_start: 0.7933 (tmm) cc_final: 0.7617 (tmm) outliers start: 12 outliers final: 2 residues processed: 108 average time/residue: 0.2894 time to fit residues: 44.4189 Evaluate side-chains 91 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 1016 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 40 optimal weight: 0.0270 chunk 95 optimal weight: 0.0000 overall best weight: 1.0048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A1023 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14328 Z= 0.142 Angle : 0.531 10.055 20476 Z= 0.261 Chirality : 0.032 0.206 2496 Planarity : 0.004 0.064 1776 Dihedral : 22.866 176.308 4769 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.36 % Allowed : 9.65 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.63 (0.26), residues: 1092 helix: 1.52 (0.23), residues: 570 sheet: 0.12 (0.50), residues: 91 loop : -1.01 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 581 HIS 0.004 0.001 HIS A 609 PHE 0.015 0.001 PHE A 47 TYR 0.021 0.001 TYR A 18 ARG 0.009 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 ARG cc_start: 0.7352 (mtm110) cc_final: 0.7081 (ptt-90) REVERT: E 76 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8120 (mmmt) REVERT: A 813 MET cc_start: 0.7993 (tmm) cc_final: 0.7510 (tmm) outliers start: 13 outliers final: 8 residues processed: 91 average time/residue: 0.2567 time to fit residues: 34.5595 Evaluate side-chains 90 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 TYR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1016 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 0.2980 chunk 34 optimal weight: 20.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14328 Z= 0.173 Angle : 0.527 10.301 20476 Z= 0.262 Chirality : 0.032 0.175 2496 Planarity : 0.004 0.032 1776 Dihedral : 22.812 175.507 4769 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.47 % Allowed : 11.02 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.90 (0.26), residues: 1092 helix: 1.75 (0.22), residues: 570 sheet: 0.14 (0.50), residues: 91 loop : -0.88 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 60 HIS 0.004 0.001 HIS A 482 PHE 0.011 0.001 PHE A 331 TYR 0.013 0.001 TYR F 43 ARG 0.004 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8113 (mmmt) outliers start: 14 outliers final: 9 residues processed: 92 average time/residue: 0.2439 time to fit residues: 33.7373 Evaluate side-chains 88 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 1016 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 0.0270 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 HIS A 754 HIS A 827 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14328 Z= 0.228 Angle : 0.558 10.474 20476 Z= 0.279 Chirality : 0.034 0.228 2496 Planarity : 0.004 0.032 1776 Dihedral : 22.829 175.274 4769 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.31 % Allowed : 11.54 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.91 (0.26), residues: 1092 helix: 1.73 (0.22), residues: 572 sheet: 0.26 (0.51), residues: 92 loop : -0.86 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 60 HIS 0.005 0.001 HIS A 482 PHE 0.027 0.002 PHE A 47 TYR 0.015 0.001 TYR F 43 ARG 0.005 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8151 (mmmt) REVERT: E 94 LEU cc_start: 0.9390 (mp) cc_final: 0.9165 (tp) outliers start: 22 outliers final: 16 residues processed: 89 average time/residue: 0.2266 time to fit residues: 31.5090 Evaluate side-chains 88 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 83 HIS Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 827 GLN Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1090 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 chunk 66 optimal weight: 0.8980 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14328 Z= 0.130 Angle : 0.508 11.286 20476 Z= 0.252 Chirality : 0.032 0.168 2496 Planarity : 0.004 0.031 1776 Dihedral : 22.798 174.826 4769 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.89 % Allowed : 13.12 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 1.07 (0.26), residues: 1092 helix: 1.89 (0.22), residues: 574 sheet: 0.28 (0.51), residues: 92 loop : -0.84 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 60 HIS 0.011 0.001 HIS A 754 PHE 0.014 0.001 PHE A 27 TYR 0.010 0.001 TYR F 43 ARG 0.003 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 ARG cc_start: 0.7261 (mtm110) cc_final: 0.7016 (ptt-90) REVERT: E 76 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8197 (mmmt) REVERT: E 94 LEU cc_start: 0.9386 (mp) cc_final: 0.9156 (tp) outliers start: 18 outliers final: 13 residues processed: 93 average time/residue: 0.2441 time to fit residues: 34.6979 Evaluate side-chains 92 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain A residue 752 HIS Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1129 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 0.8980 chunk 14 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 126 optimal weight: 0.0980 chunk 79 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14328 Z= 0.127 Angle : 0.501 14.172 20476 Z= 0.246 Chirality : 0.031 0.172 2496 Planarity : 0.003 0.031 1776 Dihedral : 22.671 175.154 4769 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.89 % Allowed : 13.64 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1092 helix: 2.10 (0.22), residues: 572 sheet: 0.36 (0.51), residues: 92 loop : -0.85 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 60 HIS 0.004 0.001 HIS A 754 PHE 0.014 0.001 PHE A 27 TYR 0.008 0.001 TYR F 43 ARG 0.003 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 ARG cc_start: 0.7212 (mtm110) cc_final: 0.6951 (ptt-90) REVERT: E 76 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8247 (mmmt) REVERT: E 94 LEU cc_start: 0.9378 (mp) cc_final: 0.9144 (tp) REVERT: E 98 LEU cc_start: 0.7659 (tt) cc_final: 0.7441 (tt) outliers start: 18 outliers final: 14 residues processed: 97 average time/residue: 0.2357 time to fit residues: 35.0259 Evaluate side-chains 94 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1129 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 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 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14328 Z= 0.193 Angle : 0.521 10.741 20476 Z= 0.258 Chirality : 0.032 0.185 2496 Planarity : 0.004 0.030 1776 Dihedral : 22.664 175.556 4769 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.10 % Allowed : 13.54 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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 (0.26), residues: 1092 helix: 2.07 (0.22), residues: 572 sheet: 0.19 (0.51), residues: 92 loop : -0.84 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.005 0.001 HIS A 482 PHE 0.019 0.002 PHE E 26 TYR 0.012 0.001 TYR F 43 ARG 0.003 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 1.437 Fit side-chains revert: symmetry clash REVERT: E 76 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8254 (mmmt) REVERT: A 813 MET cc_start: 0.8222 (tmm) cc_final: 0.7922 (tmm) outliers start: 20 outliers final: 17 residues processed: 87 average time/residue: 0.2337 time to fit residues: 31.5010 Evaluate side-chains 91 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.9990 chunk 110 optimal weight: 0.0370 chunk 117 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 124 optimal weight: 0.0570 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14328 Z= 0.146 Angle : 0.500 11.005 20476 Z= 0.247 Chirality : 0.031 0.173 2496 Planarity : 0.003 0.031 1776 Dihedral : 22.621 175.428 4769 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.78 % Allowed : 14.06 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 1.27 (0.27), residues: 1092 helix: 2.12 (0.23), residues: 572 sheet: 0.26 (0.52), residues: 92 loop : -0.81 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 60 HIS 0.003 0.001 HIS A 609 PHE 0.017 0.001 PHE A 776 TYR 0.010 0.001 TYR F 43 ARG 0.004 0.000 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 76 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8258 (mmmt) REVERT: E 78 ARG cc_start: 0.8698 (tpp-160) cc_final: 0.8344 (tpp-160) REVERT: A 813 MET cc_start: 0.8190 (tmm) cc_final: 0.7860 (tmm) outliers start: 17 outliers final: 15 residues processed: 88 average time/residue: 0.2523 time to fit residues: 33.7553 Evaluate side-chains 92 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 86 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 120 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14328 Z= 0.144 Angle : 0.508 11.095 20476 Z= 0.247 Chirality : 0.031 0.207 2496 Planarity : 0.004 0.049 1776 Dihedral : 22.565 175.578 4769 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.68 % Allowed : 14.69 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 1.30 (0.27), residues: 1092 helix: 2.16 (0.22), residues: 572 sheet: 0.23 (0.52), residues: 92 loop : -0.80 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.003 0.000 HIS A 482 PHE 0.019 0.001 PHE A 776 TYR 0.010 0.001 TYR F 43 ARG 0.002 0.000 ARG A 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: E 76 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8291 (mmmt) REVERT: E 78 ARG cc_start: 0.8697 (tpp-160) cc_final: 0.8348 (tpp-160) REVERT: A 813 MET cc_start: 0.8192 (tmm) cc_final: 0.7854 (tmm) outliers start: 16 outliers final: 15 residues processed: 85 average time/residue: 0.2327 time to fit residues: 31.3282 Evaluate side-chains 90 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 10.9990 chunk 95 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 40.0000 chunk 104 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 5 optimal weight: 0.0570 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.100063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.064956 restraints weight = 48566.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.066809 restraints weight = 24167.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.067873 restraints weight = 16983.710| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14328 Z= 0.143 Angle : 0.503 11.311 20476 Z= 0.246 Chirality : 0.031 0.168 2496 Planarity : 0.003 0.032 1776 Dihedral : 22.516 175.803 4769 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.68 % Allowed : 14.90 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 1.32 (0.27), residues: 1092 helix: 2.18 (0.23), residues: 572 sheet: 0.18 (0.52), residues: 92 loop : -0.79 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 547 HIS 0.003 0.000 HIS A 609 PHE 0.016 0.001 PHE A 776 TYR 0.010 0.001 TYR F 43 ARG 0.002 0.000 ARG A 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2200.34 seconds wall clock time: 40 minutes 47.86 seconds (2447.86 seconds total)