Starting phenix.real_space_refine (version: dev) on Mon Feb 20 19:00:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmc_0446/02_2023/6nmc_0446.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmc_0446/02_2023/6nmc_0446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmc_0446/02_2023/6nmc_0446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmc_0446/02_2023/6nmc_0446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmc_0446/02_2023/6nmc_0446.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmc_0446/02_2023/6nmc_0446.pdb" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A ARG 737": "NH1" <-> "NH2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A GLU 885": "OE1" <-> "OE2" Residue "A GLU 939": "OE1" <-> "OE2" Residue "A GLU 947": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 11": "NH1" <-> "NH2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12808 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1202, 9931 Classifications: {'peptide': 1202} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 25, 'TRANS': 1172} Chain breaks: 3 Chain: "G" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 535 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna2p': 8, 'rna3p': 16} Chain: "B" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1305 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain breaks: 1 Chain: "C" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1029 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 7.55, per 1000 atoms: 0.59 Number of scatterers: 12808 At special positions: 0 Unit cell: (132.184, 108.732, 105.534, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 25 15.00 Mg 2 11.99 O 2548 8.00 N 2098 7.00 C 8096 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: 5.43 Conformation dependent library (CDL) restraints added in 1.6 seconds 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2838 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 13 sheets defined 53.0% alpha, 4.8% beta 4 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 37 through 66 removed outlier: 5.043A pdb=" N TYR A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LYS A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 73 through 83 removed outlier: 4.073A pdb=" N LEU A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 111 removed outlier: 3.737A pdb=" N GLU A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 removed outlier: 4.475A pdb=" N PHE A 119 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.881A pdb=" N ILE A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 124 " --> pdb=" O LYS A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 124' Processing helix chain 'A' and resid 136 through 142 removed outlier: 4.147A pdb=" N LEU A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 148 through 154 removed outlier: 4.162A pdb=" N GLY A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.846A pdb=" N ARG A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.927A pdb=" N SER A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.856A pdb=" N PHE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.719A pdb=" N LYS A 265 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 312 through 327 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 341 through 353 removed outlier: 4.155A pdb=" N SER A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 371 removed outlier: 4.142A pdb=" N ILE A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 Processing helix chain 'A' and resid 396 through 404 Processing helix chain 'A' and resid 409 through 433 removed outlier: 4.363A pdb=" N LYS A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.623A pdb=" N ASP A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.702A pdb=" N ALA A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 560 through 563 removed outlier: 4.068A pdb=" N ALA A 563 " --> pdb=" O LYS A 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 609 through 619 Processing helix chain 'A' and resid 628 through 646 removed outlier: 4.445A pdb=" N LYS A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 635 " --> pdb=" O ASP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 652 removed outlier: 3.940A pdb=" N ASN A 651 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 663 removed outlier: 3.882A pdb=" N TYR A 663 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 718 through 727 Processing helix chain 'A' and resid 786 through 790 removed outlier: 3.800A pdb=" N PHE A 789 " --> pdb=" O ASP A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 4.058A pdb=" N ARG A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 822 " --> pdb=" O VAL A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 886 removed outlier: 3.711A pdb=" N GLU A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 4.443A pdb=" N VAL A 908 " --> pdb=" O ILE A 904 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N HIS A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 952 removed outlier: 3.702A pdb=" N TYR A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 956 Processing helix chain 'A' and resid 1020 through 1030 removed outlier: 4.398A pdb=" N LYS A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1111 through 1116 Processing helix chain 'A' and resid 1120 through 1136 removed outlier: 4.183A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A1129 " --> pdb=" O SER A1125 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU A1130 " --> pdb=" O SER A1126 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A1133 " --> pdb=" O ALA A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1169 removed outlier: 4.165A pdb=" N ALA A1169 " --> pdb=" O ARG A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1199 removed outlier: 3.774A pdb=" N ILE A1187 " --> pdb=" O GLY A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1225 Processing helix chain 'B' and resid 3 through 20 removed outlier: 3.508A pdb=" N GLU B 10 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 4.287A pdb=" N ALA B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.529A pdb=" N GLU B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 124 through 162 removed outlier: 4.589A pdb=" N GLU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 removed outlier: 4.288A pdb=" N ALA C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.528A pdb=" N GLU C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.741A pdb=" N THR C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 162 removed outlier: 3.815A pdb=" N LEU C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 579 through 580 removed outlier: 3.853A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA3, first strand: chain 'A' and resid 521 through 522 removed outlier: 3.642A pdb=" N PHE A 521 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 746 " --> pdb=" O PHE A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 584 through 585 Processing sheet with id=AA5, first strand: chain 'A' and resid 736 through 738 removed outlier: 3.657A pdb=" N ARG A 737 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 758 through 759 removed outlier: 3.692A pdb=" N HIS A 759 " --> pdb=" O VAL A 783 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 783 " --> pdb=" O HIS A 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 764 through 765 Processing sheet with id=AA8, first strand: chain 'A' and resid 828 through 832 removed outlier: 3.594A pdb=" N VAL A 842 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 841 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN A 853 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 843 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 858 through 862 removed outlier: 4.332A pdb=" N ILE A 868 " --> pdb=" O ASN A 861 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 922 through 925 removed outlier: 6.708A pdb=" N ILE A 922 " --> pdb=" O PHE A 994 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE A 996 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU A 924 " --> pdb=" O ILE A 996 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1047 through 1048 removed outlier: 3.845A pdb=" N LEU A1047 " --> pdb=" O TRP A1063 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A1063 " --> pdb=" O LEU A1047 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1070 through 1073 removed outlier: 3.878A pdb=" N ARG A1071 " --> pdb=" O VAL A1089 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A1089 " --> pdb=" O ARG A1071 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1138 through 1140 506 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 4.62 Time building geometry restraints manager: 5.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 4109 1.35 - 1.50: 4532 1.50 - 1.66: 4415 1.66 - 1.81: 24 1.81 - 1.96: 41 Bond restraints: 13121 Sorted by residual: bond pdb=" SD MET A 531 " pdb=" CE MET A 531 " ideal model delta sigma weight residual 1.791 1.963 -0.172 2.50e-02 1.60e+03 4.74e+01 bond pdb=" SD MET A 626 " pdb=" CE MET A 626 " ideal model delta sigma weight residual 1.791 1.963 -0.172 2.50e-02 1.60e+03 4.73e+01 bond pdb=" CG MET A 531 " pdb=" SD MET A 531 " ideal model delta sigma weight residual 1.803 1.963 -0.160 2.50e-02 1.60e+03 4.11e+01 bond pdb=" SD MET A 603 " pdb=" CE MET A 603 " ideal model delta sigma weight residual 1.791 1.951 -0.160 2.50e-02 1.60e+03 4.08e+01 bond pdb=" CG MET A 626 " pdb=" SD MET A 626 " ideal model delta sigma weight residual 1.803 1.962 -0.159 2.50e-02 1.60e+03 4.04e+01 ... (remaining 13116 not shown) Histogram of bond angle deviations from ideal: 96.34 - 104.58: 204 104.58 - 112.82: 6679 112.82 - 121.06: 7515 121.06 - 129.31: 3274 129.31 - 137.55: 84 Bond angle restraints: 17756 Sorted by residual: angle pdb=" N MET A 626 " pdb=" CA MET A 626 " pdb=" C MET A 626 " ideal model delta sigma weight residual 113.16 105.09 8.07 1.24e+00 6.50e-01 4.23e+01 angle pdb=" C PHE A 220 " pdb=" CA PHE A 220 " pdb=" CB PHE A 220 " ideal model delta sigma weight residual 109.29 119.29 -10.00 1.82e+00 3.02e-01 3.02e+01 angle pdb=" CA TRP B 100 " pdb=" C TRP B 100 " pdb=" O TRP B 100 " ideal model delta sigma weight residual 121.10 115.55 5.55 1.10e+00 8.26e-01 2.55e+01 angle pdb=" CA TRP C 100 " pdb=" C TRP C 100 " pdb=" O TRP C 100 " ideal model delta sigma weight residual 121.10 115.60 5.50 1.10e+00 8.26e-01 2.50e+01 angle pdb=" C GLU A 88 " pdb=" N LYS A 89 " pdb=" CA LYS A 89 " ideal model delta sigma weight residual 122.07 129.01 -6.94 1.43e+00 4.89e-01 2.35e+01 ... (remaining 17751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 7653 35.60 - 71.19: 205 71.19 - 106.79: 11 106.79 - 142.38: 0 142.38 - 177.98: 1 Dihedral angle restraints: 7870 sinusoidal: 3472 harmonic: 4398 Sorted by residual: dihedral pdb=" O4' U G 16 " pdb=" C1' U G 16 " pdb=" N1 U G 16 " pdb=" C2 U G 16 " ideal model delta sinusoidal sigma weight residual 232.00 54.02 177.98 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C ASP A 625 " pdb=" N ASP A 625 " pdb=" CA ASP A 625 " pdb=" CB ASP A 625 " ideal model delta harmonic sigma weight residual -122.60 -137.57 14.97 0 2.50e+00 1.60e-01 3.59e+01 dihedral pdb=" CA GLU A 476 " pdb=" C GLU A 476 " pdb=" N GLY A 477 " pdb=" CA GLY A 477 " ideal model delta harmonic sigma weight residual -180.00 -150.39 -29.61 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 7867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1597 0.098 - 0.196: 267 0.196 - 0.293: 18 0.293 - 0.391: 5 0.391 - 0.489: 2 Chirality restraints: 1889 Sorted by residual: chirality pdb=" CA ASP A 625 " pdb=" N ASP A 625 " pdb=" C ASP A 625 " pdb=" CB ASP A 625 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CB ILE A 798 " pdb=" CA ILE A 798 " pdb=" CG1 ILE A 798 " pdb=" CG2 ILE A 798 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CB ILE B 113 " pdb=" CA ILE B 113 " pdb=" CG1 ILE B 113 " pdb=" CG2 ILE B 113 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 1886 not shown) Planarity restraints: 2188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 102 " 0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ASN C 102 " -0.061 2.00e-02 2.50e+03 pdb=" O ASN C 102 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE C 103 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 128 " -0.044 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO A 129 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 599 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C SER A 599 " -0.045 2.00e-02 2.50e+03 pdb=" O SER A 599 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS A 600 " 0.015 2.00e-02 2.50e+03 ... (remaining 2185 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 266 2.59 - 3.17: 11018 3.17 - 3.75: 20420 3.75 - 4.32: 26700 4.32 - 4.90: 42382 Nonbonded interactions: 100786 Sorted by model distance: nonbonded pdb="MG MG G 101 " pdb=" O HOH G 202 " model vdw 2.015 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 201 " model vdw 2.031 2.170 nonbonded pdb=" OP2 A G 19 " pdb="MG MG A1301 " model vdw 2.032 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 203 " model vdw 2.036 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH A1401 " model vdw 2.045 2.170 ... (remaining 100781 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 25 5.49 5 Mg 2 5.21 5 S 39 5.16 5 C 8096 2.51 5 N 2098 2.21 5 O 2548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.260 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: 2.250 Check model and map are aligned: 0.190 Process input model: 37.850 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.014 0.172 13121 Z= 0.861 Angle : 1.160 10.765 17756 Z= 0.683 Chirality : 0.073 0.489 1889 Planarity : 0.007 0.065 2188 Dihedral : 16.403 177.976 5032 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.19 % Favored : 89.40 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.17), residues: 1462 helix: -2.34 (0.15), residues: 695 sheet: -3.03 (0.45), residues: 112 loop : -3.24 (0.20), residues: 655 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 359 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 9 residues processed: 385 average time/residue: 0.3162 time to fit residues: 163.8598 Evaluate side-chains 204 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 195 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1348 time to fit residues: 4.4071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 116 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 33 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN A 941 GLN A 963 ASN ** A1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 ASN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 13121 Z= 0.169 Angle : 0.642 12.672 17756 Z= 0.341 Chirality : 0.044 0.221 1889 Planarity : 0.004 0.053 2188 Dihedral : 9.719 172.652 1908 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.12 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.20), residues: 1462 helix: -0.96 (0.18), residues: 718 sheet: -2.66 (0.46), residues: 119 loop : -2.76 (0.22), residues: 625 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 288 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 290 average time/residue: 0.3026 time to fit residues: 121.5110 Evaluate side-chains 195 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1649 time to fit residues: 2.2910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN A1139 ASN B 18 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 13121 Z= 0.316 Angle : 0.686 11.304 17756 Z= 0.372 Chirality : 0.043 0.181 1889 Planarity : 0.004 0.060 2188 Dihedral : 9.521 172.126 1908 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.05 % Favored : 92.89 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.94 (0.22), residues: 1462 helix: -0.16 (0.19), residues: 728 sheet: -2.24 (0.51), residues: 106 loop : -2.50 (0.24), residues: 628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.2850 time to fit residues: 93.2424 Evaluate side-chains 171 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 70 optimal weight: 0.0060 chunk 15 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 overall best weight: 5.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 HIS B 20 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN B 71 ASN C 91 HIS C 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 13121 Z= 0.279 Angle : 0.642 11.786 17756 Z= 0.350 Chirality : 0.043 0.195 1889 Planarity : 0.004 0.049 2188 Dihedral : 9.309 173.280 1908 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.47 (0.22), residues: 1462 helix: 0.22 (0.20), residues: 723 sheet: -2.26 (0.49), residues: 104 loop : -2.19 (0.25), residues: 635 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2914 time to fit residues: 94.2563 Evaluate side-chains 172 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.566 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN B 47 ASN C 91 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 13121 Z= 0.287 Angle : 0.651 11.838 17756 Z= 0.355 Chirality : 0.043 0.163 1889 Planarity : 0.004 0.072 2188 Dihedral : 9.252 173.797 1908 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1462 helix: 0.37 (0.20), residues: 719 sheet: -2.58 (0.44), residues: 117 loop : -1.97 (0.25), residues: 626 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.2839 time to fit residues: 88.8932 Evaluate side-chains 172 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.517 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 144 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 HIS ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 ASN C 91 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.6261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 13121 Z= 0.355 Angle : 0.706 11.411 17756 Z= 0.387 Chirality : 0.045 0.234 1889 Planarity : 0.005 0.071 2188 Dihedral : 9.326 173.703 1908 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.41 (0.22), residues: 1462 helix: 0.26 (0.19), residues: 720 sheet: -2.63 (0.43), residues: 117 loop : -2.01 (0.25), residues: 625 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 210 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 212 average time/residue: 0.2858 time to fit residues: 85.7686 Evaluate side-chains 150 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.623 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 143 optimal weight: 0.0060 chunk 89 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN B 47 ASN C 91 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 13121 Z= 0.199 Angle : 0.631 15.958 17756 Z= 0.336 Chirality : 0.043 0.189 1889 Planarity : 0.004 0.047 2188 Dihedral : 9.120 173.771 1908 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.15 (0.22), residues: 1462 helix: 0.46 (0.20), residues: 720 sheet: -2.48 (0.44), residues: 117 loop : -1.86 (0.25), residues: 625 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.2740 time to fit residues: 83.1248 Evaluate side-chains 167 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.553 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN B 45 HIS B 47 ASN C 91 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.6704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 13121 Z= 0.302 Angle : 0.675 15.224 17756 Z= 0.363 Chirality : 0.044 0.202 1889 Planarity : 0.004 0.055 2188 Dihedral : 9.162 171.794 1908 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.14 (0.22), residues: 1462 helix: 0.40 (0.20), residues: 717 sheet: -2.50 (0.45), residues: 111 loop : -1.77 (0.25), residues: 634 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.2843 time to fit residues: 79.3854 Evaluate side-chains 157 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.643 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 1.9990 chunk 137 optimal weight: 30.0000 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN A 895 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.6801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 13121 Z= 0.193 Angle : 0.631 15.175 17756 Z= 0.332 Chirality : 0.042 0.200 1889 Planarity : 0.003 0.039 2188 Dihedral : 8.922 172.407 1908 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.23), residues: 1462 helix: 0.59 (0.20), residues: 716 sheet: -2.40 (0.45), residues: 111 loop : -1.63 (0.26), residues: 635 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2724 time to fit residues: 84.0748 Evaluate side-chains 156 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 30.0000 chunk 86 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 98 optimal weight: 0.0980 chunk 148 optimal weight: 40.0000 chunk 136 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.6983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 13121 Z= 0.192 Angle : 0.639 14.818 17756 Z= 0.334 Chirality : 0.043 0.226 1889 Planarity : 0.003 0.037 2188 Dihedral : 8.900 171.957 1908 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.84 (0.23), residues: 1462 helix: 0.63 (0.20), residues: 721 sheet: -2.34 (0.45), residues: 111 loop : -1.61 (0.26), residues: 630 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2616 time to fit residues: 80.0764 Evaluate side-chains 164 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 30.0000 chunk 103 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN B 45 HIS ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.073493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.050934 restraints weight = 57677.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050521 restraints weight = 31577.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.050869 restraints weight = 25025.197| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 13121 Z= 0.252 Angle : 0.652 15.069 17756 Z= 0.346 Chirality : 0.043 0.198 1889 Planarity : 0.004 0.042 2188 Dihedral : 8.883 170.547 1908 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1462 helix: 0.54 (0.20), residues: 733 sheet: -2.36 (0.44), residues: 113 loop : -1.61 (0.26), residues: 616 =============================================================================== Job complete usr+sys time: 2454.60 seconds wall clock time: 46 minutes 45.29 seconds (2805.29 seconds total)