Starting phenix.real_space_refine on Fri Mar 15 21:16:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmc_0446/03_2024/6nmc_0446.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmc_0446/03_2024/6nmc_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_0446/03_2024/6nmc_0446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmc_0446/03_2024/6nmc_0446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmc_0446/03_2024/6nmc_0446.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmc_0446/03_2024/6nmc_0446.pdb" } resolution = 4.24 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= 0.001 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 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. 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.20, per 1000 atoms: 0.56 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: 5.76 Conformation dependent library (CDL) restraints added in 2.1 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: 4.36 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: 4.42 Time building geometry restraints manager: 5.82 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 GLY A 477 " pdb=" N LYS A 478 " pdb=" CA LYS A 478 " ideal model delta sigma weight residual 121.70 133.39 -11.69 1.80e+00 3.09e-01 4.22e+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 ... (remaining 17751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 7688 35.60 - 71.19: 238 71.19 - 106.79: 13 106.79 - 142.38: 0 142.38 - 177.98: 1 Dihedral angle restraints: 7940 sinusoidal: 3542 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 7937 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 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: 0.350 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.810 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 39.860 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 1.162 11.689 17756 Z= 0.685 Chirality : 0.073 0.489 1889 Planarity : 0.007 0.065 2188 Dihedral : 16.981 177.976 5102 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 % Allowed : 14.04 % Favored : 83.51 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP C 100 HIS 0.008 0.002 HIS B 42 PHE 0.033 0.004 PHE A1161 TYR 0.029 0.003 TYR A 237 ARG 0.004 0.001 ARG A 508 *********************** 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 : 1.507 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 REVERT: A 81 PHE cc_start: 0.9173 (t80) cc_final: 0.8924 (t80) REVERT: A 142 ASN cc_start: 0.8986 (t0) cc_final: 0.8695 (t0) REVERT: A 173 PHE cc_start: 0.9203 (t80) cc_final: 0.8996 (t80) REVERT: A 200 HIS cc_start: 0.9264 (m-70) cc_final: 0.9020 (m-70) REVERT: A 231 GLN cc_start: 0.9530 (pt0) cc_final: 0.8739 (pp30) REVERT: A 256 ASN cc_start: 0.9400 (m-40) cc_final: 0.9065 (p0) REVERT: A 325 PHE cc_start: 0.8755 (m-80) cc_final: 0.8358 (m-80) REVERT: A 407 ASP cc_start: 0.8416 (m-30) cc_final: 0.8190 (t0) REVERT: A 420 GLN cc_start: 0.9315 (tt0) cc_final: 0.9091 (tm-30) REVERT: A 435 LEU cc_start: 0.9605 (tp) cc_final: 0.9219 (tt) REVERT: A 459 LEU cc_start: 0.9348 (mt) cc_final: 0.8923 (mm) REVERT: A 490 PHE cc_start: 0.8855 (t80) cc_final: 0.8499 (t80) REVERT: A 498 LEU cc_start: 0.9226 (mt) cc_final: 0.8527 (mt) REVERT: A 555 LEU cc_start: 0.9372 (tp) cc_final: 0.8911 (tt) REVERT: A 675 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8431 (tm-30) REVERT: A 914 LEU cc_start: 0.9523 (tp) cc_final: 0.9159 (mt) REVERT: A 1013 LEU cc_start: 0.9050 (mp) cc_final: 0.8850 (mm) REVERT: A 1035 MET cc_start: 0.8363 (ptm) cc_final: 0.7682 (ppp) REVERT: A 1049 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: A 1186 ASN cc_start: 0.8612 (m-40) cc_final: 0.8398 (m110) REVERT: A 1195 ILE cc_start: 0.9621 (mt) cc_final: 0.9393 (tp) REVERT: B 97 PHE cc_start: 0.8225 (m-10) cc_final: 0.7792 (m-10) REVERT: B 100 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.7696 (p90) REVERT: B 140 MET cc_start: 0.9227 (mmp) cc_final: 0.8907 (mmp) REVERT: B 148 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8125 (mm110) REVERT: B 152 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8615 (tptp) REVERT: C 105 ASN cc_start: 0.8370 (m-40) cc_final: 0.8104 (m-40) REVERT: C 108 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7930 (mm-30) outliers start: 33 outliers final: 9 residues processed: 385 average time/residue: 0.3107 time to fit residues: 160.7518 Evaluate side-chains 219 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 207 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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: 3.9990 chunk 116 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 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 873 HIS A 963 ASN ** A1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13121 Z= 0.185 Angle : 0.635 8.882 17756 Z= 0.344 Chirality : 0.043 0.225 1889 Planarity : 0.004 0.053 2188 Dihedral : 11.975 171.936 1978 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.34 % Favored : 94.60 % Rotamer: Outliers : 0.22 % Allowed : 3.94 % Favored : 95.84 % 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: -2.72 (0.20), residues: 1462 helix: -0.90 (0.18), residues: 723 sheet: -2.65 (0.49), residues: 111 loop : -2.70 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 100 HIS 0.003 0.001 HIS B 161 PHE 0.023 0.002 PHE A 61 TYR 0.027 0.002 TYR A 840 ARG 0.007 0.001 ARG A 883 *********************** 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 295 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 292 time to evaluate : 1.512 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: A 13 LEU cc_start: 0.9622 (tp) cc_final: 0.9396 (tt) REVERT: A 147 PHE cc_start: 0.7383 (t80) cc_final: 0.6872 (t80) REVERT: A 161 MET cc_start: 0.9054 (mtm) cc_final: 0.8812 (mtp) REVERT: A 179 ASN cc_start: 0.8864 (m110) cc_final: 0.8646 (m110) REVERT: A 200 HIS cc_start: 0.9233 (m-70) cc_final: 0.9017 (m-70) REVERT: A 231 GLN cc_start: 0.9276 (pt0) cc_final: 0.9042 (pp30) REVERT: A 235 ASP cc_start: 0.9056 (m-30) cc_final: 0.8739 (m-30) REVERT: A 256 ASN cc_start: 0.9351 (m-40) cc_final: 0.8841 (p0) REVERT: A 276 LEU cc_start: 0.9031 (mt) cc_final: 0.8324 (tp) REVERT: A 321 LEU cc_start: 0.9662 (mt) cc_final: 0.9442 (mt) REVERT: A 384 ASP cc_start: 0.9407 (t0) cc_final: 0.9153 (m-30) REVERT: A 427 LYS cc_start: 0.9640 (tmtt) cc_final: 0.9400 (tptp) REVERT: A 435 LEU cc_start: 0.9491 (tp) cc_final: 0.8910 (tt) REVERT: A 490 PHE cc_start: 0.8763 (t80) cc_final: 0.8483 (t80) REVERT: A 498 LEU cc_start: 0.9040 (mt) cc_final: 0.8777 (mt) REVERT: A 542 TYR cc_start: 0.7693 (m-80) cc_final: 0.7254 (m-80) REVERT: A 671 ARG cc_start: 0.8914 (ttm110) cc_final: 0.8602 (ttm110) REVERT: A 842 VAL cc_start: 0.9548 (t) cc_final: 0.9109 (m) REVERT: A 971 LEU cc_start: 0.9388 (mt) cc_final: 0.8835 (tp) REVERT: A 986 MET cc_start: 0.7735 (ppp) cc_final: 0.7392 (ppp) REVERT: A 1035 MET cc_start: 0.8509 (ptm) cc_final: 0.8165 (ppp) REVERT: A 1182 ASN cc_start: 0.8078 (t0) cc_final: 0.7757 (t0) REVERT: B 47 ASN cc_start: 0.8530 (p0) cc_final: 0.8312 (p0) REVERT: B 58 PHE cc_start: 0.5645 (m-80) cc_final: 0.5343 (m-80) REVERT: B 152 LYS cc_start: 0.9155 (ttmm) cc_final: 0.8946 (tptt) REVERT: C 45 HIS cc_start: 0.8043 (p-80) cc_final: 0.7814 (p-80) REVERT: C 105 ASN cc_start: 0.8316 (m-40) cc_final: 0.7902 (p0) REVERT: C 129 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7690 (mm-30) outliers start: 3 outliers final: 0 residues processed: 295 average time/residue: 0.2814 time to fit residues: 114.5725 Evaluate side-chains 203 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.616 ------------------------------------------------------------------------------- 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: 5.9990 chunk 112 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 overall best weight: 3.1584 ------------------------------------------------------------------------------- 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 279 GLN A 468 ASN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 944 GLN A1136 GLN A1139 ASN ** A1182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN C 91 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4533 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= 0.212 Angle : 0.613 8.809 17756 Z= 0.332 Chirality : 0.042 0.239 1889 Planarity : 0.004 0.058 2188 Dihedral : 11.678 172.037 1978 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.29 % Favored : 93.64 % Rotamer: Outliers : 0.15 % Allowed : 4.83 % Favored : 95.02 % 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: -1.86 (0.22), residues: 1462 helix: -0.13 (0.19), residues: 729 sheet: -2.20 (0.50), residues: 107 loop : -2.41 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 355 HIS 0.004 0.001 HIS C 42 PHE 0.024 0.002 PHE A1161 TYR 0.034 0.002 TYR C 106 ARG 0.004 0.000 ARG C 41 *********************** 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 251 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 249 time to evaluate : 1.373 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: A 13 LEU cc_start: 0.9647 (tp) cc_final: 0.9407 (tt) REVERT: A 71 LEU cc_start: 0.8859 (tp) cc_final: 0.8499 (tp) REVERT: A 162 PHE cc_start: 0.8830 (m-80) cc_final: 0.8473 (m-80) REVERT: A 179 ASN cc_start: 0.8567 (m110) cc_final: 0.8365 (m110) REVERT: A 231 GLN cc_start: 0.9336 (pt0) cc_final: 0.9066 (pp30) REVERT: A 235 ASP cc_start: 0.9058 (m-30) cc_final: 0.8815 (m-30) REVERT: A 321 LEU cc_start: 0.9660 (mt) cc_final: 0.9450 (mt) REVERT: A 350 ASP cc_start: 0.9054 (t70) cc_final: 0.8766 (t0) REVERT: A 355 TRP cc_start: 0.7399 (m-10) cc_final: 0.6887 (m-10) REVERT: A 387 LYS cc_start: 0.9421 (mmmm) cc_final: 0.9146 (ptpt) REVERT: A 390 LYS cc_start: 0.9609 (mmpt) cc_final: 0.9309 (pttm) REVERT: A 407 ASP cc_start: 0.8372 (t0) cc_final: 0.8117 (t0) REVERT: A 424 GLU cc_start: 0.9234 (tp30) cc_final: 0.8951 (tp30) REVERT: A 427 LYS cc_start: 0.9681 (tmtt) cc_final: 0.9420 (tptp) REVERT: A 461 ASP cc_start: 0.8949 (p0) cc_final: 0.8717 (p0) REVERT: A 490 PHE cc_start: 0.8844 (t80) cc_final: 0.8603 (t80) REVERT: A 498 LEU cc_start: 0.9323 (mt) cc_final: 0.8849 (mt) REVERT: A 675 GLU cc_start: 0.8887 (tp30) cc_final: 0.8505 (tp30) REVERT: A 832 ASP cc_start: 0.8319 (t0) cc_final: 0.8011 (t0) REVERT: A 971 LEU cc_start: 0.9447 (mt) cc_final: 0.9001 (tp) REVERT: A 986 MET cc_start: 0.7673 (ppp) cc_final: 0.7340 (ppp) REVERT: A 1035 MET cc_start: 0.8522 (ptm) cc_final: 0.8271 (ppp) REVERT: A 1128 MET cc_start: 0.8884 (mmp) cc_final: 0.8156 (tpp) REVERT: A 1135 LEU cc_start: 0.9300 (mm) cc_final: 0.9073 (mm) REVERT: A 1182 ASN cc_start: 0.8043 (t0) cc_final: 0.7741 (t0) REVERT: B 47 ASN cc_start: 0.8666 (p0) cc_final: 0.8397 (p0) REVERT: B 94 ASP cc_start: 0.8271 (p0) cc_final: 0.8056 (p0) REVERT: B 125 ASP cc_start: 0.8218 (p0) cc_final: 0.7676 (p0) REVERT: B 148 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8870 (mm-40) REVERT: B 152 LYS cc_start: 0.9229 (ttmm) cc_final: 0.8833 (tttm) outliers start: 2 outliers final: 0 residues processed: 250 average time/residue: 0.2768 time to fit residues: 96.5241 Evaluate side-chains 198 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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: 5.9990 chunk 101 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 142 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN C 91 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13121 Z= 0.170 Angle : 0.578 10.249 17756 Z= 0.314 Chirality : 0.042 0.199 1889 Planarity : 0.003 0.045 2188 Dihedral : 11.503 172.708 1978 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % 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: -1.49 (0.22), residues: 1462 helix: 0.21 (0.20), residues: 725 sheet: -1.95 (0.51), residues: 107 loop : -2.26 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 355 HIS 0.006 0.001 HIS C 45 PHE 0.022 0.002 PHE A 147 TYR 0.026 0.001 TYR A 840 ARG 0.004 0.000 ARG B 155 *********************** 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 260 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.567 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: A 13 LEU cc_start: 0.9588 (tp) cc_final: 0.9356 (tt) REVERT: A 71 LEU cc_start: 0.8839 (tp) cc_final: 0.8436 (tp) REVERT: A 162 PHE cc_start: 0.8897 (m-80) cc_final: 0.8463 (m-80) REVERT: A 256 ASN cc_start: 0.9383 (m110) cc_final: 0.8858 (p0) REVERT: A 321 LEU cc_start: 0.9665 (mt) cc_final: 0.9457 (mt) REVERT: A 350 ASP cc_start: 0.8976 (t70) cc_final: 0.8728 (t0) REVERT: A 355 TRP cc_start: 0.7624 (m-10) cc_final: 0.7281 (m-10) REVERT: A 390 LYS cc_start: 0.9613 (mmpt) cc_final: 0.9216 (ptpp) REVERT: A 407 ASP cc_start: 0.8443 (t0) cc_final: 0.8213 (t0) REVERT: A 427 LYS cc_start: 0.9683 (tmtt) cc_final: 0.9415 (tptp) REVERT: A 476 GLU cc_start: 0.8887 (pm20) cc_final: 0.8392 (pp20) REVERT: A 478 LYS cc_start: 0.9221 (ptpp) cc_final: 0.8711 (mtmm) REVERT: A 498 LEU cc_start: 0.9033 (mt) cc_final: 0.8688 (mt) REVERT: A 671 ARG cc_start: 0.8990 (mtm110) cc_final: 0.8732 (ttm110) REVERT: A 675 GLU cc_start: 0.8692 (tp30) cc_final: 0.8456 (tm-30) REVERT: A 832 ASP cc_start: 0.8342 (t0) cc_final: 0.8030 (t0) REVERT: A 944 GLN cc_start: 0.9164 (pt0) cc_final: 0.8744 (pt0) REVERT: A 971 LEU cc_start: 0.9437 (mt) cc_final: 0.8846 (tp) REVERT: A 986 MET cc_start: 0.7697 (ppp) cc_final: 0.7042 (ptm) REVERT: A 1035 MET cc_start: 0.8497 (ptm) cc_final: 0.8269 (ppp) REVERT: A 1128 MET cc_start: 0.8867 (mmp) cc_final: 0.8133 (tpp) REVERT: A 1135 LEU cc_start: 0.9312 (mm) cc_final: 0.9002 (mm) REVERT: A 1218 TRP cc_start: 0.9405 (t-100) cc_final: 0.9187 (t-100) REVERT: B 152 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8925 (tptt) REVERT: C 105 ASN cc_start: 0.8475 (p0) cc_final: 0.7834 (p0) REVERT: C 109 LEU cc_start: 0.8545 (mp) cc_final: 0.8248 (mp) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2869 time to fit residues: 103.6529 Evaluate side-chains 193 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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: 9.9990 chunk 81 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 263 ASN ** 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 822 HIS B 20 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13121 Z= 0.359 Angle : 0.691 9.225 17756 Z= 0.379 Chirality : 0.045 0.277 1889 Planarity : 0.004 0.073 2188 Dihedral : 11.620 171.976 1978 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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: 737 sheet: -2.21 (0.47), residues: 112 loop : -2.19 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 999 HIS 0.011 0.002 HIS C 45 PHE 0.026 0.002 PHE A1161 TYR 0.029 0.002 TYR A 840 ARG 0.005 0.001 ARG A 18 *********************** 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 232 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.529 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: A 71 LEU cc_start: 0.8902 (tp) cc_final: 0.8445 (tp) REVERT: A 161 MET cc_start: 0.9105 (mtm) cc_final: 0.8857 (mtp) REVERT: A 162 PHE cc_start: 0.8960 (m-80) cc_final: 0.8494 (m-80) REVERT: A 256 ASN cc_start: 0.9370 (m110) cc_final: 0.8883 (m-40) REVERT: A 321 LEU cc_start: 0.9669 (mt) cc_final: 0.9469 (mt) REVERT: A 350 ASP cc_start: 0.8988 (t70) cc_final: 0.8748 (t0) REVERT: A 355 TRP cc_start: 0.8074 (m-10) cc_final: 0.7609 (m-10) REVERT: A 383 ASP cc_start: 0.9300 (t70) cc_final: 0.8963 (t0) REVERT: A 384 ASP cc_start: 0.9485 (t0) cc_final: 0.8974 (m-30) REVERT: A 387 LYS cc_start: 0.8953 (ptpp) cc_final: 0.8456 (pttm) REVERT: A 427 LYS cc_start: 0.9766 (tmtt) cc_final: 0.9480 (tptp) REVERT: A 476 GLU cc_start: 0.8912 (pm20) cc_final: 0.8483 (pp20) REVERT: A 478 LYS cc_start: 0.9294 (ptpp) cc_final: 0.8780 (mtmm) REVERT: A 490 PHE cc_start: 0.8815 (t80) cc_final: 0.8600 (t80) REVERT: A 558 MET cc_start: 0.8850 (mpp) cc_final: 0.8605 (mpp) REVERT: A 671 ARG cc_start: 0.9042 (mtm110) cc_final: 0.8825 (ttm110) REVERT: A 832 ASP cc_start: 0.8704 (t0) cc_final: 0.8287 (t0) REVERT: A 944 GLN cc_start: 0.9401 (pt0) cc_final: 0.8963 (pt0) REVERT: A 986 MET cc_start: 0.7816 (ppp) cc_final: 0.7431 (ptm) REVERT: A 1035 MET cc_start: 0.8573 (ptm) cc_final: 0.7930 (ppp) REVERT: A 1128 MET cc_start: 0.8966 (mmp) cc_final: 0.8173 (tpp) REVERT: B 152 LYS cc_start: 0.9253 (ttmm) cc_final: 0.8861 (tttm) REVERT: C 105 ASN cc_start: 0.8461 (p0) cc_final: 0.7935 (p0) REVERT: C 109 LEU cc_start: 0.9076 (mp) cc_final: 0.8445 (mp) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2822 time to fit residues: 91.7126 Evaluate side-chains 171 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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: 9.9990 chunk 28 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 35 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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 399 GLN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 HIS B 47 ASN C 71 ASN C 91 HIS C 148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13121 Z= 0.215 Angle : 0.613 9.581 17756 Z= 0.333 Chirality : 0.043 0.242 1889 Planarity : 0.004 0.044 2188 Dihedral : 11.511 173.225 1978 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.15 % Allowed : 2.30 % Favored : 97.55 % 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 (0.23), residues: 1462 helix: 0.49 (0.20), residues: 731 sheet: -2.56 (0.45), residues: 117 loop : -1.93 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 999 HIS 0.012 0.001 HIS C 42 PHE 0.019 0.002 PHE A1161 TYR 0.029 0.002 TYR A 840 ARG 0.007 0.000 ARG A 385 *********************** 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 242 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 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 REVERT: A 71 LEU cc_start: 0.8721 (tp) cc_final: 0.8340 (tp) REVERT: A 161 MET cc_start: 0.9132 (mtm) cc_final: 0.8920 (mtp) REVERT: A 162 PHE cc_start: 0.8920 (m-80) cc_final: 0.8452 (m-80) REVERT: A 179 ASN cc_start: 0.9001 (m110) cc_final: 0.8747 (m110) REVERT: A 256 ASN cc_start: 0.9263 (m110) cc_final: 0.8658 (p0) REVERT: A 355 TRP cc_start: 0.8134 (m-10) cc_final: 0.7928 (m100) REVERT: A 383 ASP cc_start: 0.9348 (t70) cc_final: 0.8893 (t0) REVERT: A 384 ASP cc_start: 0.9501 (t0) cc_final: 0.8973 (m-30) REVERT: A 387 LYS cc_start: 0.9014 (ptpp) cc_final: 0.8298 (pttm) REVERT: A 407 ASP cc_start: 0.8520 (t70) cc_final: 0.8292 (t70) REVERT: A 427 LYS cc_start: 0.9751 (tmtt) cc_final: 0.9459 (tptp) REVERT: A 476 GLU cc_start: 0.8830 (pm20) cc_final: 0.8614 (pp20) REVERT: A 490 PHE cc_start: 0.8819 (t80) cc_final: 0.8581 (t80) REVERT: A 498 LEU cc_start: 0.9121 (mt) cc_final: 0.8864 (mt) REVERT: A 499 LYS cc_start: 0.9326 (mmtm) cc_final: 0.9009 (mmtm) REVERT: A 671 ARG cc_start: 0.9030 (mtm110) cc_final: 0.8802 (ttm110) REVERT: A 832 ASP cc_start: 0.8347 (t0) cc_final: 0.8018 (t0) REVERT: A 944 GLN cc_start: 0.9405 (pt0) cc_final: 0.8986 (pt0) REVERT: A 952 ASP cc_start: 0.9003 (m-30) cc_final: 0.8692 (m-30) REVERT: A 986 MET cc_start: 0.7516 (ppp) cc_final: 0.7016 (ptm) REVERT: A 1035 MET cc_start: 0.8595 (ptm) cc_final: 0.8276 (ppp) REVERT: A 1128 MET cc_start: 0.8916 (mmp) cc_final: 0.8157 (tpp) REVERT: B 20 ASN cc_start: 0.8873 (m110) cc_final: 0.8225 (m110) REVERT: B 36 GLN cc_start: 0.8791 (pt0) cc_final: 0.8460 (pt0) REVERT: B 152 LYS cc_start: 0.9257 (ttmm) cc_final: 0.8885 (tttm) REVERT: C 45 HIS cc_start: 0.7855 (p-80) cc_final: 0.7527 (p-80) outliers start: 2 outliers final: 0 residues processed: 242 average time/residue: 0.2815 time to fit residues: 96.1655 Evaluate side-chains 178 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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: 6.9990 chunk 16 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 ASN C 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13121 Z= 0.202 Angle : 0.609 9.079 17756 Z= 0.329 Chirality : 0.043 0.217 1889 Planarity : 0.003 0.039 2188 Dihedral : 11.424 173.363 1978 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.07 % Allowed : 1.41 % Favored : 98.51 % 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: -0.96 (0.23), residues: 1462 helix: 0.66 (0.20), residues: 725 sheet: -2.45 (0.47), residues: 111 loop : -1.85 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A1218 HIS 0.007 0.001 HIS C 42 PHE 0.019 0.002 PHE A1161 TYR 0.031 0.002 TYR A 494 ARG 0.004 0.000 ARG A1189 *********************** 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 232 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 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: A 71 LEU cc_start: 0.8741 (tp) cc_final: 0.8336 (tp) REVERT: A 178 GLU cc_start: 0.8933 (pm20) cc_final: 0.8378 (pm20) REVERT: A 179 ASN cc_start: 0.8737 (m110) cc_final: 0.7481 (m110) REVERT: A 256 ASN cc_start: 0.9241 (m110) cc_final: 0.8456 (p0) REVERT: A 313 GLU cc_start: 0.9090 (pm20) cc_final: 0.8878 (pm20) REVERT: A 350 ASP cc_start: 0.8855 (t70) cc_final: 0.8646 (t0) REVERT: A 383 ASP cc_start: 0.9359 (t0) cc_final: 0.9003 (t0) REVERT: A 384 ASP cc_start: 0.9535 (t0) cc_final: 0.9284 (m-30) REVERT: A 407 ASP cc_start: 0.8532 (t70) cc_final: 0.8328 (t70) REVERT: A 427 LYS cc_start: 0.9776 (tmtt) cc_final: 0.9489 (tptp) REVERT: A 558 MET cc_start: 0.9000 (mpp) cc_final: 0.8749 (mpp) REVERT: A 832 ASP cc_start: 0.8350 (t0) cc_final: 0.7964 (t0) REVERT: A 944 GLN cc_start: 0.9407 (pt0) cc_final: 0.8971 (pt0) REVERT: A 952 ASP cc_start: 0.8968 (m-30) cc_final: 0.8640 (m-30) REVERT: A 986 MET cc_start: 0.7481 (ppp) cc_final: 0.6859 (ptm) REVERT: A 1035 MET cc_start: 0.8532 (ptm) cc_final: 0.8298 (ppp) REVERT: A 1128 MET cc_start: 0.8913 (mmp) cc_final: 0.8158 (tpp) REVERT: B 36 GLN cc_start: 0.8758 (pt0) cc_final: 0.8428 (pt0) REVERT: B 47 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8345 (p0) REVERT: B 136 TYR cc_start: 0.9042 (t80) cc_final: 0.8744 (t80) REVERT: B 152 LYS cc_start: 0.9243 (ttmm) cc_final: 0.8905 (tttm) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.2697 time to fit residues: 88.5769 Evaluate side-chains 177 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 1.557 ------------------------------------------------------------------------------- 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: 0.7980 chunk 57 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 13 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN C 91 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13121 Z= 0.195 Angle : 0.613 9.191 17756 Z= 0.330 Chirality : 0.043 0.214 1889 Planarity : 0.003 0.037 2188 Dihedral : 11.379 173.504 1978 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -0.95 (0.23), residues: 1462 helix: 0.61 (0.20), residues: 737 sheet: -2.44 (0.46), residues: 111 loop : -1.81 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 999 HIS 0.010 0.001 HIS C 42 PHE 0.016 0.001 PHE A1161 TYR 0.028 0.001 TYR A 840 ARG 0.003 0.000 ARG B 155 *********************** 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 238 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.603 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: A 71 LEU cc_start: 0.8710 (tp) cc_final: 0.8308 (tp) REVERT: A 256 ASN cc_start: 0.9309 (m110) cc_final: 0.8720 (p0) REVERT: A 313 GLU cc_start: 0.9071 (pm20) cc_final: 0.8860 (pm20) REVERT: A 350 ASP cc_start: 0.8805 (t70) cc_final: 0.8567 (t0) REVERT: A 383 ASP cc_start: 0.9360 (t0) cc_final: 0.8978 (t0) REVERT: A 384 ASP cc_start: 0.9529 (t0) cc_final: 0.9288 (m-30) REVERT: A 390 LYS cc_start: 0.9618 (mmpt) cc_final: 0.9205 (ptpt) REVERT: A 427 LYS cc_start: 0.9766 (tmtt) cc_final: 0.9467 (tptp) REVERT: A 461 ASP cc_start: 0.9124 (t0) cc_final: 0.8819 (p0) REVERT: A 490 PHE cc_start: 0.8794 (t80) cc_final: 0.8562 (t80) REVERT: A 558 MET cc_start: 0.8978 (mpp) cc_final: 0.8673 (mpp) REVERT: A 832 ASP cc_start: 0.8242 (t0) cc_final: 0.7833 (t0) REVERT: A 835 GLU cc_start: 0.7830 (mp0) cc_final: 0.7504 (mp0) REVERT: A 944 GLN cc_start: 0.9410 (pt0) cc_final: 0.8962 (pt0) REVERT: A 952 ASP cc_start: 0.8914 (m-30) cc_final: 0.8622 (m-30) REVERT: A 986 MET cc_start: 0.7401 (ppp) cc_final: 0.6745 (ptm) REVERT: A 1035 MET cc_start: 0.8534 (ptm) cc_final: 0.8239 (ppp) REVERT: A 1128 MET cc_start: 0.8884 (mmp) cc_final: 0.8204 (tpp) REVERT: B 130 LEU cc_start: 0.9369 (mt) cc_final: 0.8476 (mt) REVERT: B 152 LYS cc_start: 0.9270 (ttmm) cc_final: 0.8928 (tttm) REVERT: C 86 PHE cc_start: 0.6564 (p90) cc_final: 0.6356 (p90) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.3091 time to fit residues: 104.9423 Evaluate side-chains 181 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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: 0.0010 chunk 137 optimal weight: 30.0000 chunk 125 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 overall best weight: 5.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN B 36 GLN B 47 ASN C 91 HIS C 148 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.6601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13121 Z= 0.293 Angle : 0.678 8.975 17756 Z= 0.370 Chirality : 0.045 0.228 1889 Planarity : 0.004 0.063 2188 Dihedral : 11.500 172.545 1978 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.07 % Allowed : 0.67 % Favored : 99.26 % 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: -0.97 (0.23), residues: 1462 helix: 0.60 (0.20), residues: 728 sheet: -2.50 (0.46), residues: 113 loop : -1.77 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1086 HIS 0.007 0.001 HIS C 45 PHE 0.021 0.002 PHE A1161 TYR 0.035 0.002 TYR A 840 ARG 0.004 0.001 ARG C 41 *********************** 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 218 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 1.505 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: A 71 LEU cc_start: 0.8842 (tp) cc_final: 0.8493 (tp) REVERT: A 179 ASN cc_start: 0.8794 (m110) cc_final: 0.8592 (m110) REVERT: A 256 ASN cc_start: 0.9248 (m110) cc_final: 0.8644 (p0) REVERT: A 313 GLU cc_start: 0.9222 (pm20) cc_final: 0.8896 (pm20) REVERT: A 350 ASP cc_start: 0.8878 (t70) cc_final: 0.8649 (t0) REVERT: A 384 ASP cc_start: 0.9541 (t0) cc_final: 0.9181 (m-30) REVERT: A 387 LYS cc_start: 0.9119 (ptpp) cc_final: 0.8832 (pttm) REVERT: A 427 LYS cc_start: 0.9772 (tmtt) cc_final: 0.9511 (tptp) REVERT: A 461 ASP cc_start: 0.9127 (t0) cc_final: 0.8897 (p0) REVERT: A 490 PHE cc_start: 0.8862 (t80) cc_final: 0.8565 (t80) REVERT: A 558 MET cc_start: 0.9049 (mpp) cc_final: 0.8695 (mpp) REVERT: A 832 ASP cc_start: 0.8585 (t0) cc_final: 0.8137 (t0) REVERT: A 944 GLN cc_start: 0.9461 (pt0) cc_final: 0.8988 (pt0) REVERT: A 952 ASP cc_start: 0.8989 (m-30) cc_final: 0.8662 (m-30) REVERT: A 986 MET cc_start: 0.7374 (ppp) cc_final: 0.6729 (ptm) REVERT: A 1035 MET cc_start: 0.8600 (ptm) cc_final: 0.7875 (ppp) REVERT: A 1128 MET cc_start: 0.8860 (mmp) cc_final: 0.8423 (tpp) REVERT: B 20 ASN cc_start: 0.8729 (m110) cc_final: 0.8226 (m-40) REVERT: B 94 ASP cc_start: 0.8480 (p0) cc_final: 0.8235 (p0) REVERT: B 152 LYS cc_start: 0.9270 (ttmm) cc_final: 0.8915 (tttm) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.2685 time to fit residues: 83.2431 Evaluate side-chains 175 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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: 5.9990 chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** 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: 0.7982 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 13121 Z= 0.198 Angle : 0.616 9.251 17756 Z= 0.331 Chirality : 0.043 0.192 1889 Planarity : 0.003 0.035 2188 Dihedral : 11.349 173.481 1978 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.07 % Allowed : 0.37 % Favored : 99.55 % 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: -0.83 (0.23), residues: 1462 helix: 0.67 (0.20), residues: 732 sheet: -2.41 (0.45), residues: 113 loop : -1.66 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 100 HIS 0.012 0.001 HIS C 42 PHE 0.019 0.001 PHE C 101 TYR 0.027 0.001 TYR B 136 ARG 0.005 0.000 ARG B 155 ********************** 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 225 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 1.599 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: A 71 LEU cc_start: 0.8751 (tp) cc_final: 0.8407 (tp) REVERT: A 256 ASN cc_start: 0.9298 (m110) cc_final: 0.8687 (p0) REVERT: A 313 GLU cc_start: 0.9154 (pm20) cc_final: 0.8860 (pm20) REVERT: A 350 ASP cc_start: 0.8846 (t70) cc_final: 0.8571 (t0) REVERT: A 383 ASP cc_start: 0.9361 (t0) cc_final: 0.8999 (t0) REVERT: A 384 ASP cc_start: 0.9544 (t0) cc_final: 0.9336 (m-30) REVERT: A 427 LYS cc_start: 0.9758 (tmtt) cc_final: 0.9475 (tptp) REVERT: A 469 TYR cc_start: 0.8971 (t80) cc_final: 0.8720 (t80) REVERT: A 490 PHE cc_start: 0.8898 (t80) cc_final: 0.8549 (t80) REVERT: A 558 MET cc_start: 0.9033 (mpp) cc_final: 0.8640 (mpp) REVERT: A 832 ASP cc_start: 0.8312 (t0) cc_final: 0.7954 (t0) REVERT: A 944 GLN cc_start: 0.9401 (pt0) cc_final: 0.8922 (pt0) REVERT: A 952 ASP cc_start: 0.8913 (m-30) cc_final: 0.8579 (m-30) REVERT: A 986 MET cc_start: 0.7178 (ppp) cc_final: 0.6515 (ptm) REVERT: A 1035 MET cc_start: 0.8573 (ptm) cc_final: 0.8239 (ppp) REVERT: A 1128 MET cc_start: 0.8874 (mmp) cc_final: 0.8452 (tpp) REVERT: B 152 LYS cc_start: 0.9242 (ttmm) cc_final: 0.8889 (tttm) REVERT: B 164 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8523 (mm-40) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.2592 time to fit residues: 83.4222 Evaluate side-chains 178 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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: 8.9990 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 103 optimal weight: 0.4980 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN B 47 ASN C 71 ASN C 91 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.072982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.050226 restraints weight = 58171.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.049609 restraints weight = 34513.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.049977 restraints weight = 25414.475| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.6843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13121 Z= 0.297 Angle : 0.677 9.227 17756 Z= 0.369 Chirality : 0.045 0.315 1889 Planarity : 0.004 0.067 2188 Dihedral : 11.483 172.250 1978 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.07 % Allowed : 0.37 % Favored : 99.55 % 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: -0.92 (0.23), residues: 1462 helix: 0.60 (0.20), residues: 737 sheet: -2.48 (0.45), residues: 113 loop : -1.72 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1086 HIS 0.006 0.001 HIS C 42 PHE 0.020 0.002 PHE A1161 TYR 0.019 0.002 TYR B 12 ARG 0.004 0.001 ARG A 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2652.18 seconds wall clock time: 49 minutes 7.46 seconds (2947.46 seconds total)