Starting phenix.real_space_refine on Sat Dec 9 10:57:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtf_0064/12_2023/6gtf_0064.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtf_0064/12_2023/6gtf_0064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtf_0064/12_2023/6gtf_0064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtf_0064/12_2023/6gtf_0064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtf_0064/12_2023/6gtf_0064.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtf_0064/12_2023/6gtf_0064.pdb" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 66 5.49 5 S 17 5.16 5 C 6602 2.51 5 N 1908 2.21 5 O 2278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A TYR 822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1081": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1185": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10871 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 9496 Classifications: {'peptide': 1280} Incomplete info: {'backbone_only': 239, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 28, 'TRANS': 1251} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1576 Unresolved non-hydrogen dihedrals: 714 Unresolved non-hydrogen chiralities: 310 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 17, 'TRP:plan': 1, 'ASP:plan': 25, 'PHE:plan': 14, 'GLU:plan': 23, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 545 Chain: "B" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 616 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 10} Link IDs: {'rna2p': 8, 'rna3p': 20} Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 427 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 6.52, per 1000 atoms: 0.60 Number of scatterers: 10871 At special positions: 0 Unit cell: (100.672, 133.12, 103.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 66 15.00 O 2278 8.00 N 1908 7.00 C 6602 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: 4.70 Conformation dependent library (CDL) restraints added in 2.0 seconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 4 sheets defined 35.9% alpha, 4.1% beta 4 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 removed outlier: 4.069A pdb=" N ARG A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.540A pdb=" N ILE A 65 " --> pdb=" O ILE A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 74 through 89 removed outlier: 3.848A pdb=" N VAL A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 114 removed outlier: 3.705A pdb=" N GLN A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.617A pdb=" N LEU A 122 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 123' Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.895A pdb=" N ASN A 148 " --> pdb=" O GLN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 removed outlier: 3.604A pdb=" N ILE A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.738A pdb=" N ARG A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 187 " --> pdb=" O HIS A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 182 through 187' Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.564A pdb=" N LYS A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 313 through 319 removed outlier: 3.744A pdb=" N LYS A 317 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 4.147A pdb=" N MET A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.903A pdb=" N ASP A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.827A pdb=" N GLU A 419 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 removed outlier: 3.851A pdb=" N GLU A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 4.173A pdb=" N ALA A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 493 removed outlier: 3.503A pdb=" N GLU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.967A pdb=" N GLN A 507 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 522 Processing helix chain 'A' and resid 523 through 528 removed outlier: 3.629A pdb=" N ASP A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 539 through 544 removed outlier: 4.346A pdb=" N ILE A 542 " --> pdb=" O LYS A 539 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 543 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A 544 " --> pdb=" O LYS A 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 539 through 544' Processing helix chain 'A' and resid 561 through 572 removed outlier: 3.519A pdb=" N GLU A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.577A pdb=" N ASN A 638 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 removed outlier: 3.503A pdb=" N ILE A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 673 removed outlier: 3.814A pdb=" N PHE A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.600A pdb=" N TYR A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.543A pdb=" N LEU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 693 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 728 removed outlier: 5.370A pdb=" N PHE A 720 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'A' and resid 755 through 760 Processing helix chain 'A' and resid 770 through 779 removed outlier: 3.677A pdb=" N ILE A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 4.588A pdb=" N PHE A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.257A pdb=" N SER A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 907 removed outlier: 3.964A pdb=" N LEU A 902 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 954 No H-bonds generated for 'chain 'A' and resid 952 through 954' Processing helix chain 'A' and resid 955 through 962 removed outlier: 3.646A pdb=" N ILE A 960 " --> pdb=" O LYS A 956 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 999 removed outlier: 3.847A pdb=" N MET A 980 " --> pdb=" O ASN A 976 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU A 982 " --> pdb=" O LYS A 978 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLN A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 988 " --> pdb=" O TYR A 984 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 989 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N HIS A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 995 " --> pdb=" O GLU A 991 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 996 " --> pdb=" O ILE A 992 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1033 removed outlier: 3.593A pdb=" N LYS A1029 " --> pdb=" O GLN A1025 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1110 removed outlier: 3.710A pdb=" N GLN A1106 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1181 removed outlier: 3.655A pdb=" N GLU A1175 " --> pdb=" O THR A1171 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS A1176 " --> pdb=" O LYS A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1197 removed outlier: 4.269A pdb=" N ILE A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1212 removed outlier: 3.791A pdb=" N LYS A1206 " --> pdb=" O LYS A1202 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A1207 " --> pdb=" O PHE A1203 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER A1209 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A1210 " --> pdb=" O LYS A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1275 removed outlier: 4.113A pdb=" N HIS A1261 " --> pdb=" O ASN A1257 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A1262 " --> pdb=" O GLY A1258 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY A1263 " --> pdb=" O ALA A1259 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1269 " --> pdb=" O LYS A1265 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN A1275 " --> pdb=" O GLY A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1295 removed outlier: 4.525A pdb=" N GLU A1293 " --> pdb=" O GLU A1289 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A1295 " --> pdb=" O TYR A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing sheet with id=AA1, first strand: chain 'A' and resid 596 through 598 removed outlier: 4.029A pdb=" N PHE A 596 " --> pdb=" O TYR A 832 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU A 830 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 878 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 11.970A pdb=" N ALA A 619 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N TYR A 659 " --> pdb=" O ALA A 619 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU A 621 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 657 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 912 through 913 removed outlier: 6.582A pdb=" N HIS A 912 " --> pdb=" O ILE A1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 927 through 928 Processing sheet with id=AA4, first strand: chain 'A' and resid 1125 through 1129 removed outlier: 3.562A pdb=" N ILE A1144 " --> pdb=" O PHE A1126 " (cutoff:3.500A) 198 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 12 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2010 1.32 - 1.44: 3170 1.44 - 1.57: 5874 1.57 - 1.69: 129 1.69 - 1.81: 27 Bond restraints: 11210 Sorted by residual: bond pdb=" CB TRP A 808 " pdb=" CG TRP A 808 " ideal model delta sigma weight residual 1.498 1.392 0.106 3.10e-02 1.04e+03 1.17e+01 bond pdb=" CB ARG A 18 " pdb=" CG ARG A 18 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.92e+00 bond pdb=" CB PHE A 941 " pdb=" CG PHE A 941 " ideal model delta sigma weight residual 1.502 1.447 0.055 2.30e-02 1.89e+03 5.74e+00 bond pdb=" C1' DC C 4 " pdb=" N1 DC C 4 " ideal model delta sigma weight residual 1.490 1.420 0.070 3.00e-02 1.11e+03 5.44e+00 bond pdb=" CB GLN A 24 " pdb=" CG GLN A 24 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.28e+00 ... (remaining 11205 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.12: 393 105.12 - 112.45: 5110 112.45 - 119.78: 4418 119.78 - 127.11: 5153 127.11 - 134.44: 198 Bond angle restraints: 15272 Sorted by residual: angle pdb=" C GLN A1245 " pdb=" N ALA A1246 " pdb=" CA ALA A1246 " ideal model delta sigma weight residual 120.94 134.44 -13.50 1.90e+00 2.77e-01 5.05e+01 angle pdb=" C GLY A 892 " pdb=" N ALA A 893 " pdb=" CA ALA A 893 " ideal model delta sigma weight residual 122.35 130.65 -8.30 1.46e+00 4.69e-01 3.23e+01 angle pdb=" N PHE A 211 " pdb=" CA PHE A 211 " pdb=" C PHE A 211 " ideal model delta sigma weight residual 114.75 108.13 6.62 1.26e+00 6.30e-01 2.76e+01 angle pdb=" CA GLU A 41 " pdb=" CB GLU A 41 " pdb=" CG GLU A 41 " ideal model delta sigma weight residual 114.10 124.31 -10.21 2.00e+00 2.50e-01 2.61e+01 angle pdb=" N VAL A 253 " pdb=" CA VAL A 253 " pdb=" C VAL A 253 " ideal model delta sigma weight residual 110.05 104.77 5.28 1.09e+00 8.42e-01 2.35e+01 ... (remaining 15267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.78: 5633 18.78 - 37.56: 450 37.56 - 56.34: 182 56.34 - 75.11: 51 75.11 - 93.89: 12 Dihedral angle restraints: 6328 sinusoidal: 3013 harmonic: 3315 Sorted by residual: dihedral pdb=" CA ASP A1227 " pdb=" C ASP A1227 " pdb=" N TYR A1228 " pdb=" CA TYR A1228 " ideal model delta harmonic sigma weight residual 180.00 -147.66 -32.34 0 5.00e+00 4.00e-02 4.18e+01 dihedral pdb=" CA LYS A1084 " pdb=" C LYS A1084 " pdb=" N ILE A1085 " pdb=" CA ILE A1085 " ideal model delta harmonic sigma weight residual -180.00 -148.64 -31.36 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA ASP A 40 " pdb=" C ASP A 40 " pdb=" N GLU A 41 " pdb=" CA GLU A 41 " ideal model delta harmonic sigma weight residual -180.00 -149.10 -30.90 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 6325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1123 0.069 - 0.138: 342 0.138 - 0.207: 52 0.207 - 0.276: 5 0.276 - 0.344: 3 Chirality restraints: 1525 Sorted by residual: chirality pdb=" C1' U B -16 " pdb=" O4' U B -16 " pdb=" C2' U B -16 " pdb=" N1 U B -16 " both_signs ideal model delta sigma weight residual False 2.47 2.12 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB ILE A 974 " pdb=" CA ILE A 974 " pdb=" CG1 ILE A 974 " pdb=" CG2 ILE A 974 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CG LEU A 914 " pdb=" CB LEU A 914 " pdb=" CD1 LEU A 914 " pdb=" CD2 LEU A 914 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1522 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 669 " -0.061 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO A 670 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1231 " 0.050 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO A1232 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A1232 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1232 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C B -11 " -0.036 2.00e-02 2.50e+03 1.92e-02 8.27e+00 pdb=" N1 C B -11 " 0.042 2.00e-02 2.50e+03 pdb=" C2 C B -11 " 0.007 2.00e-02 2.50e+03 pdb=" O2 C B -11 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C B -11 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C B -11 " -0.010 2.00e-02 2.50e+03 pdb=" N4 C B -11 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C B -11 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C B -11 " 0.006 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 211 2.60 - 3.18: 9059 3.18 - 3.75: 16871 3.75 - 4.33: 23040 4.33 - 4.90: 35787 Nonbonded interactions: 84968 Sorted by model distance: nonbonded pdb=" OE2 GLU A 920 " pdb=" OH TYR A1024 " model vdw 2.030 2.440 nonbonded pdb=" OE2 GLU A 594 " pdb=" N LYS A 834 " model vdw 2.101 2.520 nonbonded pdb=" N ALA A 665 " pdb=" OE2 GLU A 758 " model vdw 2.111 2.520 nonbonded pdb=" OP2 A B -18 " pdb=" N4 C B -11 " model vdw 2.121 2.520 nonbonded pdb=" NZ LYS A1221 " pdb=" OD2 ASP A1227 " model vdw 2.186 2.520 ... (remaining 84963 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: 0.580 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: 3.440 Check model and map are aligned: 0.170 Set scattering table: 0.090 Process input model: 35.290 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.106 11210 Z= 0.590 Angle : 1.173 14.437 15272 Z= 0.651 Chirality : 0.065 0.344 1525 Planarity : 0.007 0.092 1810 Dihedral : 16.898 93.892 4348 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.54 % Favored : 84.46 % Rotamer: Outliers : 0.43 % Allowed : 5.17 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -5.84 (0.17), residues: 1274 helix: -4.50 (0.11), residues: 458 sheet: -3.90 (0.40), residues: 106 loop : -3.52 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP A1142 HIS 0.018 0.004 HIS A 881 PHE 0.036 0.004 PHE A 596 TYR 0.046 0.004 TYR A 178 ARG 0.012 0.002 ARG A 833 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 1.194 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: 4 outliers final: 1 residues processed: 216 average time/residue: 0.3156 time to fit residues: 89.0431 Evaluate side-chains 128 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1070 time to fit residues: 1.6991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 10.0000 chunk 100 optimal weight: 0.0570 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 40.0000 chunk 63 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN A 271 ASN A 301 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN A 694 HIS A 697 HIS A 759 ASN A 779 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS A 835 GLN A 843 HIS A 887 ASN A 922 HIS A 942 ASN A 952 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN A1043 ASN A1239 ASN ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11210 Z= 0.206 Angle : 0.673 7.124 15272 Z= 0.370 Chirality : 0.045 0.315 1525 Planarity : 0.005 0.069 1810 Dihedral : 19.509 101.493 2161 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 2.26 % Allowed : 12.82 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.02 (0.19), residues: 1274 helix: -3.53 (0.16), residues: 496 sheet: -3.48 (0.42), residues: 106 loop : -3.17 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 175 HIS 0.003 0.001 HIS A 183 PHE 0.013 0.002 PHE A 622 TYR 0.036 0.002 TYR A1099 ARG 0.004 0.000 ARG A1053 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 1.227 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 outliers start: 21 outliers final: 11 residues processed: 167 average time/residue: 0.2877 time to fit residues: 64.8629 Evaluate side-chains 130 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1318 time to fit residues: 4.0924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.0770 chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 40.0000 chunk 120 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 41 optimal weight: 40.0000 chunk 97 optimal weight: 0.7980 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 24 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN A 938 GLN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11210 Z= 0.199 Angle : 0.625 9.233 15272 Z= 0.340 Chirality : 0.043 0.268 1525 Planarity : 0.004 0.060 1810 Dihedral : 19.135 99.134 2161 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 2.16 % Allowed : 15.30 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.20), residues: 1274 helix: -2.93 (0.19), residues: 503 sheet: -3.35 (0.43), residues: 105 loop : -3.10 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 175 HIS 0.005 0.001 HIS A 183 PHE 0.024 0.002 PHE A 888 TYR 0.030 0.002 TYR A1099 ARG 0.004 0.000 ARG A 746 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 147 average time/residue: 0.2702 time to fit residues: 55.0241 Evaluate side-chains 125 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1804 time to fit residues: 4.6495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 30.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11210 Z= 0.385 Angle : 0.775 9.012 15272 Z= 0.416 Chirality : 0.049 0.339 1525 Planarity : 0.005 0.062 1810 Dihedral : 19.336 101.371 2161 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer: Outliers : 3.34 % Allowed : 16.16 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.21), residues: 1274 helix: -2.74 (0.19), residues: 509 sheet: -3.71 (0.40), residues: 105 loop : -3.14 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 175 HIS 0.010 0.002 HIS A 183 PHE 0.022 0.003 PHE A 888 TYR 0.027 0.003 TYR A 659 ARG 0.005 0.001 ARG A 833 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 1.317 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: 31 outliers final: 16 residues processed: 140 average time/residue: 0.2604 time to fit residues: 50.8912 Evaluate side-chains 129 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1054 time to fit residues: 4.6335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 88 optimal weight: 0.0370 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN A 856 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11210 Z= 0.183 Angle : 0.606 7.375 15272 Z= 0.331 Chirality : 0.043 0.273 1525 Planarity : 0.004 0.047 1810 Dihedral : 18.977 94.983 2161 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 1.94 % Allowed : 18.86 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.21), residues: 1274 helix: -2.34 (0.20), residues: 505 sheet: -3.54 (0.41), residues: 104 loop : -2.92 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 808 HIS 0.004 0.001 HIS A 697 PHE 0.011 0.001 PHE A 264 TYR 0.029 0.002 TYR A 773 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.190 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: 18 outliers final: 6 residues processed: 135 average time/residue: 0.2502 time to fit residues: 47.7507 Evaluate side-chains 114 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1005 time to fit residues: 2.8047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 50.0000 chunk 115 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 0.0470 chunk 67 optimal weight: 9.9990 overall best weight: 2.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11210 Z= 0.210 Angle : 0.606 8.550 15272 Z= 0.330 Chirality : 0.043 0.272 1525 Planarity : 0.003 0.040 1810 Dihedral : 18.798 92.898 2161 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 2.16 % Allowed : 21.34 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.21), residues: 1274 helix: -2.05 (0.21), residues: 509 sheet: -3.37 (0.42), residues: 102 loop : -2.92 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 175 HIS 0.004 0.001 HIS A1261 PHE 0.012 0.001 PHE A 888 TYR 0.027 0.002 TYR A 773 ARG 0.004 0.000 ARG A 833 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 134 average time/residue: 0.2575 time to fit residues: 48.0394 Evaluate side-chains 119 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1393 time to fit residues: 3.4777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 0.0020 overall best weight: 1.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11210 Z= 0.185 Angle : 0.594 9.161 15272 Z= 0.321 Chirality : 0.043 0.261 1525 Planarity : 0.003 0.034 1810 Dihedral : 18.640 90.815 2161 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.75 % Allowed : 22.84 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.22), residues: 1274 helix: -1.75 (0.22), residues: 493 sheet: -3.04 (0.44), residues: 98 loop : -2.78 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 175 HIS 0.003 0.001 HIS A 881 PHE 0.010 0.001 PHE A 888 TYR 0.027 0.002 TYR A 773 ARG 0.003 0.000 ARG A 746 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.289 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: 7 outliers final: 4 residues processed: 125 average time/residue: 0.2612 time to fit residues: 45.9996 Evaluate side-chains 116 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.123 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1106 time to fit residues: 2.9197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 50.0000 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN A 835 GLN A 856 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11210 Z= 0.249 Angle : 0.644 10.921 15272 Z= 0.343 Chirality : 0.045 0.285 1525 Planarity : 0.003 0.035 1810 Dihedral : 18.621 94.343 2161 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 1.08 % Allowed : 22.31 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.22), residues: 1274 helix: -1.65 (0.23), residues: 486 sheet: -3.08 (0.43), residues: 102 loop : -2.76 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 808 HIS 0.005 0.001 HIS A1261 PHE 0.017 0.002 PHE A 596 TYR 0.023 0.002 TYR A 112 ARG 0.005 0.001 ARG A 833 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 1.190 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: 10 outliers final: 7 residues processed: 119 average time/residue: 0.2520 time to fit residues: 42.8579 Evaluate side-chains 115 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1555 time to fit residues: 3.2039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 52 optimal weight: 40.0000 chunk 93 optimal weight: 0.0170 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 overall best weight: 1.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11210 Z= 0.179 Angle : 0.586 10.127 15272 Z= 0.314 Chirality : 0.043 0.263 1525 Planarity : 0.003 0.033 1810 Dihedral : 18.460 89.386 2161 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.11 % Allowed : 23.49 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.22), residues: 1274 helix: -1.44 (0.23), residues: 491 sheet: -2.86 (0.44), residues: 105 loop : -2.67 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1142 HIS 0.004 0.001 HIS A1261 PHE 0.013 0.001 PHE A 596 TYR 0.044 0.002 TYR A 773 ARG 0.003 0.000 ARG A 833 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 1.264 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: 1 outliers final: 1 residues processed: 117 average time/residue: 0.2815 time to fit residues: 46.6648 Evaluate side-chains 109 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1051 time to fit residues: 1.8710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 105 optimal weight: 0.0070 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11210 Z= 0.186 Angle : 0.597 10.152 15272 Z= 0.322 Chirality : 0.043 0.256 1525 Planarity : 0.003 0.038 1810 Dihedral : 18.407 88.819 2161 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.32 % Allowed : 23.49 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.23), residues: 1274 helix: -1.31 (0.24), residues: 493 sheet: -2.79 (0.44), residues: 105 loop : -2.66 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP A 141 HIS 0.004 0.001 HIS A1261 PHE 0.013 0.001 PHE A 596 TYR 0.030 0.002 TYR A 112 ARG 0.004 0.000 ARG A 833 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.423 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: 3 outliers final: 3 residues processed: 117 average time/residue: 0.2588 time to fit residues: 42.9823 Evaluate side-chains 111 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2097 time to fit residues: 2.5400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 30.0000 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 40.0000 chunk 108 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 92 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.154635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.127113 restraints weight = 24412.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.127467 restraints weight = 13307.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.128596 restraints weight = 11011.261| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11210 Z= 0.192 Angle : 0.602 10.235 15272 Z= 0.323 Chirality : 0.042 0.259 1525 Planarity : 0.003 0.036 1810 Dihedral : 18.365 88.409 2161 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.43 % Allowed : 23.92 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.23), residues: 1274 helix: -1.26 (0.24), residues: 494 sheet: -2.72 (0.44), residues: 105 loop : -2.64 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 141 HIS 0.006 0.001 HIS A 58 PHE 0.014 0.001 PHE A 753 TYR 0.038 0.002 TYR A 248 ARG 0.006 0.000 ARG A 746 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2135.62 seconds wall clock time: 40 minutes 0.70 seconds (2400.70 seconds total)