Starting phenix.real_space_refine on Sun Jul 21 17:47:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsn_36624/07_2024/8jsn_36624_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsn_36624/07_2024/8jsn_36624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsn_36624/07_2024/8jsn_36624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsn_36624/07_2024/8jsn_36624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsn_36624/07_2024/8jsn_36624_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsn_36624/07_2024/8jsn_36624_neut.cif" } resolution = 3.4 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= 0.001 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 Zn 1 6.06 5 P 10 5.49 5 S 76 5.16 5 C 9442 2.51 5 N 2512 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14856 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1362, 10897 Classifications: {'peptide': 1362} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 70, 'TRANS': 1289} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1989 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2015 Chain: "C" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 737 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 511 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 509 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9157 SG CYS A1150 49.587 45.472 97.801 1.00111.98 S ATOM 9179 SG CYS A1153 52.209 42.626 97.805 1.00122.87 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER B 266 " occ=0.31 ... (10 atoms not shown) pdb=" OG BSER B 266 " occ=0.69 Time building chain proxies: 9.92, per 1000 atoms: 0.67 Number of scatterers: 14856 At special positions: 0 Unit cell: (180.94, 133.63, 113.71, 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) Zn 1 29.99 S 76 16.00 P 10 15.00 O 2815 8.00 N 2512 7.00 C 9442 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: 5.77 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A1347 " pdb="ZN ZN A2301 " - pdb=" ND1 HIS A1345 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1153 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1150 " Number of angles added : 1 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3546 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 8 sheets defined 58.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.727A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.871A pdb=" N LYS A 54 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 72 through 75 removed outlier: 3.666A pdb=" N PHE A 75 " --> pdb=" O PRO A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 76 through 83 Processing helix chain 'A' and resid 100 through 122 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 145 through 163 removed outlier: 3.832A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 214 through 223 removed outlier: 3.620A pdb=" N LYS A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 261 removed outlier: 3.504A pdb=" N ILE A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 317 through 334 Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 361 through 369 Processing helix chain 'A' and resid 381 through 391 removed outlier: 3.551A pdb=" N ALA A 385 " --> pdb=" O HIS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 422 removed outlier: 3.518A pdb=" N ILE A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 457 through 464 removed outlier: 3.501A pdb=" N HIS A 463 " --> pdb=" O GLU A 460 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 464 " --> pdb=" O PHE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 498 removed outlier: 3.655A pdb=" N TRP A 494 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASP A 495 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A 497 " --> pdb=" O TRP A 494 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 498 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.752A pdb=" N LEU A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.617A pdb=" N LEU A 542 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 584 removed outlier: 3.676A pdb=" N ASP A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.969A pdb=" N GLU A 600 " --> pdb=" O THR A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 610 Processing helix chain 'A' and resid 636 through 640 removed outlier: 3.686A pdb=" N PHE A 640 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 Proline residue: A 647 - end of helix removed outlier: 3.590A pdb=" N TYR A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 712 through 731 Processing helix chain 'A' and resid 759 through 783 removed outlier: 4.251A pdb=" N GLN A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 820 removed outlier: 3.600A pdb=" N THR A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 850 removed outlier: 3.853A pdb=" N GLU A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 875 removed outlier: 3.533A pdb=" N ARG A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 889 removed outlier: 3.928A pdb=" N LEU A 888 " --> pdb=" O ASP A 884 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 889' Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 927 through 943 removed outlier: 3.503A pdb=" N ILE A 943 " --> pdb=" O TYR A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 955 removed outlier: 4.235A pdb=" N LYS A 955 " --> pdb=" O PRO A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'A' and resid 974 through 978 removed outlier: 3.623A pdb=" N GLN A 978 " --> pdb=" O PRO A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 994 removed outlier: 3.701A pdb=" N LEU A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1005 removed outlier: 3.510A pdb=" N LEU A1004 " --> pdb=" O LEU A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1021 Processing helix chain 'A' and resid 1027 through 1036 removed outlier: 3.789A pdb=" N ALA A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1048 Processing helix chain 'A' and resid 1052 through 1059 Processing helix chain 'A' and resid 1059 through 1064 Processing helix chain 'A' and resid 1069 through 1085 removed outlier: 3.559A pdb=" N ARG A1073 " --> pdb=" O PRO A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1101 removed outlier: 4.085A pdb=" N ALA A1099 " --> pdb=" O ILE A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1134 through 1138 Processing helix chain 'A' and resid 1150 through 1155 Processing helix chain 'A' and resid 1182 through 1184 No H-bonds generated for 'chain 'A' and resid 1182 through 1184' Processing helix chain 'A' and resid 1213 through 1230 Processing helix chain 'A' and resid 1235 through 1245 removed outlier: 3.817A pdb=" N ILE A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS A1241 " --> pdb=" O ASP A1237 " (cutoff:3.500A) Proline residue: A1242 - end of helix Processing helix chain 'A' and resid 1266 through 1273 removed outlier: 3.676A pdb=" N ARG A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1290 removed outlier: 3.556A pdb=" N THR A1290 " --> pdb=" O ASN A1287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1287 through 1290' Processing helix chain 'A' and resid 1296 through 1300 Processing helix chain 'A' and resid 1315 through 1331 Processing helix chain 'B' and resid 82 through 119 Processing helix chain 'B' and resid 123 through 149 removed outlier: 3.557A pdb=" N THR B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.608A pdb=" N ALA B 164 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 removed outlier: 3.517A pdb=" N SER B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 220 through 231 removed outlier: 3.764A pdb=" N HIS B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 254 removed outlier: 3.752A pdb=" N GLN B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 removed outlier: 3.524A pdb=" N ILE B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 270 " --> pdb=" O ASER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.724A pdb=" N GLN B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS B 309 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 116 removed outlier: 4.525A pdb=" N ASN C 116 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 143 removed outlier: 3.909A pdb=" N ASP C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 165 Processing helix chain 'D' and resid 83 through 112 Processing helix chain 'D' and resid 113 through 117 removed outlier: 3.883A pdb=" N ASN D 116 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 146 removed outlier: 3.875A pdb=" N TYR D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP D 123 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N MET D 124 " --> pdb=" O PRO D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 117 Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.547A pdb=" N TYR E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 removed outlier: 3.565A pdb=" N VAL C 146 " --> pdb=" O TYR B 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 549 through 552 Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 740 removed outlier: 3.938A pdb=" N LYS A 734 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 801 Processing sheet with id=AA6, first strand: chain 'A' and resid 1139 through 1141 Processing sheet with id=AA7, first strand: chain 'A' and resid 1175 through 1176 removed outlier: 4.113A pdb=" N SER A1175 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 296 745 hydrogen bonds defined for protein. 2134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 6.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4639 1.34 - 1.46: 2192 1.46 - 1.57: 8248 1.57 - 1.69: 19 1.69 - 1.81: 111 Bond restraints: 15209 Sorted by residual: bond pdb=" C ALA B 291 " pdb=" N PRO B 292 " ideal model delta sigma weight residual 1.331 1.370 -0.039 8.70e-03 1.32e+04 1.97e+01 bond pdb=" CA PRO B 292 " pdb=" C PRO B 292 " ideal model delta sigma weight residual 1.514 1.538 -0.024 5.50e-03 3.31e+04 1.93e+01 bond pdb=" N VAL B 294 " pdb=" CA VAL B 294 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.27e-02 6.20e+03 8.00e+00 bond pdb=" C PRO B 292 " pdb=" O PRO B 292 " ideal model delta sigma weight residual 1.246 1.222 0.024 8.50e-03 1.38e+04 7.74e+00 bond pdb=" N GLU C 178 " pdb=" CA GLU C 178 " ideal model delta sigma weight residual 1.462 1.488 -0.026 1.26e-02 6.30e+03 4.30e+00 ... (remaining 15204 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.52: 529 106.52 - 113.39: 8331 113.39 - 120.26: 5421 120.26 - 127.13: 6243 127.13 - 133.99: 195 Bond angle restraints: 20719 Sorted by residual: angle pdb=" N PRO B 292 " pdb=" CA PRO B 292 " pdb=" C PRO B 292 " ideal model delta sigma weight residual 110.47 115.68 -5.21 9.60e-01 1.09e+00 2.95e+01 angle pdb=" C LEU C 118 " pdb=" N LYS C 119 " pdb=" CA LYS C 119 " ideal model delta sigma weight residual 121.80 132.29 -10.49 2.44e+00 1.68e-01 1.85e+01 angle pdb=" N ILE A1103 " pdb=" CA ILE A1103 " pdb=" C ILE A1103 " ideal model delta sigma weight residual 111.62 108.85 2.77 7.90e-01 1.60e+00 1.23e+01 angle pdb=" N PRO B 292 " pdb=" CA PRO B 292 " pdb=" CB PRO B 292 " ideal model delta sigma weight residual 103.19 105.14 -1.95 5.60e-01 3.19e+00 1.21e+01 angle pdb=" C SER A 750 " pdb=" N VAL A 751 " pdb=" CA VAL A 751 " ideal model delta sigma weight residual 121.97 128.16 -6.19 1.80e+00 3.09e-01 1.18e+01 ... (remaining 20714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 8980 35.63 - 71.27: 202 71.27 - 106.90: 19 106.90 - 142.54: 0 142.54 - 178.17: 1 Dihedral angle restraints: 9202 sinusoidal: 3739 harmonic: 5463 Sorted by residual: dihedral pdb=" O4' C G 7 " pdb=" C1' C G 7 " pdb=" N1 C G 7 " pdb=" C2 C G 7 " ideal model delta sinusoidal sigma weight residual -128.00 50.17 -178.17 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA SER A 431 " pdb=" C SER A 431 " pdb=" N ASP A 432 " pdb=" CA ASP A 432 " ideal model delta harmonic sigma weight residual 180.00 154.46 25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA HIS A 466 " pdb=" C HIS A 466 " pdb=" N PRO A 467 " pdb=" CA PRO A 467 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 9199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1900 0.046 - 0.092: 387 0.092 - 0.139: 90 0.139 - 0.185: 4 0.185 - 0.231: 2 Chirality restraints: 2383 Sorted by residual: chirality pdb=" CB ILE A 454 " pdb=" CA ILE A 454 " pdb=" CG1 ILE A 454 " pdb=" CG2 ILE A 454 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB VAL B 294 " pdb=" CA VAL B 294 " pdb=" CG1 VAL B 294 " pdb=" CG2 VAL B 294 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" CB ILE B 280 " pdb=" CA ILE B 280 " pdb=" CG1 ILE B 280 " pdb=" CG2 ILE B 280 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2380 not shown) Planarity restraints: 2616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1145 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.62e+00 pdb=" N PRO A1146 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A1146 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1146 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1085 " 0.012 2.00e-02 2.50e+03 1.28e-02 4.07e+00 pdb=" CG TRP A1085 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A1085 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A1085 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1085 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1085 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1085 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1085 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1085 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1085 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 127 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C THR D 127 " 0.032 2.00e-02 2.50e+03 pdb=" O THR D 127 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE D 128 " -0.011 2.00e-02 2.50e+03 ... (remaining 2613 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2661 2.77 - 3.30: 14371 3.30 - 3.83: 23359 3.83 - 4.37: 26543 4.37 - 4.90: 47958 Nonbonded interactions: 114892 Sorted by model distance: nonbonded pdb=" O MET D 124 " pdb=" OG1 THR D 127 " model vdw 2.234 2.440 nonbonded pdb=" O ARG D 110 " pdb=" OG SER D 113 " model vdw 2.289 2.440 nonbonded pdb=" NH1 ARG A1029 " pdb=" OD1 ASN A1272 " model vdw 2.294 2.520 nonbonded pdb=" OE1 GLU A1218 " pdb=" NH2 ARG A1247 " model vdw 2.295 2.520 nonbonded pdb=" O ALA A1097 " pdb=" OG1 THR A1101 " model vdw 2.301 2.440 ... (remaining 114887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 82 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 118 or (resid 119 and (name N or n \ ame CA or name C or name O or name CB )) or resid 120 through 146)) selection = (chain 'E' and (resid 82 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 132 or (resid 133 and (name N or \ name CA or name C or name O or name CB )) or resid 134 through 146)) } 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=0.31 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 45.500 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.003 0.050 15209 Z= 0.173 Angle : 0.577 10.485 20719 Z= 0.309 Chirality : 0.039 0.231 2383 Planarity : 0.004 0.054 2616 Dihedral : 15.437 178.169 5656 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.65 % Favored : 93.86 % Rotamer: Outliers : 0.06 % Allowed : 0.49 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1843 helix: 1.71 (0.17), residues: 972 sheet: 1.17 (0.59), residues: 88 loop : -1.16 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A1085 HIS 0.005 0.001 HIS A 795 PHE 0.013 0.001 PHE A 548 TYR 0.013 0.001 TYR D 122 ARG 0.004 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 1.730 Fit side-chains REVERT: A 894 LEU cc_start: 0.8835 (tp) cc_final: 0.8555 (tp) REVERT: B 115 GLU cc_start: 0.8905 (tp30) cc_final: 0.8704 (tp30) REVERT: B 124 MET cc_start: 0.6170 (ptp) cc_final: 0.5807 (ptp) REVERT: B 305 ARG cc_start: 0.7081 (tpp-160) cc_final: 0.6619 (ttp-170) REVERT: C 133 ARG cc_start: 0.7850 (ttp-110) cc_final: 0.7594 (ttt-90) outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.2884 time to fit residues: 105.0695 Evaluate side-chains 207 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9980 chunk 139 optimal weight: 8.9990 chunk 77 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.0970 chunk 74 optimal weight: 0.3980 chunk 144 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 107 optimal weight: 0.0870 chunk 167 optimal weight: 2.9990 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 723 GLN ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15209 Z= 0.142 Angle : 0.540 10.258 20719 Z= 0.274 Chirality : 0.039 0.195 2383 Planarity : 0.004 0.055 2616 Dihedral : 8.771 177.477 2164 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.76 % Favored : 93.75 % Rotamer: Outliers : 0.86 % Allowed : 7.08 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.21), residues: 1843 helix: 2.08 (0.17), residues: 980 sheet: 1.16 (0.60), residues: 88 loop : -1.13 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1085 HIS 0.004 0.001 HIS A 352 PHE 0.012 0.001 PHE A 270 TYR 0.027 0.001 TYR D 122 ARG 0.004 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 217 time to evaluate : 1.701 Fit side-chains REVERT: A 894 LEU cc_start: 0.8873 (tp) cc_final: 0.8636 (tp) REVERT: A 918 GLU cc_start: 0.8457 (tp30) cc_final: 0.8226 (tm-30) REVERT: B 115 GLU cc_start: 0.8905 (tp30) cc_final: 0.8704 (tp30) REVERT: B 305 ARG cc_start: 0.7115 (tpp-160) cc_final: 0.6422 (ttm170) REVERT: C 133 ARG cc_start: 0.7887 (ttp-110) cc_final: 0.7573 (ttt-90) outliers start: 14 outliers final: 11 residues processed: 222 average time/residue: 0.2906 time to fit residues: 92.8570 Evaluate side-chains 209 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 198 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain E residue 132 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 0.0060 chunk 167 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN A 663 ASN A 723 GLN A 761 GLN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 ASN A 998 ASN B 98 GLN ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15209 Z= 0.304 Angle : 0.598 10.260 20719 Z= 0.305 Chirality : 0.042 0.162 2383 Planarity : 0.004 0.055 2616 Dihedral : 8.929 179.616 2164 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.20 % Favored : 93.32 % Rotamer: Outliers : 1.91 % Allowed : 9.66 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.20), residues: 1843 helix: 1.98 (0.17), residues: 986 sheet: 1.31 (0.63), residues: 83 loop : -1.26 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1085 HIS 0.005 0.001 HIS A 392 PHE 0.023 0.002 PHE A 548 TYR 0.021 0.002 TYR D 122 ARG 0.005 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 1.750 Fit side-chains REVERT: A 767 ASP cc_start: 0.7573 (t0) cc_final: 0.7335 (t0) REVERT: A 801 PHE cc_start: 0.7086 (t80) cc_final: 0.6725 (t80) REVERT: A 1221 GLU cc_start: 0.6881 (mp0) cc_final: 0.6673 (mp0) REVERT: B 305 ARG cc_start: 0.7212 (tpp-160) cc_final: 0.6439 (ttm170) REVERT: C 133 ARG cc_start: 0.7890 (ttp-110) cc_final: 0.7585 (ttt-90) REVERT: D 126 LYS cc_start: 0.8337 (mttm) cc_final: 0.7935 (mmtp) REVERT: D 132 ASN cc_start: 0.8894 (t0) cc_final: 0.8625 (m-40) outliers start: 31 outliers final: 26 residues processed: 230 average time/residue: 0.2952 time to fit residues: 98.1392 Evaluate side-chains 222 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 128 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 1.9990 chunk 125 optimal weight: 0.0030 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 112 optimal weight: 0.2980 chunk 167 optimal weight: 0.2980 chunk 177 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 159 optimal weight: 9.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 795 HIS A 924 ASN B 88 GLN ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15209 Z= 0.133 Angle : 0.529 10.424 20719 Z= 0.269 Chirality : 0.038 0.155 2383 Planarity : 0.004 0.054 2616 Dihedral : 8.804 178.514 2164 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.49 % Favored : 94.02 % Rotamer: Outliers : 1.42 % Allowed : 11.02 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1843 helix: 2.18 (0.17), residues: 984 sheet: 1.22 (0.63), residues: 83 loop : -1.20 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 664 HIS 0.005 0.001 HIS A 352 PHE 0.018 0.001 PHE A 801 TYR 0.019 0.001 TYR D 122 ARG 0.003 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 1.716 Fit side-chains REVERT: A 663 ASN cc_start: 0.8882 (p0) cc_final: 0.8558 (p0) REVERT: A 1252 VAL cc_start: 0.7850 (t) cc_final: 0.7609 (p) REVERT: B 211 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7352 (mm-30) REVERT: B 278 ILE cc_start: 0.7693 (mm) cc_final: 0.7377 (mt) REVERT: B 305 ARG cc_start: 0.7102 (tpp-160) cc_final: 0.6474 (ttm170) REVERT: C 133 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7560 (ttt-90) REVERT: D 132 ASN cc_start: 0.8863 (t0) cc_final: 0.8608 (m-40) outliers start: 23 outliers final: 15 residues processed: 223 average time/residue: 0.2831 time to fit residues: 92.6749 Evaluate side-chains 217 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 128 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 90 optimal weight: 0.3980 chunk 159 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 ASN ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 15209 Z= 0.309 Angle : 0.603 10.241 20719 Z= 0.309 Chirality : 0.042 0.171 2383 Planarity : 0.004 0.054 2616 Dihedral : 8.989 179.929 2164 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.52 % Favored : 92.99 % Rotamer: Outliers : 2.52 % Allowed : 11.38 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.20), residues: 1843 helix: 1.99 (0.17), residues: 980 sheet: 1.22 (0.63), residues: 78 loop : -1.34 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 191 HIS 0.007 0.001 HIS A 392 PHE 0.023 0.002 PHE A 548 TYR 0.015 0.002 TYR A 534 ARG 0.003 0.000 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 1.595 Fit side-chains REVERT: A 427 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8334 (p90) REVERT: A 767 ASP cc_start: 0.7607 (t0) cc_final: 0.7331 (t0) REVERT: A 1295 SER cc_start: 0.8316 (p) cc_final: 0.7980 (p) REVERT: B 211 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7599 (mm-30) REVERT: B 278 ILE cc_start: 0.7791 (mm) cc_final: 0.7439 (mt) REVERT: B 305 ARG cc_start: 0.7109 (tpp-160) cc_final: 0.6415 (ttm170) REVERT: C 133 ARG cc_start: 0.7904 (ttp-110) cc_final: 0.7660 (ttt-90) REVERT: D 132 ASN cc_start: 0.8943 (t0) cc_final: 0.8692 (m-40) outliers start: 41 outliers final: 28 residues processed: 240 average time/residue: 0.2786 time to fit residues: 98.7112 Evaluate side-chains 232 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 203 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 129 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 147 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 ASN ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15209 Z= 0.160 Angle : 0.548 10.473 20719 Z= 0.279 Chirality : 0.039 0.157 2383 Planarity : 0.004 0.054 2616 Dihedral : 8.885 178.939 2164 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.65 % Favored : 93.86 % Rotamer: Outliers : 1.85 % Allowed : 12.80 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1843 helix: 2.12 (0.17), residues: 984 sheet: 1.35 (0.63), residues: 81 loop : -1.31 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1085 HIS 0.005 0.001 HIS A 352 PHE 0.013 0.001 PHE A 411 TYR 0.023 0.001 TYR D 122 ARG 0.002 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 208 time to evaluate : 1.708 Fit side-chains REVERT: A 663 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8859 (p0) REVERT: A 950 LEU cc_start: 0.9007 (mm) cc_final: 0.8797 (mm) REVERT: A 1295 SER cc_start: 0.8306 (p) cc_final: 0.7993 (p) REVERT: B 211 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 278 ILE cc_start: 0.7760 (mm) cc_final: 0.7419 (mt) REVERT: B 305 ARG cc_start: 0.7142 (tpp-160) cc_final: 0.6460 (ttm170) REVERT: C 123 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7074 (p0) REVERT: C 133 ARG cc_start: 0.7871 (ttp-110) cc_final: 0.7635 (ttt-90) REVERT: D 132 ASN cc_start: 0.8888 (t0) cc_final: 0.8636 (m-40) outliers start: 30 outliers final: 26 residues processed: 228 average time/residue: 0.2859 time to fit residues: 95.2997 Evaluate side-chains 230 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 123 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15209 Z= 0.236 Angle : 0.571 10.506 20719 Z= 0.292 Chirality : 0.040 0.161 2383 Planarity : 0.004 0.053 2616 Dihedral : 8.917 179.014 2164 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.09 % Favored : 93.42 % Rotamer: Outliers : 2.34 % Allowed : 12.62 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.21), residues: 1843 helix: 2.07 (0.17), residues: 981 sheet: 1.14 (0.63), residues: 83 loop : -1.35 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.005 0.001 HIS A 352 PHE 0.018 0.002 PHE A 548 TYR 0.018 0.001 TYR D 122 ARG 0.002 0.000 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 1.685 Fit side-chains REVERT: A 663 ASN cc_start: 0.9106 (OUTLIER) cc_final: 0.8854 (p0) REVERT: A 1295 SER cc_start: 0.8348 (p) cc_final: 0.8062 (p) REVERT: B 305 ARG cc_start: 0.7153 (tpp-160) cc_final: 0.6466 (ttm170) REVERT: C 123 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7127 (p0) REVERT: C 133 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7659 (ttt-90) REVERT: D 132 ASN cc_start: 0.8931 (t0) cc_final: 0.8685 (m-40) outliers start: 38 outliers final: 30 residues processed: 228 average time/residue: 0.2881 time to fit residues: 95.4489 Evaluate side-chains 235 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 203 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 123 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 112 optimal weight: 0.0980 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15209 Z= 0.176 Angle : 0.555 10.794 20719 Z= 0.284 Chirality : 0.039 0.168 2383 Planarity : 0.004 0.053 2616 Dihedral : 8.862 178.492 2164 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.71 % Favored : 93.80 % Rotamer: Outliers : 1.91 % Allowed : 13.29 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1843 helix: 2.12 (0.17), residues: 980 sheet: 1.34 (0.63), residues: 81 loop : -1.32 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 191 HIS 0.005 0.001 HIS A 352 PHE 0.013 0.001 PHE A 411 TYR 0.021 0.001 TYR D 122 ARG 0.002 0.000 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 209 time to evaluate : 1.763 Fit side-chains REVERT: A 767 ASP cc_start: 0.7470 (t0) cc_final: 0.7184 (t0) REVERT: A 950 LEU cc_start: 0.9011 (mm) cc_final: 0.8805 (mm) REVERT: A 1221 GLU cc_start: 0.6871 (mp0) cc_final: 0.6669 (mp0) REVERT: A 1295 SER cc_start: 0.8321 (p) cc_final: 0.8025 (p) REVERT: B 188 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7933 (mmm160) REVERT: B 211 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7676 (mm-30) REVERT: B 305 ARG cc_start: 0.7118 (tpp-160) cc_final: 0.6446 (ttm170) REVERT: C 123 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7161 (p0) REVERT: C 133 ARG cc_start: 0.7852 (ttp-110) cc_final: 0.7627 (ttt-90) REVERT: D 132 ASN cc_start: 0.8890 (t0) cc_final: 0.8653 (m-40) outliers start: 31 outliers final: 26 residues processed: 229 average time/residue: 0.2905 time to fit residues: 95.7223 Evaluate side-chains 234 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 123 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 165 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15209 Z= 0.180 Angle : 0.557 10.744 20719 Z= 0.284 Chirality : 0.039 0.169 2383 Planarity : 0.004 0.053 2616 Dihedral : 8.832 178.183 2164 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.98 % Favored : 93.53 % Rotamer: Outliers : 1.97 % Allowed : 13.54 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1843 helix: 2.13 (0.17), residues: 980 sheet: 1.36 (0.63), residues: 81 loop : -1.33 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 191 HIS 0.005 0.001 HIS A 352 PHE 0.014 0.001 PHE A 411 TYR 0.019 0.001 TYR D 122 ARG 0.002 0.000 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 211 time to evaluate : 1.692 Fit side-chains REVERT: A 767 ASP cc_start: 0.7477 (t0) cc_final: 0.7144 (t0) REVERT: A 1295 SER cc_start: 0.8328 (p) cc_final: 0.8034 (p) REVERT: B 188 ARG cc_start: 0.8153 (mmm-85) cc_final: 0.7930 (mmm160) REVERT: B 211 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7616 (mm-30) REVERT: B 305 ARG cc_start: 0.7106 (tpp-160) cc_final: 0.6449 (ttm170) REVERT: C 123 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7135 (p0) REVERT: C 133 ARG cc_start: 0.7852 (ttp-110) cc_final: 0.7629 (ttt-90) REVERT: D 132 ASN cc_start: 0.8882 (t0) cc_final: 0.8640 (m-40) outliers start: 32 outliers final: 29 residues processed: 232 average time/residue: 0.2992 time to fit residues: 99.6150 Evaluate side-chains 235 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.3980 chunk 106 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 168 optimal weight: 0.3980 chunk 145 optimal weight: 0.0270 chunk 15 optimal weight: 0.5980 chunk 112 optimal weight: 0.0000 chunk 89 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 overall best weight: 0.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 723 GLN ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15209 Z= 0.141 Angle : 0.545 10.896 20719 Z= 0.277 Chirality : 0.039 0.173 2383 Planarity : 0.004 0.053 2616 Dihedral : 8.715 177.054 2164 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.38 % Favored : 94.13 % Rotamer: Outliers : 1.42 % Allowed : 14.03 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1843 helix: 2.17 (0.17), residues: 986 sheet: 1.35 (0.63), residues: 81 loop : -1.23 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1085 HIS 0.005 0.000 HIS A 352 PHE 0.012 0.001 PHE A 369 TYR 0.023 0.001 TYR D 122 ARG 0.002 0.000 ARG E 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 208 time to evaluate : 1.684 Fit side-chains REVERT: A 1295 SER cc_start: 0.8277 (p) cc_final: 0.7977 (p) REVERT: B 188 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7894 (mmm160) REVERT: B 211 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7604 (mm-30) REVERT: B 305 ARG cc_start: 0.7031 (tpp-160) cc_final: 0.6674 (ttp-170) REVERT: C 123 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.7034 (p0) REVERT: C 133 ARG cc_start: 0.7807 (ttp-110) cc_final: 0.7601 (ttt-90) REVERT: D 132 ASN cc_start: 0.8795 (t0) cc_final: 0.8556 (m-40) outliers start: 23 outliers final: 19 residues processed: 223 average time/residue: 0.2956 time to fit residues: 95.4406 Evaluate side-chains 219 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 199 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 150 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 723 GLN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 HIS ** 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 = 0.3730 r_free = 0.3730 target = 0.143849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.108527 restraints weight = 35938.773| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.27 r_work: 0.2911 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15209 Z= 0.180 Angle : 0.568 10.770 20719 Z= 0.288 Chirality : 0.039 0.169 2383 Planarity : 0.004 0.054 2616 Dihedral : 8.728 177.488 2164 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.38 % Favored : 94.08 % Rotamer: Outliers : 1.35 % Allowed : 14.77 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.21), residues: 1843 helix: 2.11 (0.17), residues: 986 sheet: 1.34 (0.63), residues: 81 loop : -1.25 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 191 HIS 0.013 0.001 HIS B 260 PHE 0.013 0.001 PHE A 411 TYR 0.021 0.001 TYR D 122 ARG 0.002 0.000 ARG B 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3544.26 seconds wall clock time: 63 minutes 34.80 seconds (3814.80 seconds total)