Starting phenix.real_space_refine on Sat Mar 23 16:54:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sok_40660/03_2024/8sok_40660.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sok_40660/03_2024/8sok_40660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sok_40660/03_2024/8sok_40660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sok_40660/03_2024/8sok_40660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sok_40660/03_2024/8sok_40660.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sok_40660/03_2024/8sok_40660.pdb" } resolution = 4.1 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= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 922 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 9 5.49 5 S 103 5.16 5 C 11795 2.51 5 N 3210 2.21 5 O 3455 1.98 5 H 18588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37162 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 18208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1158, 18208 Classifications: {'peptide': 1158} Link IDs: {'PCIS': 6, 'PTRANS': 88, 'TRANS': 1063} Chain breaks: 2 Chain: "B" Number of atoms: 5825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 5825 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 13, 'TRANS': 347} Chain: "C" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1897 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "D" Number of atoms: 9937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 9937 Classifications: {'peptide': 630} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 602} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 972 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "F" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 321 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" 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 15624 SG CYS A1043 78.333 92.219 70.385 1.00100.31 S ATOM 15666 SG CYS A1046 75.634 94.882 69.285 1.00 99.09 S ATOM 15802 SG CYS A1055 78.501 95.084 67.535 1.00101.81 S ATOM 15902 SG CYS A1062 79.128 95.208 71.402 1.00 99.71 S ATOM 31926 SG CYS D 382 66.292 102.038 150.553 1.00111.08 S ATOM 31973 SG CYS D 385 66.188 105.294 148.770 1.00111.92 S ATOM 33829 SG CYS D 503 69.540 103.437 150.222 1.00110.86 S ATOM 33879 SG CYS D 506 66.905 105.275 152.391 1.00116.20 S Time building chain proxies: 15.91, per 1000 atoms: 0.43 Number of scatterers: 37162 At special positions: 0 Unit cell: (111.8, 153.94, 190.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 103 16.00 P 9 15.00 O 3455 8.00 N 3210 7.00 C 11795 6.00 H 18588 1.00 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: 28.56 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1055 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1062 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1043 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1046 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 382 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 506 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 385 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 503 " Number of angles added : 12 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4412 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 30 sheets defined 29.2% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 Processing helix chain 'A' and resid 37 through 52 removed outlier: 4.062A pdb=" N LEU A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 88 through 97 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 216 through 219 removed outlier: 3.879A pdb=" N LEU A 219 " --> pdb=" O ARG A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 265 through 274 removed outlier: 4.290A pdb=" N VAL A 270 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 388 through 393 removed outlier: 3.625A pdb=" N ARG A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 388 through 393' Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.926A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 461 removed outlier: 3.641A pdb=" N TYR A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 478 removed outlier: 4.489A pdb=" N TRP A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 507 through 515 removed outlier: 3.673A pdb=" N LEU A 513 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 551 through 567 removed outlier: 4.344A pdb=" N GLU A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 Processing helix chain 'A' and resid 582 through 591 Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 671 through 677 Processing helix chain 'A' and resid 803 through 808 Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 865 through 870 removed outlier: 4.492A pdb=" N ASP A 870 " --> pdb=" O GLN A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 removed outlier: 3.894A pdb=" N ALA A 874 " --> pdb=" O VAL A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 913 removed outlier: 3.680A pdb=" N VAL A 912 " --> pdb=" O CYS A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 951 through 955 Processing helix chain 'A' and resid 1011 through 1017 Processing helix chain 'A' and resid 1092 through 1097 Processing helix chain 'A' and resid 1100 through 1112 Processing helix chain 'A' and resid 1136 through 1148 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 30 through 37 removed outlier: 4.098A pdb=" N LEU B 35 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 125 Processing helix chain 'B' and resid 160 through 177 Proline residue: B 171 - end of helix Processing helix chain 'B' and resid 200 through 220 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 241 through 248 removed outlier: 3.730A pdb=" N HIS B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 removed outlier: 5.508A pdb=" N ASN B 253 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 277 Processing helix chain 'B' and resid 297 through 310 removed outlier: 3.980A pdb=" N ILE B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 Processing helix chain 'B' and resid 340 through 355 removed outlier: 3.538A pdb=" N GLU B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 17 removed outlier: 3.955A pdb=" N VAL C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'D' and resid 13 through 17 Processing helix chain 'D' and resid 126 through 143 Processing helix chain 'D' and resid 152 through 156 Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 210 through 215 removed outlier: 6.006A pdb=" N ASN D 215 " --> pdb=" O ARG D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 4.093A pdb=" N HIS D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.565A pdb=" N ARG D 273 " --> pdb=" O SER D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 297 removed outlier: 3.841A pdb=" N SER D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 322 removed outlier: 3.885A pdb=" N GLU D 320A" --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 320D" --> pdb=" O SER D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 353 Processing helix chain 'D' and resid 373 through 376 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 410 through 414 Processing helix chain 'D' and resid 447 through 450 Processing helix chain 'D' and resid 459 through 468 Processing helix chain 'D' and resid 511 through 518 Processing helix chain 'D' and resid 525 through 533 Processing helix chain 'D' and resid 576 through 591 Processing helix chain 'D' and resid 596 through 600 Processing helix chain 'E' and resid 176 through 193 Processing helix chain 'E' and resid 205 through 215 Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.570A pdb=" N LEU E 240 " --> pdb=" O ILE E 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 68 removed outlier: 6.329A pdb=" N SER A 66 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 114 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL A 68 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N THR A 116 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N LEU A 179 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N SER A 143 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N LEU A 181 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLU A 145 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 68 removed outlier: 6.329A pdb=" N SER A 66 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 114 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL A 68 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N THR A 116 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU A 113 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 204 removed outlier: 5.855A pdb=" N ILE A 201 " --> pdb=" O GLN A 316 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 318 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 203 " --> pdb=" O LEU A 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 237 through 238 removed outlier: 8.675A pdb=" N TRP A 299 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER A 260 " --> pdb=" O TRP A 299 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR A 301 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE A 262 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 238 removed outlier: 6.519A pdb=" N ILE A 246 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 233 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER A 248 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 352 Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 361 removed outlier: 6.214A pdb=" N LEU A 356 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N CYS A 400 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 373 through 375 removed outlier: 6.629A pdb=" N GLY A 380 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 593 through 596 removed outlier: 3.970A pdb=" N LEU A 595 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 593 through 596 removed outlier: 3.970A pdb=" N LEU A 595 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 687 " --> pdb=" O GLU A 662 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 628 through 631 removed outlier: 4.047A pdb=" N VAL A 611 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 742 through 744 Processing sheet with id=AB4, first strand: chain 'A' and resid 742 through 744 removed outlier: 7.316A pdb=" N TYR A 764 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS A 738 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 766 " --> pdb=" O CYS A 736 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 732 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLY A 772 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER A 730 " --> pdb=" O GLY A 772 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLN A 774 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY A 728 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 899 through 901 removed outlier: 6.300A pdb=" N ARG A 966 " --> pdb=" O LEU A 995 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 905 through 907 Processing sheet with id=AB7, first strand: chain 'A' and resid 1024 through 1027 removed outlier: 5.574A pdb=" N GLU A1160 " --> pdb=" O CYS A1198 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N CYS A1198 " --> pdb=" O GLU A1160 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG A1089 " --> pdb=" O CYS A1198 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N SER A1200 " --> pdb=" O ARG A1089 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A1036 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A1076 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A1034 " --> pdb=" O LEU A1076 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLU A1078 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A1032 " --> pdb=" O GLU A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1175 through 1178 Processing sheet with id=AB9, first strand: chain 'B' and resid 38 through 39 removed outlier: 3.548A pdb=" N LYS B 38 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 56 through 68 removed outlier: 6.436A pdb=" N GLY B 76 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 66 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER B 74 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU B 68 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N PHE B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N ARG B 145 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN B 85 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TRP B 89 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR B 151 " --> pdb=" O TRP B 89 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG B 135 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR B 152 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG B 133 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS B 154 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N THR B 131 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 59 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 223 through 225 Processing sheet with id=AC3, first strand: chain 'B' and resid 322 through 323 Processing sheet with id=AC4, first strand: chain 'C' and resid 24 through 36 removed outlier: 11.593A pdb=" N GLY C 30 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 10.317A pdb=" N GLN C 47 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU C 32 " --> pdb=" O MET C 45 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N MET C 45 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 13.852A pdb=" N SER C 87 " --> pdb=" O GLN C 52 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N GLN C 54 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N VAL C 89 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU C 56 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA C 91 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N CYS C 58 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL C 93 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU C 76 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU C 94 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 74 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N CYS C 96 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU C 72 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER C 24 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 36 through 37 removed outlier: 6.506A pdb=" N VAL D 50 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL D 29 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL D 25 " --> pdb=" O HIS D 82 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N HIS D 82 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLY D 27 " --> pdb=" O ARG D 80 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARG D 80 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D 29 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE D 78 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 36 through 37 removed outlier: 8.131A pdb=" N THR D 93 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR D 58 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 204 through 205 removed outlier: 6.240A pdb=" N LEU D 168 " --> pdb=" O TRP D 184 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TRP D 184 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 10.761A pdb=" N THR D 217 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N PHE D 263 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP D 219 " --> pdb=" O PHE D 263 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N LEU D 265 " --> pdb=" O ASP D 219 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU D 221 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N MET D 258 " --> pdb=" O MET D 251 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE D 238 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 204 through 205 removed outlier: 6.472A pdb=" N LEU D 164 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR D 242 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N CYS D 166 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ARG D 240 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU D 168 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE D 238 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE D 238 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 335 through 337 Processing sheet with id=AD1, first strand: chain 'D' and resid 387 through 389 removed outlier: 3.504A pdb=" N ALA D 557 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 10.479A pdb=" N TYR D 622 " --> pdb=" O VAL D 554 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU D 556 " --> pdb=" O TYR D 622 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ILE D 624 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TYR D 558 " --> pdb=" O ILE D 624 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE D 606 " --> pdb=" O PHE D 625 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 419 through 426 removed outlier: 3.656A pdb=" N ARG D 432 " --> pdb=" O THR D 426 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU D 452 " --> pdb=" O VAL D 439 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 493 through 495 removed outlier: 3.848A pdb=" N LEU D 493 " --> pdb=" O HIS D 500 " (cutoff:3.500A) 727 hydrogen bonds defined for protein. 1842 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: 15.50 Time building geometry restraints manager: 29.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 18509 1.03 - 1.23: 407 1.23 - 1.43: 7519 1.43 - 1.63: 11036 1.63 - 1.82: 135 Bond restraints: 37606 Sorted by residual: bond pdb=" N LYS B 320 " pdb=" H LYS B 320 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CG LYS B 320 " pdb=" HG3 LYS B 320 " ideal model delta sigma weight residual 0.970 1.091 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" NZ LYS B 320 " pdb=" HZ1 LYS B 320 " ideal model delta sigma weight residual 0.890 1.010 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" NZ LYS B 320 " pdb=" HZ2 LYS B 320 " ideal model delta sigma weight residual 0.890 1.010 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" CB LYS B 320 " pdb=" HB3 LYS B 320 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 37601 not shown) Histogram of bond angle deviations from ideal: 67.53 - 80.87: 10 80.87 - 94.20: 0 94.20 - 107.54: 2528 107.54 - 120.88: 56526 120.88 - 134.21: 9099 Bond angle restraints: 68163 Sorted by residual: angle pdb=" C PRO D 592 " pdb=" CA PRO D 592 " pdb=" HA PRO D 592 " ideal model delta sigma weight residual 109.00 67.53 41.47 3.00e+00 1.11e-01 1.91e+02 angle pdb=" CB PRO D 592 " pdb=" CA PRO D 592 " pdb=" HA PRO D 592 " ideal model delta sigma weight residual 109.00 73.62 35.38 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N PRO D 592 " pdb=" CA PRO D 592 " pdb=" HA PRO D 592 " ideal model delta sigma weight residual 110.00 74.82 35.18 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB GLU E 180 " pdb=" CA GLU E 180 " pdb=" HA GLU E 180 " ideal model delta sigma weight residual 109.00 73.89 35.11 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C GLU E 180 " pdb=" CA GLU E 180 " pdb=" HA GLU E 180 " ideal model delta sigma weight residual 109.00 74.33 34.67 3.00e+00 1.11e-01 1.34e+02 ... (remaining 68158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 17116 32.09 - 64.19: 559 64.19 - 96.28: 44 96.28 - 128.37: 0 128.37 - 160.46: 2 Dihedral angle restraints: 17721 sinusoidal: 9809 harmonic: 7912 Sorted by residual: dihedral pdb=" CA PHE A 158 " pdb=" C PHE A 158 " pdb=" N LEU A 159 " pdb=" CA LEU A 159 " ideal model delta harmonic sigma weight residual 180.00 151.64 28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA GLN A 387 " pdb=" C GLN A 387 " pdb=" N PHE A 388 " pdb=" CA PHE A 388 " ideal model delta harmonic sigma weight residual 180.00 152.57 27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA SER A1158 " pdb=" C SER A1158 " pdb=" N PHE A1159 " pdb=" CA PHE A1159 " ideal model delta harmonic sigma weight residual 180.00 -154.30 -25.70 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 17718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.853: 2951 0.853 - 1.707: 0 1.707 - 2.560: 0 2.560 - 3.414: 0 3.414 - 4.267: 1 Chirality restraints: 2952 Sorted by residual: chirality pdb=" C3' DA F 3 " pdb=" C4' DA F 3 " pdb=" O3' DA F 3 " pdb=" C2' DA F 3 " both_signs ideal model delta sigma weight residual False -2.66 1.61 -4.27 2.00e-01 2.50e+01 4.55e+02 chirality pdb=" CA GLU E 180 " pdb=" N GLU E 180 " pdb=" C GLU E 180 " pdb=" CB GLU E 180 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA PRO D 592 " pdb=" N PRO D 592 " pdb=" C PRO D 592 " pdb=" CB PRO D 592 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2949 not shown) Planarity restraints: 5476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 325 " 0.021 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" N VAL D 326 " -0.065 2.00e-02 2.50e+03 pdb=" CA VAL D 326 " 0.016 2.00e-02 2.50e+03 pdb=" H VAL D 326 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 325 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C GLU D 325 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU D 325 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL D 326 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 818 " -0.254 9.50e-02 1.11e+02 8.47e-02 7.76e+00 pdb=" NE ARG A 818 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 818 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 818 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 818 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 818 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 818 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 818 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 818 " -0.002 2.00e-02 2.50e+03 ... (remaining 5473 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1538 2.16 - 2.77: 73303 2.77 - 3.38: 103293 3.38 - 3.99: 130634 3.99 - 4.60: 202877 Nonbonded interactions: 511645 Sorted by model distance: nonbonded pdb=" HG SER A 730 " pdb=" O LEU A 819 " model vdw 1.550 1.850 nonbonded pdb=" O CYS A 424 " pdb=" H GLY A 427 " model vdw 1.556 1.850 nonbonded pdb=" OE1 GLU D 67 " pdb=" H GLU D 67 " model vdw 1.558 1.850 nonbonded pdb=" HG SER A1158 " pdb=" OG SER A1200 " model vdw 1.559 1.850 nonbonded pdb=" OD1 ASP D 163 " pdb=" H SER D 243 " model vdw 1.563 1.850 ... (remaining 511640 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.590 Extract box with map and model: 11.300 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 120.980 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.110 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 19018 Z= 0.335 Angle : 0.762 8.951 25894 Z= 0.424 Chirality : 0.090 4.267 2952 Planarity : 0.007 0.111 3287 Dihedral : 13.707 160.463 7092 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.79 % Favored : 89.65 % Rotamer: Outliers : 1.02 % Allowed : 4.89 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -3.40 (0.15), residues: 2319 helix: -2.16 (0.19), residues: 513 sheet: -2.51 (0.20), residues: 521 loop : -2.18 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 781 HIS 0.012 0.001 HIS A 812 PHE 0.020 0.002 PHE A 567 TYR 0.027 0.002 TYR B 30 ARG 0.007 0.001 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 229 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 PHE cc_start: 0.6668 (p90) cc_final: 0.6026 (p90) REVERT: A 272 HIS cc_start: 0.8462 (t70) cc_final: 0.8090 (t70) REVERT: A 448 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7265 (m-80) REVERT: B 240 ASN cc_start: 0.7707 (p0) cc_final: 0.7491 (p0) REVERT: B 320 LYS cc_start: 0.4468 (OUTLIER) cc_final: 0.4182 (tppt) REVERT: B 323 HIS cc_start: 0.7415 (t-90) cc_final: 0.6815 (t-90) REVERT: D 26 TYR cc_start: -0.0946 (OUTLIER) cc_final: -0.1724 (t80) outliers start: 21 outliers final: 7 residues processed: 249 average time/residue: 0.7401 time to fit residues: 276.7622 Evaluate side-chains 180 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 9.9990 chunk 175 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 110 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 19018 Z= 0.229 Angle : 0.639 6.288 25894 Z= 0.339 Chirality : 0.092 4.423 2952 Planarity : 0.005 0.057 3287 Dihedral : 9.895 159.292 2623 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.50 (0.16), residues: 2319 helix: -0.96 (0.21), residues: 518 sheet: -1.99 (0.20), residues: 545 loop : -1.78 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 95 HIS 0.008 0.001 HIS A 84 PHE 0.011 0.001 PHE A 602 TYR 0.019 0.002 TYR D 26 ARG 0.006 0.000 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 3.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 240 ASN cc_start: 0.7610 (p0) cc_final: 0.7357 (p0) REVERT: B 318 MET cc_start: 0.6585 (mmp) cc_final: 0.6267 (mmp) REVERT: B 323 HIS cc_start: 0.7354 (t-90) cc_final: 0.6763 (t-90) REVERT: C 14 GLU cc_start: 0.6476 (mp0) cc_final: 0.5932 (mp0) REVERT: D 144 MET cc_start: 0.4538 (ttp) cc_final: 0.4103 (ttt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.6984 time to fit residues: 224.0079 Evaluate side-chains 176 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 175 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 HIS ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 19018 Z= 0.378 Angle : 0.683 6.954 25894 Z= 0.361 Chirality : 0.092 4.426 2952 Planarity : 0.005 0.082 3287 Dihedral : 9.794 159.778 2623 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.87 % Favored : 90.04 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.41 (0.17), residues: 2319 helix: -0.66 (0.22), residues: 523 sheet: -1.97 (0.20), residues: 553 loop : -1.80 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 594 HIS 0.006 0.001 HIS A1092 PHE 0.016 0.002 PHE B 23 TYR 0.026 0.002 TYR A 467 ARG 0.015 0.001 ARG A 731 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 318 MET cc_start: 0.6646 (mmp) cc_final: 0.6369 (mmp) REVERT: B 323 HIS cc_start: 0.7418 (t-90) cc_final: 0.6900 (t-90) REVERT: C 14 GLU cc_start: 0.6540 (mp0) cc_final: 0.5918 (mp0) REVERT: D 144 MET cc_start: 0.4629 (ttp) cc_final: 0.4181 (ttt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.6822 time to fit residues: 210.1302 Evaluate side-chains 172 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 19018 Z= 0.418 Angle : 0.702 10.030 25894 Z= 0.371 Chirality : 0.092 4.437 2952 Planarity : 0.005 0.075 3287 Dihedral : 9.801 160.360 2623 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.18 % Favored : 89.74 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.42 (0.17), residues: 2319 helix: -0.56 (0.22), residues: 523 sheet: -2.03 (0.21), residues: 550 loop : -1.85 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 594 HIS 0.006 0.001 HIS A1092 PHE 0.041 0.002 PHE A 986 TYR 0.032 0.002 TYR B 30 ARG 0.014 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 LEU cc_start: 0.8608 (mm) cc_final: 0.8401 (mm) REVERT: A 395 MET cc_start: 0.8326 (mmm) cc_final: 0.8044 (mmm) REVERT: B 318 MET cc_start: 0.6730 (mmp) cc_final: 0.6478 (mmp) REVERT: B 323 HIS cc_start: 0.7469 (t-90) cc_final: 0.6927 (t70) REVERT: D 144 MET cc_start: 0.4740 (ttp) cc_final: 0.4287 (ttt) REVERT: D 168 LEU cc_start: 0.7028 (tp) cc_final: 0.6815 (tt) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.7176 time to fit residues: 219.4965 Evaluate side-chains 165 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 191 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 0.8980 chunk 201 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1017 GLN ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 19018 Z= 0.190 Angle : 0.570 5.611 25894 Z= 0.298 Chirality : 0.092 4.438 2952 Planarity : 0.004 0.047 3287 Dihedral : 9.353 158.528 2623 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.03 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.03 (0.17), residues: 2319 helix: -0.19 (0.23), residues: 524 sheet: -1.83 (0.21), residues: 545 loop : -1.61 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 207 HIS 0.004 0.001 HIS A 533 PHE 0.014 0.001 PHE A 158 TYR 0.013 0.001 TYR B 30 ARG 0.009 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 LEU cc_start: 0.8572 (pt) cc_final: 0.8296 (pt) REVERT: A 272 HIS cc_start: 0.8383 (t70) cc_final: 0.8181 (t70) REVERT: A 391 LEU cc_start: 0.8416 (mm) cc_final: 0.8212 (mm) REVERT: A 395 MET cc_start: 0.8260 (mmm) cc_final: 0.7878 (mmm) REVERT: B 240 ASN cc_start: 0.7594 (p0) cc_final: 0.7329 (p0) REVERT: B 318 MET cc_start: 0.6726 (mmp) cc_final: 0.6489 (mmp) REVERT: B 323 HIS cc_start: 0.7316 (t-90) cc_final: 0.6806 (t70) REVERT: C 14 GLU cc_start: 0.6377 (mp0) cc_final: 0.5752 (mp0) REVERT: D 144 MET cc_start: 0.4549 (ttp) cc_final: 0.4095 (ttt) REVERT: D 251 MET cc_start: 0.7096 (mmm) cc_final: 0.6842 (mmm) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.6863 time to fit residues: 211.4267 Evaluate side-chains 169 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 4.9990 chunk 201 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 224 optimal weight: 8.9990 chunk 186 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 GLN ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 19018 Z= 0.181 Angle : 0.541 5.740 25894 Z= 0.283 Chirality : 0.091 4.439 2952 Planarity : 0.004 0.043 3287 Dihedral : 9.179 158.147 2623 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.33 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.80 (0.17), residues: 2319 helix: 0.03 (0.23), residues: 523 sheet: -1.69 (0.21), residues: 549 loop : -1.46 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 207 HIS 0.004 0.001 HIS D 499 PHE 0.011 0.001 PHE A 158 TYR 0.012 0.001 TYR B 30 ARG 0.007 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 LEU cc_start: 0.8545 (pt) cc_final: 0.8254 (pt) REVERT: A 272 HIS cc_start: 0.8365 (t70) cc_final: 0.8164 (t70) REVERT: A 395 MET cc_start: 0.8246 (mmm) cc_final: 0.7687 (tpp) REVERT: B 240 ASN cc_start: 0.7600 (p0) cc_final: 0.7311 (p0) REVERT: B 318 MET cc_start: 0.6676 (mmp) cc_final: 0.6431 (mmp) REVERT: B 323 HIS cc_start: 0.7297 (t-90) cc_final: 0.6788 (t70) REVERT: C 14 GLU cc_start: 0.6292 (mp0) cc_final: 0.5678 (mp0) REVERT: D 144 MET cc_start: 0.4470 (ttp) cc_final: 0.4010 (ttt) REVERT: D 251 MET cc_start: 0.7121 (mmm) cc_final: 0.6722 (mmm) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.7286 time to fit residues: 212.1600 Evaluate side-chains 166 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 163 optimal weight: 0.7980 chunk 188 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1009 HIS ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 19018 Z= 0.241 Angle : 0.562 5.886 25894 Z= 0.294 Chirality : 0.091 4.441 2952 Planarity : 0.004 0.042 3287 Dihedral : 9.182 158.584 2623 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.88 % Favored : 91.03 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.76 (0.17), residues: 2319 helix: 0.13 (0.23), residues: 523 sheet: -1.71 (0.21), residues: 560 loop : -1.44 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 594 HIS 0.005 0.001 HIS D 499 PHE 0.011 0.001 PHE B 23 TYR 0.016 0.001 TYR A 467 ARG 0.008 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7656 (mt) cc_final: 0.7431 (mt) REVERT: A 233 LEU cc_start: 0.8583 (pt) cc_final: 0.8298 (pt) REVERT: A 272 HIS cc_start: 0.8388 (t70) cc_final: 0.8163 (t70) REVERT: A 395 MET cc_start: 0.8261 (mmm) cc_final: 0.7920 (mmm) REVERT: A 564 TRP cc_start: 0.7228 (m100) cc_final: 0.6701 (m100) REVERT: B 240 ASN cc_start: 0.7622 (p0) cc_final: 0.7359 (p0) REVERT: B 318 MET cc_start: 0.6786 (mmp) cc_final: 0.6540 (mmp) REVERT: B 323 HIS cc_start: 0.7360 (t-90) cc_final: 0.6867 (t70) REVERT: C 14 GLU cc_start: 0.6406 (mp0) cc_final: 0.5707 (mp0) REVERT: D 144 MET cc_start: 0.4500 (ttp) cc_final: 0.3915 (ttt) REVERT: D 251 MET cc_start: 0.7398 (mmm) cc_final: 0.7037 (mmm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.7212 time to fit residues: 203.8015 Evaluate side-chains 159 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 2.9990 chunk 133 optimal weight: 0.0060 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 214 optimal weight: 20.0000 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1009 HIS ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 19018 Z= 0.229 Angle : 0.553 6.170 25894 Z= 0.288 Chirality : 0.091 4.441 2952 Planarity : 0.004 0.042 3287 Dihedral : 9.137 158.582 2623 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.41 % Favored : 91.50 % Rotamer: Outliers : 0.05 % Allowed : 0.73 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.72 (0.17), residues: 2319 helix: 0.18 (0.23), residues: 523 sheet: -1.69 (0.21), residues: 561 loop : -1.42 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 299 HIS 0.004 0.001 HIS D 499 PHE 0.011 0.001 PHE A 763 TYR 0.014 0.001 TYR A 467 ARG 0.007 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7650 (mt) cc_final: 0.7242 (mp) REVERT: A 233 LEU cc_start: 0.8567 (pt) cc_final: 0.8270 (pt) REVERT: A 395 MET cc_start: 0.8245 (mmm) cc_final: 0.7898 (mmm) REVERT: A 564 TRP cc_start: 0.7220 (m100) cc_final: 0.6677 (m100) REVERT: A 1009 HIS cc_start: 0.6688 (OUTLIER) cc_final: 0.6300 (t-170) REVERT: B 240 ASN cc_start: 0.7681 (p0) cc_final: 0.7402 (p0) REVERT: B 318 MET cc_start: 0.6779 (mmp) cc_final: 0.6515 (mmp) REVERT: B 323 HIS cc_start: 0.7305 (t-90) cc_final: 0.6827 (t70) REVERT: C 14 GLU cc_start: 0.6382 (mp0) cc_final: 0.5703 (mp0) REVERT: D 144 MET cc_start: 0.4469 (ttp) cc_final: 0.3882 (ttt) REVERT: D 251 MET cc_start: 0.7348 (mmm) cc_final: 0.7051 (mmm) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.7295 time to fit residues: 200.5812 Evaluate side-chains 163 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 4.9990 chunk 208 optimal weight: 20.0000 chunk 214 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 19018 Z= 0.208 Angle : 0.542 6.172 25894 Z= 0.282 Chirality : 0.091 4.441 2952 Planarity : 0.004 0.042 3287 Dihedral : 9.056 158.426 2623 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.41 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.61 (0.18), residues: 2319 helix: 0.29 (0.23), residues: 523 sheet: -1.64 (0.21), residues: 556 loop : -1.35 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 594 HIS 0.005 0.001 HIS A 533 PHE 0.009 0.001 PHE B 23 TYR 0.012 0.001 TYR A 764 ARG 0.007 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 LEU cc_start: 0.8448 (pt) cc_final: 0.8145 (pt) REVERT: A 272 HIS cc_start: 0.8400 (t70) cc_final: 0.8189 (t70) REVERT: A 395 MET cc_start: 0.8231 (mmm) cc_final: 0.7873 (mmm) REVERT: B 240 ASN cc_start: 0.7715 (p0) cc_final: 0.7425 (p0) REVERT: B 318 MET cc_start: 0.6784 (mmp) cc_final: 0.6514 (mmp) REVERT: B 323 HIS cc_start: 0.7293 (t-90) cc_final: 0.6811 (t70) REVERT: C 14 GLU cc_start: 0.6362 (mp0) cc_final: 0.5698 (mp0) REVERT: D 144 MET cc_start: 0.4502 (ttp) cc_final: 0.3926 (ttt) REVERT: D 251 MET cc_start: 0.7376 (mmm) cc_final: 0.7115 (mmm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.7406 time to fit residues: 202.8020 Evaluate side-chains 162 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 231 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 chunk 184 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 146 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 GLN ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 19018 Z= 0.189 Angle : 0.531 6.261 25894 Z= 0.275 Chirality : 0.091 4.441 2952 Planarity : 0.004 0.088 3287 Dihedral : 8.952 158.135 2623 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.42 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.48 (0.18), residues: 2319 helix: 0.42 (0.23), residues: 525 sheet: -1.54 (0.21), residues: 565 loop : -1.28 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 594 HIS 0.006 0.001 HIS A 533 PHE 0.013 0.001 PHE A 801 TYR 0.011 0.001 TYR A 764 ARG 0.007 0.000 ARG A 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 LEU cc_start: 0.8401 (pt) cc_final: 0.8110 (pt) REVERT: A 395 MET cc_start: 0.8202 (mmm) cc_final: 0.7856 (mmm) REVERT: B 240 ASN cc_start: 0.7716 (p0) cc_final: 0.7393 (p0) REVERT: B 318 MET cc_start: 0.6793 (mmp) cc_final: 0.6502 (mmp) REVERT: B 323 HIS cc_start: 0.7257 (t-90) cc_final: 0.6767 (t70) REVERT: C 14 GLU cc_start: 0.6285 (mp0) cc_final: 0.5636 (mp0) REVERT: D 144 MET cc_start: 0.4462 (ttp) cc_final: 0.3884 (ttt) REVERT: D 251 MET cc_start: 0.7318 (mmm) cc_final: 0.7075 (mmm) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.6832 time to fit residues: 193.1289 Evaluate side-chains 163 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 169 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 161 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1009 HIS ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 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 = 0.4512 r_free = 0.4512 target = 0.140159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.123200 restraints weight = 179296.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.124735 restraints weight = 256202.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.124439 restraints weight = 105319.952| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 19018 Z= 0.209 Angle : 0.531 6.127 25894 Z= 0.276 Chirality : 0.091 4.441 2952 Planarity : 0.004 0.084 3287 Dihedral : 8.905 158.317 2623 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.32 % Favored : 91.59 % Rotamer: Outliers : 0.05 % Allowed : 0.39 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.42 (0.18), residues: 2319 helix: 0.56 (0.24), residues: 520 sheet: -1.51 (0.21), residues: 557 loop : -1.29 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 594 HIS 0.005 0.001 HIS A 533 PHE 0.011 0.001 PHE A 986 TYR 0.012 0.001 TYR A 205 ARG 0.006 0.000 ARG A 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6584.84 seconds wall clock time: 118 minutes 43.08 seconds (7123.08 seconds total)