Starting phenix.real_space_refine on Sun Nov 17 22:32:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgi_45580/11_2024/9cgi_45580.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgi_45580/11_2024/9cgi_45580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgi_45580/11_2024/9cgi_45580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgi_45580/11_2024/9cgi_45580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgi_45580/11_2024/9cgi_45580.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgi_45580/11_2024/9cgi_45580.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 9355 2.51 5 N 2513 2.21 5 O 2787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14751 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1314, 10576 Classifications: {'peptide': 1314} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1262} Chain breaks: 3 Chain: "B" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 806 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "C" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1606 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain breaks: 2 Chain: "D" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 927 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "E" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 836 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Time building chain proxies: 8.87, per 1000 atoms: 0.60 Number of scatterers: 14751 At special positions: 0 Unit cell: (102.699, 110.667, 197.429, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2787 8.00 N 2513 7.00 C 9355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1191 " - pdb=" SG CYS A1429 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.29 Conformation dependent library (CDL) restraints added in 1.9 seconds 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3512 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 11 sheets defined 64.4% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 23 through 33 removed outlier: 3.697A pdb=" N ALA A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 104 through 137 removed outlier: 3.779A pdb=" N ILE A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LYS A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 155 Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 166 through 188 removed outlier: 3.612A pdb=" N PHE A 170 " --> pdb=" O TRP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.966A pdb=" N ARG A 193 " --> pdb=" O PRO A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 255 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.951A pdb=" N ARG A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 273 " --> pdb=" O TRP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 282 through 288 removed outlier: 3.832A pdb=" N ILE A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 removed outlier: 3.621A pdb=" N VAL A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 327 removed outlier: 4.028A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 346 removed outlier: 3.531A pdb=" N ARG A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.678A pdb=" N PHE A 359 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 360 " --> pdb=" O PHE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 removed outlier: 3.730A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N HIS A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 411 Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 479 through 487 removed outlier: 3.933A pdb=" N TRP A 483 " --> pdb=" O LYS A 480 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ASP A 484 " --> pdb=" O ASP A 481 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL A 486 " --> pdb=" O TRP A 483 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR A 487 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.513A pdb=" N VAL A 491 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.676A pdb=" N VAL A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 574 Processing helix chain 'A' and resid 577 through 581 removed outlier: 3.619A pdb=" N LYS A 580 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU A 581 " --> pdb=" O TYR A 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 577 through 581' Processing helix chain 'A' and resid 587 through 598 Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 731 through 747 removed outlier: 4.985A pdb=" N ILE A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 removed outlier: 4.091A pdb=" N LYS A 757 " --> pdb=" O ASN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 removed outlier: 3.679A pdb=" N THR A 784 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 Proline residue: A 812 - end of helix Processing helix chain 'A' and resid 847 through 874 Processing helix chain 'A' and resid 904 through 910 removed outlier: 3.854A pdb=" N SER A 908 " --> pdb=" O GLN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 940 removed outlier: 3.730A pdb=" N ALA A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 964 Processing helix chain 'A' and resid 972 through 981 Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 982 through 992 Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1014 through 1029 Processing helix chain 'A' and resid 1033 through 1041 removed outlier: 3.937A pdb=" N LEU A1037 " --> pdb=" O THR A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1056 Processing helix chain 'A' and resid 1067 through 1083 removed outlier: 3.957A pdb=" N ASN A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1110 removed outlier: 3.683A pdb=" N GLU A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A1107 " --> pdb=" O GLU A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1126 Processing helix chain 'A' and resid 1126 through 1138 removed outlier: 3.851A pdb=" N LEU A1138 " --> pdb=" O ILE A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1153 Processing helix chain 'A' and resid 1156 through 1164 removed outlier: 4.025A pdb=" N LEU A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS A1164 " --> pdb=" O SER A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1178 Processing helix chain 'A' and resid 1191 through 1204 Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1220 through 1224 removed outlier: 3.594A pdb=" N ALA A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1220 through 1224' Processing helix chain 'A' and resid 1236 through 1241 Processing helix chain 'A' and resid 1291 through 1309 removed outlier: 3.501A pdb=" N GLY A1309 " --> pdb=" O THR A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1323 Processing helix chain 'A' and resid 1329 through 1337 Processing helix chain 'A' and resid 1391 through 1407 removed outlier: 3.881A pdb=" N ALA A1395 " --> pdb=" O ILE A1391 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A1396 " --> pdb=" O TYR A1392 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 484 Processing helix chain 'B' and resid 489 through 501 removed outlier: 3.855A pdb=" N HIS B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.729A pdb=" N TYR B 506 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 541 removed outlier: 3.563A pdb=" N LEU B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 527 " --> pdb=" O SER B 523 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS B 535 " --> pdb=" O MET B 531 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 536 " --> pdb=" O ARG B 532 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU B 537 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU B 538 " --> pdb=" O ASN B 534 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN B 539 " --> pdb=" O HIS B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 574 removed outlier: 3.790A pdb=" N MET B 574 " --> pdb=" O HIS B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 485 Processing helix chain 'C' and resid 489 through 501 removed outlier: 3.713A pdb=" N ARG C 495 " --> pdb=" O HIS C 491 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS C 499 " --> pdb=" O ARG C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.783A pdb=" N TYR C 506 " --> pdb=" O LEU C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 533 Processing helix chain 'C' and resid 533 through 541 removed outlier: 3.843A pdb=" N LYS C 541 " --> pdb=" O GLU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 574 Processing helix chain 'C' and resid 602 through 608 Processing helix chain 'C' and resid 634 through 638 removed outlier: 3.697A pdb=" N LEU C 637 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 672 removed outlier: 3.649A pdb=" N ARG C 661 " --> pdb=" O ASP C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 688 Processing helix chain 'C' and resid 690 through 708 removed outlier: 3.681A pdb=" N ILE C 694 " --> pdb=" O ASN C 690 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN C 708 " --> pdb=" O ILE C 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 484 Processing helix chain 'D' and resid 489 through 501 removed outlier: 3.792A pdb=" N HIS D 499 " --> pdb=" O ARG D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.595A pdb=" N TYR D 506 " --> pdb=" O LEU D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 541 removed outlier: 3.743A pdb=" N HIS D 535 " --> pdb=" O MET D 531 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS D 541 " --> pdb=" O GLU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 578 removed outlier: 3.555A pdb=" N ILE D 546 " --> pdb=" O GLU D 542 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 484 Processing helix chain 'E' and resid 489 through 501 removed outlier: 3.728A pdb=" N HIS E 499 " --> pdb=" O ARG E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.754A pdb=" N ASP E 505 " --> pdb=" O HIS E 502 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR E 506 " --> pdb=" O LEU E 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 502 through 506' Processing helix chain 'E' and resid 507 through 541 removed outlier: 4.046A pdb=" N ASP E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET E 531 " --> pdb=" O ILE E 527 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG E 532 " --> pdb=" O ASN E 528 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU E 537 " --> pdb=" O LEU E 533 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN E 539 " --> pdb=" O HIS E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 573 removed outlier: 4.049A pdb=" N ILE E 546 " --> pdb=" O GLU E 542 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE E 547 " --> pdb=" O ILE E 543 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER E 573 " --> pdb=" O GLY E 569 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 7.045A pdb=" N ILE A 21 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.199A pdb=" N MET A 84 " --> pdb=" O CYS A 227 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N TYR A 229 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 388 Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 476 removed outlier: 4.859A pdb=" N ARG A 503 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 551 through 556 removed outlier: 3.988A pdb=" N ARG A 551 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL A 537 " --> pdb=" O VAL A 763 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR A 765 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 824 through 830 removed outlier: 4.119A pdb=" N ARG A 824 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 839 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU A 834 " --> pdb=" O THR A 721 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 888 through 891 Processing sheet with id=AA9, first strand: chain 'A' and resid 1113 through 1114 Processing sheet with id=AB1, first strand: chain 'A' and resid 1225 through 1231 Processing sheet with id=AB2, first strand: chain 'A' and resid 1380 through 1381 843 hydrogen bonds defined for protein. 2421 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: 5.55 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3519 1.33 - 1.45: 2918 1.45 - 1.58: 8431 1.58 - 1.70: 0 1.70 - 1.82: 160 Bond restraints: 15028 Sorted by residual: bond pdb=" CA ALA A 87 " pdb=" C ALA A 87 " ideal model delta sigma weight residual 1.528 1.458 0.070 1.33e-02 5.65e+03 2.74e+01 bond pdb=" CA GLU A 90 " pdb=" C GLU A 90 " ideal model delta sigma weight residual 1.522 1.464 0.059 1.37e-02 5.33e+03 1.83e+01 bond pdb=" N LEU A 214 " pdb=" CA LEU A 214 " ideal model delta sigma weight residual 1.454 1.508 -0.054 1.27e-02 6.20e+03 1.81e+01 bond pdb=" CA HIS A1264 " pdb=" C HIS A1264 " ideal model delta sigma weight residual 1.524 1.498 0.026 7.00e-03 2.04e+04 1.42e+01 bond pdb=" CA ALA A 87 " pdb=" CB ALA A 87 " ideal model delta sigma weight residual 1.527 1.479 0.048 1.44e-02 4.82e+03 1.13e+01 ... (remaining 15023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 20015 3.05 - 6.10: 252 6.10 - 9.14: 31 9.14 - 12.19: 7 12.19 - 15.24: 1 Bond angle restraints: 20306 Sorted by residual: angle pdb=" N ASN A 211 " pdb=" CA ASN A 211 " pdb=" C ASN A 211 " ideal model delta sigma weight residual 109.06 97.34 11.72 1.78e+00 3.16e-01 4.34e+01 angle pdb=" N HIS A1264 " pdb=" CA HIS A1264 " pdb=" C HIS A1264 " ideal model delta sigma weight residual 111.02 102.97 8.05 1.52e+00 4.33e-01 2.81e+01 angle pdb=" CB MET B 479 " pdb=" CG MET B 479 " pdb=" SD MET B 479 " ideal model delta sigma weight residual 112.70 127.94 -15.24 3.00e+00 1.11e-01 2.58e+01 angle pdb=" C TYR A 88 " pdb=" N PRO A 89 " pdb=" CD PRO A 89 " ideal model delta sigma weight residual 120.60 109.56 11.04 2.20e+00 2.07e-01 2.52e+01 angle pdb=" N ILE A1267 " pdb=" CA ILE A1267 " pdb=" C ILE A1267 " ideal model delta sigma weight residual 107.88 114.75 -6.87 1.38e+00 5.25e-01 2.48e+01 ... (remaining 20301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8420 17.95 - 35.91: 667 35.91 - 53.86: 104 53.86 - 71.81: 14 71.81 - 89.77: 5 Dihedral angle restraints: 9210 sinusoidal: 3808 harmonic: 5402 Sorted by residual: dihedral pdb=" C THR A1140 " pdb=" N THR A1140 " pdb=" CA THR A1140 " pdb=" CB THR A1140 " ideal model delta harmonic sigma weight residual -122.00 -134.54 12.54 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" N THR A1140 " pdb=" C THR A1140 " pdb=" CA THR A1140 " pdb=" CB THR A1140 " ideal model delta harmonic sigma weight residual 123.40 135.84 -12.44 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" CA THR A 104 " pdb=" C THR A 104 " pdb=" N SER A 105 " pdb=" CA SER A 105 " ideal model delta harmonic sigma weight residual -180.00 -155.81 -24.19 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 9207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2157 0.099 - 0.198: 136 0.198 - 0.297: 9 0.297 - 0.396: 2 0.396 - 0.495: 1 Chirality restraints: 2305 Sorted by residual: chirality pdb=" CA THR A1140 " pdb=" N THR A1140 " pdb=" C THR A1140 " pdb=" CB THR A1140 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" CA ASP A1139 " pdb=" N ASP A1139 " pdb=" C ASP A1139 " pdb=" CB ASP A1139 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CA GLU A 90 " pdb=" N GLU A 90 " pdb=" C GLU A 90 " pdb=" CB GLU A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 2302 not shown) Planarity restraints: 2601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A1337 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO A1338 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A1338 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1338 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1306 " -0.021 2.00e-02 2.50e+03 1.70e-02 7.19e+00 pdb=" CG TRP A1306 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A1306 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A1306 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1306 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1306 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1306 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1306 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1306 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1306 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 489 " 0.042 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO C 490 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 490 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 490 " 0.036 5.00e-02 4.00e+02 ... (remaining 2598 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2796 2.78 - 3.31: 13596 3.31 - 3.84: 23650 3.84 - 4.37: 27817 4.37 - 4.90: 48985 Nonbonded interactions: 116844 Sorted by model distance: nonbonded pdb=" OH TYR A 12 " pdb=" OD1 ASN A 968 " model vdw 2.249 3.040 nonbonded pdb=" O ILE A1122 " pdb=" OG SER A1126 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR A1304 " pdb=" OE1 GLU A1317 " model vdw 2.272 3.040 nonbonded pdb=" OE1 GLN A 830 " pdb=" OG SER A 835 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A1214 " pdb=" O ALA A1434 " model vdw 2.302 3.040 ... (remaining 116839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'D' and resid 479 through 579) selection = (chain 'E' and resid 479 through 579) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.980 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 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 0.070 15028 Z= 0.303 Angle : 0.882 15.240 20306 Z= 0.498 Chirality : 0.054 0.495 2305 Planarity : 0.006 0.068 2601 Dihedral : 12.933 89.766 5695 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.24 % Allowed : 0.36 % Favored : 99.40 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 1819 helix: 0.70 (0.15), residues: 1049 sheet: 0.96 (0.48), residues: 107 loop : -1.36 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A1306 HIS 0.010 0.001 HIS A 427 PHE 0.041 0.003 PHE C 609 TYR 0.025 0.002 TYR A 539 ARG 0.011 0.001 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 339 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1068 ILE cc_start: 0.8302 (tp) cc_final: 0.7965 (tp) REVERT: A 1095 ASP cc_start: 0.8328 (m-30) cc_final: 0.7959 (m-30) REVERT: A 1451 VAL cc_start: 0.8366 (t) cc_final: 0.8123 (t) REVERT: C 479 MET cc_start: 0.5950 (tmm) cc_final: 0.5721 (tmm) REVERT: C 646 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8879 (mt-10) outliers start: 4 outliers final: 2 residues processed: 343 average time/residue: 1.6706 time to fit residues: 619.0475 Evaluate side-chains 205 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 547 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 106 optimal weight: 0.0770 chunk 165 optimal weight: 20.0000 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 HIS A 830 GLN A 845 ASN A 929 ASN A1066 GLN A1394 GLN C 561 ASN C 606 GLN C 651 GLN D 539 GLN D 548 ASN E 534 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15028 Z= 0.230 Angle : 0.625 9.210 20306 Z= 0.324 Chirality : 0.043 0.222 2305 Planarity : 0.005 0.060 2601 Dihedral : 4.745 41.931 1984 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.87 % Favored : 98.08 % Rotamer: Outliers : 2.76 % Allowed : 10.86 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.01 (0.20), residues: 1819 helix: 1.64 (0.16), residues: 1076 sheet: 0.91 (0.51), residues: 99 loop : -1.06 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1306 HIS 0.008 0.001 HIS A 55 PHE 0.030 0.001 PHE A 553 TYR 0.016 0.001 TYR A 419 ARG 0.005 0.001 ARG A 911 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 1.706 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: A 1095 ASP cc_start: 0.8340 (m-30) cc_final: 0.8025 (m-30) REVERT: B 518 MET cc_start: 0.4157 (ttt) cc_final: 0.3887 (ttp) REVERT: D 531 MET cc_start: 0.8164 (ppp) cc_final: 0.7921 (ppp) REVERT: E 518 MET cc_start: 0.6232 (tmm) cc_final: 0.5989 (tmm) REVERT: E 534 ASN cc_start: 0.8677 (m-40) cc_final: 0.7643 (m-40) outliers start: 46 outliers final: 11 residues processed: 238 average time/residue: 1.7293 time to fit residues: 445.3645 Evaluate side-chains 208 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain E residue 565 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 0.3980 chunk 164 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS A 929 ASN C 606 GLN C 651 GLN D 591 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15028 Z= 0.319 Angle : 0.635 10.360 20306 Z= 0.325 Chirality : 0.044 0.189 2305 Planarity : 0.005 0.050 2601 Dihedral : 4.469 21.994 1980 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.14 % Favored : 97.75 % Rotamer: Outliers : 2.70 % Allowed : 12.61 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.32 (0.20), residues: 1819 helix: 1.97 (0.16), residues: 1076 sheet: 0.75 (0.50), residues: 101 loop : -1.03 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 447 HIS 0.005 0.001 HIS A 85 PHE 0.025 0.002 PHE A 553 TYR 0.019 0.002 TYR A1420 ARG 0.008 0.001 ARG A 911 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1026 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8680 (mtp) REVERT: A 1095 ASP cc_start: 0.8343 (m-30) cc_final: 0.8041 (m-30) REVERT: A 1158 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8655 (tm) REVERT: A 1160 SER cc_start: 0.8788 (t) cc_final: 0.8493 (m) REVERT: A 1262 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8522 (ptp-170) REVERT: D 531 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7964 (ppp) outliers start: 45 outliers final: 13 residues processed: 221 average time/residue: 1.6721 time to fit residues: 401.8689 Evaluate side-chains 201 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1262 ARG Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 10.0000 chunk 124 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 GLN C 651 GLN D 548 ASN ** D 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15028 Z= 0.214 Angle : 0.582 7.973 20306 Z= 0.298 Chirality : 0.042 0.189 2305 Planarity : 0.004 0.048 2601 Dihedral : 4.283 20.839 1980 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.36 % Favored : 97.53 % Rotamer: Outliers : 2.40 % Allowed : 13.63 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.64 (0.20), residues: 1819 helix: 2.24 (0.16), residues: 1070 sheet: 0.76 (0.51), residues: 101 loop : -0.89 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1306 HIS 0.007 0.001 HIS B 535 PHE 0.021 0.001 PHE A 553 TYR 0.012 0.001 TYR A 284 ARG 0.009 0.001 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 TYR cc_start: 0.8235 (m-10) cc_final: 0.8035 (m-10) REVERT: A 1095 ASP cc_start: 0.8309 (m-30) cc_final: 0.8030 (m-30) REVERT: A 1158 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8624 (tm) REVERT: A 1160 SER cc_start: 0.8751 (t) cc_final: 0.8462 (m) REVERT: A 1245 MET cc_start: 0.8787 (ttp) cc_final: 0.8526 (ttt) REVERT: A 1262 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8486 (ptp-170) REVERT: C 665 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8498 (tttp) outliers start: 40 outliers final: 11 residues processed: 218 average time/residue: 1.7634 time to fit residues: 415.6162 Evaluate side-chains 198 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1262 ARG Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 89 optimal weight: 0.0050 chunk 157 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN A1237 GLN C 606 GLN C 648 ASN C 651 GLN D 528 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15028 Z= 0.190 Angle : 0.576 7.821 20306 Z= 0.294 Chirality : 0.042 0.186 2305 Planarity : 0.004 0.048 2601 Dihedral : 4.142 20.126 1980 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.53 % Favored : 97.36 % Rotamer: Outliers : 2.16 % Allowed : 14.23 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.83 (0.20), residues: 1819 helix: 2.37 (0.16), residues: 1073 sheet: 0.85 (0.52), residues: 100 loop : -0.77 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1248 HIS 0.007 0.001 HIS B 535 PHE 0.019 0.001 PHE A 553 TYR 0.011 0.001 TYR A 284 ARG 0.009 0.001 ARG A1180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7945 (mtp85) cc_final: 0.7717 (mtp-110) REVERT: A 472 LYS cc_start: 0.8858 (mmtm) cc_final: 0.8421 (mtmm) REVERT: A 1032 MET cc_start: 0.8805 (mtt) cc_final: 0.8432 (mtt) REVERT: A 1095 ASP cc_start: 0.8288 (m-30) cc_final: 0.8028 (m-30) REVERT: A 1160 SER cc_start: 0.8694 (t) cc_final: 0.8420 (m) REVERT: A 1245 MET cc_start: 0.8859 (ttp) cc_final: 0.8588 (ttt) REVERT: C 665 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8464 (tttp) outliers start: 36 outliers final: 12 residues processed: 218 average time/residue: 1.8163 time to fit residues: 429.1482 Evaluate side-chains 200 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain E residue 534 ASN Chi-restraints excluded: chain E residue 575 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.9734 > 50: distance: 23 - 45: 14.048 distance: 27 - 51: 24.820 distance: 34 - 55: 25.892 distance: 37 - 45: 12.946 distance: 38 - 63: 18.200 distance: 45 - 46: 9.216 distance: 46 - 47: 23.127 distance: 46 - 49: 12.667 distance: 47 - 48: 32.223 distance: 47 - 51: 16.727 distance: 48 - 74: 3.636 distance: 49 - 50: 28.730 distance: 51 - 52: 21.299 distance: 52 - 53: 5.189 distance: 53 - 54: 24.741 distance: 53 - 55: 46.105 distance: 54 - 83: 42.365 distance: 55 - 56: 26.384 distance: 56 - 57: 33.290 distance: 56 - 59: 12.548 distance: 57 - 58: 32.965 distance: 57 - 63: 17.654 distance: 58 - 89: 20.635 distance: 59 - 60: 8.521 distance: 60 - 61: 21.008 distance: 60 - 62: 35.825 distance: 63 - 64: 7.944 distance: 64 - 65: 45.486 distance: 64 - 67: 35.854 distance: 65 - 66: 38.285 distance: 65 - 74: 37.395 distance: 67 - 68: 25.405 distance: 68 - 69: 20.737 distance: 69 - 70: 19.231 distance: 70 - 71: 4.702 distance: 71 - 72: 8.238 distance: 71 - 73: 7.885 distance: 74 - 75: 15.540 distance: 75 - 76: 41.829 distance: 75 - 78: 27.854 distance: 76 - 77: 37.754 distance: 76 - 83: 30.226 distance: 78 - 79: 26.628 distance: 79 - 80: 15.082 distance: 80 - 81: 13.967 distance: 81 - 82: 17.175 distance: 83 - 84: 7.503 distance: 84 - 85: 26.165 distance: 84 - 87: 17.840 distance: 85 - 86: 25.855 distance: 85 - 89: 10.633 distance: 87 - 88: 51.375 distance: 89 - 90: 16.497 distance: 90 - 91: 17.632 distance: 91 - 92: 40.263 distance: 91 - 93: 44.632 distance: 93 - 94: 13.111 distance: 94 - 95: 40.193 distance: 94 - 97: 52.252 distance: 95 - 96: 31.226 distance: 95 - 101: 14.340 distance: 97 - 98: 20.574 distance: 98 - 99: 37.187 distance: 98 - 100: 29.234 distance: 101 - 102: 8.196 distance: 102 - 103: 57.601 distance: 102 - 105: 48.997 distance: 103 - 104: 15.040 distance: 103 - 110: 37.400 distance: 105 - 106: 36.010 distance: 106 - 107: 22.547 distance: 107 - 108: 7.667 distance: 107 - 109: 20.278 distance: 110 - 111: 31.926 distance: 110 - 116: 27.009 distance: 111 - 112: 16.785 distance: 111 - 114: 28.555 distance: 112 - 113: 31.497 distance: 112 - 117: 19.930 distance: 113 - 140: 25.450 distance: 114 - 115: 35.119 distance: 115 - 116: 31.474