Starting phenix.real_space_refine on Mon Sep 23 21:36:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzx_30262/09_2024/7bzx_30262.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzx_30262/09_2024/7bzx_30262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzx_30262/09_2024/7bzx_30262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzx_30262/09_2024/7bzx_30262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzx_30262/09_2024/7bzx_30262.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzx_30262/09_2024/7bzx_30262.cif" } resolution = 4.0 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= 0.003 sd= 0.026 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: 3 Type Number sf(0) Gaussians C 3346 2.51 5 N 1154 2.21 5 O 1152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5652 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 2850 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 466} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 552} Chain breaks: 2 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 1634 Unresolved non-hydrogen angles: 2099 Unresolved non-hydrogen dihedrals: 1341 Unresolved non-hydrogen chiralities: 168 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 27, 'TYR:plan': 17, 'ASN:plan1': 21, 'TRP:plan': 2, 'HIS:plan': 17, 'PHE:plan': 22, 'GLU:plan': 26, 'ASP:plan': 38} Unresolved non-hydrogen planarities: 834 Chain: "A" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 2802 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 459} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 545} Chain breaks: 2 Unresolved chain link angles: 26 Unresolved non-hydrogen bonds: 1618 Unresolved non-hydrogen angles: 2078 Unresolved non-hydrogen dihedrals: 1327 Unresolved non-hydrogen chiralities: 166 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 27, 'TYR:plan': 17, 'ASN:plan1': 21, 'TRP:plan': 2, 'HIS:plan': 17, 'PHE:plan': 22, 'GLU:plan': 26, 'ASP:plan': 38} Unresolved non-hydrogen planarities: 834 Time building chain proxies: 4.40, per 1000 atoms: 0.78 Number of scatterers: 5652 At special positions: 0 Unit cell: (87.55, 93.73, 82.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1152 8.00 N 1154 7.00 C 3346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.21 Conformation dependent library (CDL) restraints added in 1.6 seconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 6 sheets defined 49.6% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'B' and resid 74 through 80 Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 93 through 111 removed outlier: 3.656A pdb=" N LYS B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 133 removed outlier: 5.013A pdb=" N GLU B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 154 Processing helix chain 'B' and resid 155 through 156 No H-bonds generated for 'chain 'B' and resid 155 through 156' Processing helix chain 'B' and resid 157 through 164 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 191 through 206 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 223 through 237 Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 368 through 374 Processing helix chain 'B' and resid 374 through 379 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 400 through 416 removed outlier: 3.614A pdb=" N GLU B 414 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 449 through 463 Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 479 through 485 Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 507 through 511 removed outlier: 4.015A pdb=" N THR B 510 " --> pdb=" O ASP B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 533 through 547 Processing helix chain 'B' and resid 566 through 570 Processing helix chain 'B' and resid 595 through 605 Processing helix chain 'B' and resid 605 through 610 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 651 through 663 Processing helix chain 'B' and resid 664 through 667 Processing helix chain 'B' and resid 686 through 694 Processing helix chain 'B' and resid 697 through 708 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 91 through 111 removed outlier: 4.106A pdb=" N LYS A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A 96 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 133 removed outlier: 4.971A pdb=" N GLU A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 155 through 156 No H-bonds generated for 'chain 'A' and resid 155 through 156' Processing helix chain 'A' and resid 157 through 164 Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 223 through 237 Processing helix chain 'A' and resid 336 through 348 Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 400 through 416 removed outlier: 3.727A pdb=" N GLU A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 449 through 463 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'A' and resid 515 through 520 Processing helix chain 'A' and resid 521 through 523 No H-bonds generated for 'chain 'A' and resid 521 through 523' Processing helix chain 'A' and resid 533 through 547 Processing helix chain 'A' and resid 595 through 605 Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 651 through 663 Processing helix chain 'A' and resid 686 through 694 Processing helix chain 'A' and resid 697 through 707 Processing sheet with id=AA1, first strand: chain 'B' and resid 139 through 142 removed outlier: 5.734A pdb=" N LYS B 139 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL B 215 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 141 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY B 217 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 212 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE B 243 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA B 214 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN B 245 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B 216 " --> pdb=" O ASN B 245 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N MET B 240 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE B 358 " --> pdb=" O MET B 240 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 242 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B 360 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU B 244 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR B 327 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS B 359 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE B 329 " --> pdb=" O HIS B 359 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VAL B 361 " --> pdb=" O ILE B 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 443 through 445 removed outlier: 6.380A pdb=" N VAL B 420 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA B 470 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE B 422 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N TYR B 472 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE B 527 " --> pdb=" O CYS B 553 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG B 555 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N MET B 529 " --> pdb=" O ARG B 555 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 581 through 584 removed outlier: 6.096A pdb=" N VAL B 617 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU B 641 " --> pdb=" O ARG B 673 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N MET B 675 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR B 643 " --> pdb=" O MET B 675 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU B 677 " --> pdb=" O THR B 643 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLU B 645 " --> pdb=" O LEU B 677 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 139 through 142 removed outlier: 5.763A pdb=" N LYS A 139 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL A 215 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 141 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLY A 217 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 212 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A 243 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA A 214 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN A 245 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A 216 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 242 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 360 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU A 244 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 327 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N HIS A 359 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE A 329 " --> pdb=" O HIS A 359 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL A 361 " --> pdb=" O ILE A 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 443 through 445 removed outlier: 6.298A pdb=" N VAL A 420 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA A 470 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE A 422 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N TYR A 472 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA A 497 " --> pdb=" O PRO A 467 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N CYS A 469 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP A 499 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 471 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 527 " --> pdb=" O CYS A 553 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ARG A 555 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N MET A 529 " --> pdb=" O ARG A 555 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 581 through 584 removed outlier: 6.045A pdb=" N VAL A 617 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ALA A 590 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A 644 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 592 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLU A 646 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A 641 " --> pdb=" O ARG A 673 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N MET A 675 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR A 643 " --> pdb=" O MET A 675 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU A 677 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLU A 645 " --> pdb=" O LEU A 677 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1014 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: 2.17 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.26: 1151 1.26 - 1.34: 901 1.34 - 1.41: 276 1.41 - 1.48: 1196 1.48 - 1.56: 2122 Bond restraints: 5646 Sorted by residual: bond pdb=" N PRO B 524 " pdb=" CA PRO B 524 " ideal model delta sigma weight residual 1.467 1.399 0.068 1.17e-02 7.31e+03 3.41e+01 bond pdb=" CA THR A 256 " pdb=" C THR A 256 " ideal model delta sigma weight residual 1.522 1.470 0.052 9.30e-03 1.16e+04 3.17e+01 bond pdb=" N PRO A 557 " pdb=" CA PRO A 557 " ideal model delta sigma weight residual 1.465 1.404 0.061 1.10e-02 8.26e+03 3.08e+01 bond pdb=" N PRO A 467 " pdb=" CA PRO A 467 " ideal model delta sigma weight residual 1.467 1.402 0.065 1.19e-02 7.06e+03 2.97e+01 bond pdb=" N ALA A 618 " pdb=" CA ALA A 618 " ideal model delta sigma weight residual 1.456 1.391 0.065 1.21e-02 6.83e+03 2.92e+01 ... (remaining 5641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 6057 2.62 - 5.25: 1615 5.25 - 7.87: 132 7.87 - 10.49: 16 10.49 - 13.11: 6 Bond angle restraints: 7826 Sorted by residual: angle pdb=" C LYS B 393 " pdb=" N THR B 394 " pdb=" CA THR B 394 " ideal model delta sigma weight residual 120.54 132.72 -12.18 1.35e+00 5.49e-01 8.14e+01 angle pdb=" N PRO B 567 " pdb=" CA PRO B 567 " pdb=" C PRO B 567 " ideal model delta sigma weight residual 110.70 119.92 -9.22 1.22e+00 6.72e-01 5.72e+01 angle pdb=" N GLY A 653 " pdb=" CA GLY A 653 " pdb=" C GLY A 653 " ideal model delta sigma weight residual 112.50 104.47 8.03 1.16e+00 7.43e-01 4.79e+01 angle pdb=" C GLY B 145 " pdb=" N HIS B 146 " pdb=" CA HIS B 146 " ideal model delta sigma weight residual 120.31 130.48 -10.17 1.52e+00 4.33e-01 4.48e+01 angle pdb=" C ASN B 247 " pdb=" CA ASN B 247 " pdb=" CB ASN B 247 " ideal model delta sigma weight residual 110.79 99.71 11.08 1.66e+00 3.63e-01 4.45e+01 ... (remaining 7821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.51: 2703 6.51 - 13.02: 375 13.02 - 19.53: 107 19.53 - 26.04: 30 26.04 - 32.55: 9 Dihedral angle restraints: 3224 sinusoidal: 0 harmonic: 3224 Sorted by residual: dihedral pdb=" C THR B 112 " pdb=" N THR B 112 " pdb=" CA THR B 112 " pdb=" CB THR B 112 " ideal model delta harmonic sigma weight residual -122.00 -142.58 20.58 0 2.50e+00 1.60e-01 6.78e+01 dihedral pdb=" CA GLY B 429 " pdb=" C GLY B 429 " pdb=" N THR B 430 " pdb=" CA THR B 430 " ideal model delta harmonic sigma weight residual 180.00 147.45 32.55 0 5.00e+00 4.00e-02 4.24e+01 dihedral pdb=" N THR B 112 " pdb=" C THR B 112 " pdb=" CA THR B 112 " pdb=" CB THR B 112 " ideal model delta harmonic sigma weight residual 123.40 138.49 -15.09 0 2.50e+00 1.60e-01 3.64e+01 ... (remaining 3221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 825 0.137 - 0.273: 188 0.273 - 0.410: 21 0.410 - 0.547: 1 0.547 - 0.683: 3 Chirality restraints: 1038 Sorted by residual: chirality pdb=" CA THR B 112 " pdb=" N THR B 112 " pdb=" C THR B 112 " pdb=" CB THR B 112 " both_signs ideal model delta sigma weight residual False 2.53 1.84 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CA ASP A 507 " pdb=" N ASP A 507 " pdb=" C ASP A 507 " pdb=" CB ASP A 507 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CA PRO B 253 " pdb=" N PRO B 253 " pdb=" C PRO B 253 " pdb=" CB PRO B 253 " both_signs ideal model delta sigma weight residual False 2.72 2.16 0.56 2.00e-01 2.50e+01 7.72e+00 ... (remaining 1035 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 173 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C PHE A 173 " -0.075 2.00e-02 2.50e+03 pdb=" O PHE A 173 " 0.028 2.00e-02 2.50e+03 pdb=" N THR A 174 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 253 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C PRO A 253 " -0.066 2.00e-02 2.50e+03 pdb=" O PRO A 253 " 0.025 2.00e-02 2.50e+03 pdb=" N THR A 254 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 640 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.58e+00 pdb=" C VAL B 640 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL B 640 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU B 641 " -0.018 2.00e-02 2.50e+03 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 3416 2.97 - 3.45: 6817 3.45 - 3.93: 8153 3.93 - 4.42: 10762 4.42 - 4.90: 14735 Nonbonded interactions: 43883 Sorted by model distance: nonbonded pdb=" N GLU B 93 " pdb=" N LEU B 94 " model vdw 2.485 2.560 nonbonded pdb=" N LYS B 248 " pdb=" N GLN B 249 " model vdw 2.532 2.560 nonbonded pdb=" N ILE A 471 " pdb=" O ILE A 471 " model vdw 2.534 2.496 nonbonded pdb=" N ASP B 507 " pdb=" N GLY B 508 " model vdw 2.541 2.560 nonbonded pdb=" N THR A 254 " pdb=" O THR A 254 " model vdw 2.555 2.496 ... (remaining 43878 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 'A' selection = (chain 'B' and (resid 73 through 258 or resid 320 through 708)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.660 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2515 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 : 0.019 0.068 5646 Z= 1.391 Angle : 2.216 13.114 7826 Z= 1.609 Chirality : 0.118 0.683 1038 Planarity : 0.009 0.043 1148 Dihedral : 8.559 32.555 1148 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 1.31 % Allowed : 6.57 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.87 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.90 (0.21), residues: 1142 helix: -1.44 (0.20), residues: 505 sheet: -2.51 (0.44), residues: 111 loop : -2.20 (0.23), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 142 PHE 0.000 0.000 PHE B 107 TYR 0.000 0.000 TYR B 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.583 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0557 time to fit residues: 4.2582 Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3620 moved from start: 0.6608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5646 Z= 0.229 Angle : 0.758 8.003 7826 Z= 0.460 Chirality : 0.048 0.163 1038 Planarity : 0.004 0.019 1148 Dihedral : 6.766 28.735 1148 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.30 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: -2.00 (0.23), residues: 1142 helix: -0.53 (0.21), residues: 516 sheet: -1.92 (0.41), residues: 154 loop : -1.93 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 142 PHE 0.000 0.000 PHE B 107 TYR 0.000 0.000 TYR B 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.579 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0556 time to fit residues: 4.3092 Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 103 optimal weight: 30.0000 chunk 35 optimal weight: 30.0000 chunk 83 optimal weight: 40.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4184 moved from start: 1.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5646 Z= 0.234 Angle : 0.651 6.107 7826 Z= 0.405 Chirality : 0.046 0.134 1038 Planarity : 0.004 0.018 1148 Dihedral : 6.343 25.199 1148 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.84 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: -2.05 (0.24), residues: 1142 helix: -0.47 (0.22), residues: 508 sheet: -1.80 (0.36), residues: 164 loop : -2.12 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 142 PHE 0.000 0.000 PHE B 107 TYR 0.000 0.000 TYR B 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.610 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0558 time to fit residues: 4.3114 Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 30.0000 chunk 78 optimal weight: 30.0000 chunk 54 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 49 optimal weight: 30.0000 chunk 70 optimal weight: 30.0000 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 99 optimal weight: 50.0000 chunk 29 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4569 moved from start: 1.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5646 Z= 0.278 Angle : 0.756 7.501 7826 Z= 0.465 Chirality : 0.049 0.163 1038 Planarity : 0.004 0.018 1148 Dihedral : 7.299 26.453 1148 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.25 % Favored : 89.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: -2.66 (0.23), residues: 1142 helix: -0.99 (0.22), residues: 493 sheet: -2.20 (0.41), residues: 134 loop : -2.38 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 142 PHE 0.000 0.000 PHE B 107 TYR 0.000 0.000 TYR B 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.594 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0568 time to fit residues: 4.2751 Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 40.0000 chunk 94 optimal weight: 30.0000 chunk 76 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 40.0000 chunk 28 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4575 moved from start: 1.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5646 Z= 0.204 Angle : 0.601 6.417 7826 Z= 0.371 Chirality : 0.046 0.128 1038 Planarity : 0.003 0.016 1148 Dihedral : 6.173 23.582 1148 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.30 % Favored : 88.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: -2.59 (0.24), residues: 1142 helix: -0.78 (0.23), residues: 497 sheet: -2.30 (0.41), residues: 137 loop : -2.48 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 142 PHE 0.000 0.000 PHE B 107 TYR 0.000 0.000 TYR B 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.594 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0543 time to fit residues: 4.2128 Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.0570 chunk 21 optimal weight: 50.0000 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 30.0000 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4362 moved from start: 1.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.013 5646 Z= 0.093 Angle : 0.435 4.827 7826 Z= 0.263 Chirality : 0.044 0.127 1038 Planarity : 0.002 0.011 1148 Dihedral : 4.675 22.589 1148 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: -1.58 (0.25), residues: 1142 helix: 0.13 (0.24), residues: 510 sheet: -2.20 (0.40), residues: 141 loop : -1.92 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 142 PHE 0.000 0.000 PHE B 107 TYR 0.000 0.000 TYR B 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.602 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0607 time to fit residues: 4.5470 Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 69 optimal weight: 30.0000 chunk 67 optimal weight: 30.0000 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 overall best weight: 7.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4760 moved from start: 1.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5646 Z= 0.253 Angle : 0.671 7.958 7826 Z= 0.416 Chirality : 0.047 0.158 1038 Planarity : 0.004 0.019 1148 Dihedral : 6.746 24.985 1148 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.75 % Favored : 86.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: -2.69 (0.24), residues: 1142 helix: -0.90 (0.23), residues: 480 sheet: -2.36 (0.37), residues: 143 loop : -2.43 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 142 PHE 0.000 0.000 PHE B 107 TYR 0.000 0.000 TYR B 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.603 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0579 time to fit residues: 4.5007 Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4867 moved from start: 1.7097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5646 Z= 0.261 Angle : 0.703 6.598 7826 Z= 0.436 Chirality : 0.048 0.148 1038 Planarity : 0.004 0.017 1148 Dihedral : 7.493 33.888 1148 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.32 % Favored : 84.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.46 (0.23), residues: 1142 helix: -1.56 (0.22), residues: 474 sheet: -2.52 (0.42), residues: 114 loop : -2.93 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 142 PHE 0.000 0.000 PHE B 107 TYR 0.000 0.000 TYR B 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.527 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0555 time to fit residues: 4.2119 Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 62 optimal weight: 30.0000 chunk 44 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 chunk 93 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 109 optimal weight: 0.0170 overall best weight: 6.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4839 moved from start: 1.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5646 Z= 0.215 Angle : 0.610 5.830 7826 Z= 0.378 Chirality : 0.047 0.135 1038 Planarity : 0.003 0.016 1148 Dihedral : 6.704 29.853 1148 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.62 % Favored : 85.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: -3.45 (0.23), residues: 1142 helix: -1.36 (0.22), residues: 467 sheet: -2.67 (0.42), residues: 116 loop : -3.08 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 142 PHE 0.000 0.000 PHE B 107 TYR 0.000 0.000 TYR B 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.586 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0567 time to fit residues: 4.3896 Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 114 optimal weight: 30.0000 chunk 105 optimal weight: 20.0000 chunk 91 optimal weight: 40.0000 chunk 9 optimal weight: 0.0670 chunk 70 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 overall best weight: 7.0130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4935 moved from start: 1.8019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5646 Z= 0.244 Angle : 0.675 6.474 7826 Z= 0.418 Chirality : 0.047 0.137 1038 Planarity : 0.004 0.016 1148 Dihedral : 7.464 36.188 1148 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.99 % Favored : 83.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.72 (0.23), residues: 1142 helix: -1.62 (0.22), residues: 465 sheet: -2.55 (0.47), residues: 92 loop : -3.26 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 142 PHE 0.000 0.000 PHE B 107 TYR 0.000 0.000 TYR B 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.600 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0581 time to fit residues: 4.4340 Evaluate side-chains 34 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 13 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 91 optimal weight: 40.0000 chunk 38 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 overall best weight: 10.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.092254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.083111 restraints weight = 37560.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.084062 restraints weight = 29556.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.084798 restraints weight = 24098.174| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5730 moved from start: 1.8944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 5646 Z= 0.340 Angle : 0.841 10.034 7826 Z= 0.521 Chirality : 0.050 0.168 1038 Planarity : 0.005 0.020 1148 Dihedral : 8.680 46.177 1148 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.10 % Favored : 78.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.21), residues: 1142 helix: -2.24 (0.20), residues: 459 sheet: -2.76 (0.50), residues: 81 loop : -3.84 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 142 PHE 0.000 0.000 PHE B 107 TYR 0.000 0.000 TYR B 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 949.94 seconds wall clock time: 17 minutes 24.05 seconds (1044.05 seconds total)