Starting phenix.real_space_refine (version: dev) on Fri May 13 06:19:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/05_2022/7lh3_23335.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/05_2022/7lh3_23335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/05_2022/7lh3_23335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/05_2022/7lh3_23335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/05_2022/7lh3_23335.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/05_2022/7lh3_23335.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.007 sd= 0.020 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 31": "NH1" <-> "NH2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 502": "NH1" <-> "NH2" Residue "B ARG 558": "NH1" <-> "NH2" Residue "B TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 689": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 10452 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 6.58, per 1000 atoms: 0.63 Number of scatterers: 10452 At special positions: 0 Unit cell: (102.16, 119.078, 113.222, 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 48 16.00 O 1852 8.00 N 1690 7.00 C 6862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.38 Conformation dependent library (CDL) restraints added in 1.6 seconds 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2512 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 5 sheets defined 71.5% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 Processing helix chain 'A' and resid 41 through 48 removed outlier: 4.243A pdb=" N GLN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 75 through 105 removed outlier: 5.182A pdb=" N LEU A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLY A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 108 through 115 removed outlier: 3.988A pdb=" N GLY A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.715A pdb=" N PHE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'A' and resid 168 through 196 Processing helix chain 'A' and resid 197 through 205 removed outlier: 4.087A pdb=" N PHE A 200 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 203 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 308 removed outlier: 3.543A pdb=" N PHE A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.744A pdb=" N TYR A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 366 removed outlier: 6.430A pdb=" N VAL A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 411 through 428 removed outlier: 3.513A pdb=" N CYS A 415 " --> pdb=" O GLN A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 4.188A pdb=" N SER A 434 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 448 removed outlier: 3.847A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.875A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 Processing helix chain 'A' and resid 483 through 505 removed outlier: 3.713A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.605A pdb=" N THR A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 579 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 653 through 670 removed outlier: 3.626A pdb=" N VAL A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 691 through 694 removed outlier: 3.737A pdb=" N GLU A 694 " --> pdb=" O ARG A 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 694' Processing helix chain 'A' and resid 695 through 702 removed outlier: 3.942A pdb=" N GLU A 700 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 702 " --> pdb=" O TRP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.591A pdb=" N GLU A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 31 Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.243A pdb=" N GLN B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 75 through 105 removed outlier: 5.182A pdb=" N LEU B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLY B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 108 through 115 removed outlier: 3.987A pdb=" N GLY B 112 " --> pdb=" O PRO B 108 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.715A pdb=" N PHE B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 152 Processing helix chain 'B' and resid 168 through 196 Processing helix chain 'B' and resid 197 through 205 removed outlier: 4.086A pdb=" N PHE B 200 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 203 " --> pdb=" O PHE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 308 removed outlier: 3.543A pdb=" N PHE B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.744A pdb=" N TYR B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 366 removed outlier: 6.430A pdb=" N VAL B 341 " --> pdb=" O HIS B 337 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASP B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 411 through 428 removed outlier: 3.513A pdb=" N CYS B 415 " --> pdb=" O GLN B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 4.189A pdb=" N SER B 434 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 448 removed outlier: 3.847A pdb=" N LEU B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 removed outlier: 3.875A pdb=" N PHE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 481 Processing helix chain 'B' and resid 483 through 505 removed outlier: 3.713A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 560 removed outlier: 3.605A pdb=" N THR B 560 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 579 Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 653 through 670 removed outlier: 3.627A pdb=" N VAL B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 690 Processing helix chain 'B' and resid 691 through 694 removed outlier: 3.737A pdb=" N GLU B 694 " --> pdb=" O ARG B 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 691 through 694' Processing helix chain 'B' and resid 695 through 702 removed outlier: 3.943A pdb=" N GLU B 700 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 702 " --> pdb=" O TRP B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.590A pdb=" N GLU B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.817A pdb=" N VAL A 18 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 18 " --> pdb=" O VAL A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.607A pdb=" N GLY A 135 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 394 " --> pdb=" O GLY A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.520A pdb=" N LYS A 509 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 511 " --> pdb=" O ILE A 537 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N LYS A 513 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 11.976A pdb=" N ILE A 535 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LYS A 536 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASP A 645 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE A 538 " --> pdb=" O ASP A 645 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.606A pdb=" N GLY B 135 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 394 " --> pdb=" O GLY B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 removed outlier: 3.520A pdb=" N LYS B 509 " --> pdb=" O GLN B 539 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 511 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N LYS B 513 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 11.976A pdb=" N ILE B 535 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LYS B 536 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ASP B 645 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE B 538 " --> pdb=" O ASP B 645 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1902 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: 3.43 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3236 1.34 - 1.46: 2311 1.46 - 1.58: 5063 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 10688 Sorted by residual: bond pdb=" CA ILE A 532 " pdb=" CB ILE A 532 " ideal model delta sigma weight residual 1.537 1.529 0.008 1.29e-02 6.01e+03 4.04e-01 bond pdb=" C LEU B 71 " pdb=" N PRO B 72 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.28e-02 6.10e+03 3.41e-01 bond pdb=" C GLY A 408 " pdb=" O GLY A 408 " ideal model delta sigma weight residual 1.235 1.243 -0.008 1.35e-02 5.49e+03 3.41e-01 bond pdb=" C GLY B 408 " pdb=" O GLY B 408 " ideal model delta sigma weight residual 1.235 1.243 -0.008 1.35e-02 5.49e+03 3.36e-01 bond pdb=" N PRO B 327 " pdb=" CA PRO B 327 " ideal model delta sigma weight residual 1.459 1.467 -0.008 1.40e-02 5.10e+03 3.20e-01 ... (remaining 10683 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.18: 343 107.18 - 113.88: 6160 113.88 - 120.58: 4394 120.58 - 127.28: 3544 127.28 - 133.97: 91 Bond angle restraints: 14532 Sorted by residual: angle pdb=" N THR A 517 " pdb=" CA THR A 517 " pdb=" C THR A 517 " ideal model delta sigma weight residual 108.34 110.93 -2.59 1.31e+00 5.83e-01 3.90e+00 angle pdb=" N THR B 517 " pdb=" CA THR B 517 " pdb=" C THR B 517 " ideal model delta sigma weight residual 108.34 110.90 -2.56 1.31e+00 5.83e-01 3.81e+00 angle pdb=" N SER A 24 " pdb=" CA SER A 24 " pdb=" C SER A 24 " ideal model delta sigma weight residual 110.53 108.23 2.30 1.29e+00 6.01e-01 3.18e+00 angle pdb=" N SER B 24 " pdb=" CA SER B 24 " pdb=" C SER B 24 " ideal model delta sigma weight residual 110.53 108.26 2.27 1.29e+00 6.01e-01 3.09e+00 angle pdb=" NE ARG A 31 " pdb=" CZ ARG A 31 " pdb=" NH1 ARG A 31 " ideal model delta sigma weight residual 121.50 120.00 1.50 1.00e+00 1.00e+00 2.26e+00 ... (remaining 14527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.64: 6013 12.64 - 25.27: 243 25.27 - 37.91: 68 37.91 - 50.55: 8 50.55 - 63.18: 6 Dihedral angle restraints: 6338 sinusoidal: 2414 harmonic: 3924 Sorted by residual: dihedral pdb=" CA LEU B 184 " pdb=" CB LEU B 184 " pdb=" CG LEU B 184 " pdb=" CD1 LEU B 184 " ideal model delta sinusoidal sigma weight residual 60.00 118.45 -58.45 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LEU A 184 " pdb=" CB LEU A 184 " pdb=" CG LEU A 184 " pdb=" CD1 LEU A 184 " ideal model delta sinusoidal sigma weight residual 60.00 118.44 -58.44 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LEU B 422 " pdb=" CB LEU B 422 " pdb=" CG LEU B 422 " pdb=" CD1 LEU B 422 " ideal model delta sinusoidal sigma weight residual 180.00 123.35 56.65 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 6335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 996 0.025 - 0.050: 406 0.050 - 0.075: 210 0.075 - 0.100: 73 0.100 - 0.126: 43 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA ILE A 532 " pdb=" N ILE A 532 " pdb=" C ILE A 532 " pdb=" CB ILE A 532 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE B 532 " pdb=" N ILE B 532 " pdb=" C ILE B 532 " pdb=" CB ILE B 532 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE B 290 " pdb=" N ILE B 290 " pdb=" C ILE B 290 " pdb=" CB ILE B 290 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1725 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 542 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A 543 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 542 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO B 543 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 543 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 543 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 53 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.15e+00 pdb=" N PRO B 54 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " -0.015 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2359 2.79 - 3.31: 10623 3.31 - 3.84: 17205 3.84 - 4.37: 18938 4.37 - 4.90: 33623 Nonbonded interactions: 82748 Sorted by model distance: nonbonded pdb=" O ALA B 495 " pdb=" OG1 THR B 498 " model vdw 2.258 2.440 nonbonded pdb=" O ALA A 495 " pdb=" OG1 THR A 498 " model vdw 2.258 2.440 nonbonded pdb=" OD2 ASP A 83 " pdb=" OG1 THR A 410 " model vdw 2.316 2.440 nonbonded pdb=" O LEU B 556 " pdb=" OG1 THR B 560 " model vdw 2.316 2.440 nonbonded pdb=" O LEU A 556 " pdb=" OG1 THR A 560 " model vdw 2.317 2.440 ... (remaining 82743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6862 2.51 5 N 1690 2.21 5 O 1852 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.990 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: 4.520 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.110 Process input model: 32.270 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 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 : 0.001 0.014 10688 Z= 0.090 Angle : 0.399 5.170 14532 Z= 0.224 Chirality : 0.039 0.126 1728 Planarity : 0.003 0.029 1808 Dihedral : 7.882 63.182 3826 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.25), residues: 1352 helix: 2.34 (0.19), residues: 908 sheet: 3.14 (0.70), residues: 52 loop : -0.75 (0.32), residues: 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 302 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 306 average time/residue: 0.2510 time to fit residues: 106.0647 Evaluate side-chains 142 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 10.0000 chunk 103 optimal weight: 40.0000 chunk 57 optimal weight: 0.0010 chunk 35 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 0.4980 chunk 106 optimal weight: 50.0000 chunk 41 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 overall best weight: 3.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 454 GLN ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 454 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10688 Z= 0.162 Angle : 0.525 7.185 14532 Z= 0.260 Chirality : 0.042 0.144 1728 Planarity : 0.004 0.031 1808 Dihedral : 2.931 13.174 1456 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.25), residues: 1352 helix: 2.35 (0.19), residues: 900 sheet: 3.21 (0.73), residues: 52 loop : -0.61 (0.32), residues: 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2080 time to fit residues: 54.2650 Evaluate side-chains 133 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.331 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 84 optimal weight: 30.0000 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 40.0000 chunk 133 optimal weight: 9.9990 chunk 110 optimal weight: 30.0000 chunk 122 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 99 optimal weight: 40.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 10688 Z= 0.284 Angle : 0.610 6.886 14532 Z= 0.309 Chirality : 0.044 0.150 1728 Planarity : 0.004 0.060 1808 Dihedral : 3.510 15.891 1456 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1352 helix: 1.86 (0.18), residues: 916 sheet: 2.52 (0.74), residues: 52 loop : -0.82 (0.34), residues: 384 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.2079 time to fit residues: 51.1771 Evaluate side-chains 113 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.443 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 50.0000 chunk 59 optimal weight: 0.6980 chunk 83 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 overall best weight: 5.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10688 Z= 0.196 Angle : 0.539 6.357 14532 Z= 0.271 Chirality : 0.043 0.148 1728 Planarity : 0.004 0.035 1808 Dihedral : 3.436 16.013 1456 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.24), residues: 1352 helix: 2.04 (0.18), residues: 902 sheet: 3.30 (0.91), residues: 38 loop : -0.34 (0.34), residues: 412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.2031 time to fit residues: 52.5661 Evaluate side-chains 121 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 44 optimal weight: 0.0770 overall best weight: 6.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10688 Z= 0.217 Angle : 0.565 7.330 14532 Z= 0.282 Chirality : 0.043 0.150 1728 Planarity : 0.004 0.037 1808 Dihedral : 3.557 19.540 1456 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.24), residues: 1352 helix: 1.98 (0.18), residues: 902 sheet: 3.04 (0.92), residues: 38 loop : -0.38 (0.34), residues: 412 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1909 time to fit residues: 46.3216 Evaluate side-chains 117 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 10.0000 chunk 25 optimal weight: 40.0000 chunk 77 optimal weight: 0.0670 chunk 32 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 109 optimal weight: 0.0370 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 126 optimal weight: 50.0000 overall best weight: 4.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10688 Z= 0.162 Angle : 0.545 7.928 14532 Z= 0.268 Chirality : 0.043 0.179 1728 Planarity : 0.004 0.038 1808 Dihedral : 3.491 18.124 1456 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.24), residues: 1352 helix: 2.03 (0.18), residues: 904 sheet: 3.11 (0.91), residues: 38 loop : -0.42 (0.34), residues: 410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2205 time to fit residues: 54.0778 Evaluate side-chains 121 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.384 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 110 optimal weight: 30.0000 chunk 73 optimal weight: 8.9990 chunk 131 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10688 Z= 0.217 Angle : 0.585 7.032 14532 Z= 0.288 Chirality : 0.043 0.167 1728 Planarity : 0.004 0.038 1808 Dihedral : 3.615 18.147 1456 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.24), residues: 1352 helix: 2.00 (0.18), residues: 898 sheet: 3.00 (0.91), residues: 38 loop : -0.49 (0.34), residues: 416 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1923 time to fit residues: 44.2713 Evaluate side-chains 113 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.328 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.2980 chunk 39 optimal weight: 30.0000 chunk 25 optimal weight: 50.0000 chunk 83 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 overall best weight: 5.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10688 Z= 0.191 Angle : 0.590 7.142 14532 Z= 0.286 Chirality : 0.043 0.149 1728 Planarity : 0.004 0.037 1808 Dihedral : 3.626 18.117 1456 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1352 helix: 1.89 (0.18), residues: 914 sheet: 3.07 (0.90), residues: 38 loop : -0.62 (0.34), residues: 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1877 time to fit residues: 43.2968 Evaluate side-chains 113 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 125 optimal weight: 30.0000 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 95 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 chunk 115 optimal weight: 30.0000 chunk 121 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 10688 Z= 0.159 Angle : 0.574 7.448 14532 Z= 0.278 Chirality : 0.043 0.197 1728 Planarity : 0.004 0.039 1808 Dihedral : 3.610 18.868 1456 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1352 helix: 1.93 (0.18), residues: 908 sheet: 3.08 (0.90), residues: 38 loop : -0.69 (0.34), residues: 406 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1914 time to fit residues: 43.6268 Evaluate side-chains 123 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 85 optimal weight: 50.0000 chunk 114 optimal weight: 20.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 10688 Z= 0.272 Angle : 0.642 7.754 14532 Z= 0.317 Chirality : 0.044 0.173 1728 Planarity : 0.004 0.043 1808 Dihedral : 3.880 18.762 1456 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.24), residues: 1352 helix: 1.83 (0.18), residues: 908 sheet: 2.81 (0.90), residues: 38 loop : -0.83 (0.34), residues: 406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1924 time to fit residues: 41.4596 Evaluate side-chains 116 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 108 optimal weight: 40.0000 chunk 45 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 94 optimal weight: 50.0000 chunk 6 optimal weight: 20.0000 overall best weight: 6.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.076853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.054207 restraints weight = 51874.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.056036 restraints weight = 27449.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.057223 restraints weight = 18263.498| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10688 Z= 0.216 Angle : 0.610 8.233 14532 Z= 0.298 Chirality : 0.044 0.156 1728 Planarity : 0.004 0.042 1808 Dihedral : 3.849 19.102 1456 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1352 helix: 1.80 (0.18), residues: 908 sheet: 2.71 (0.90), residues: 38 loop : -0.80 (0.34), residues: 406 =============================================================================== Job complete usr+sys time: 1975.62 seconds wall clock time: 37 minutes 1.32 seconds (2221.32 seconds total)