Starting phenix.real_space_refine on Fri Mar 15 03:04:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/03_2024/7lh3_23335.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/03_2024/7lh3_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_23335/03_2024/7lh3_23335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/03_2024/7lh3_23335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/03_2024/7lh3_23335.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/03_2024/7lh3_23335.pdb" } resolution = 4.3 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= 0.007 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 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. 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.00, per 1000 atoms: 0.57 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: 4.14 Conformation dependent library (CDL) restraints added in 1.8 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: 1.07 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: 2.93 Time building geometry restraints manager: 4.51 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 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: 0.950 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: 0.020 Extract box with map and model: 3.890 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 30.090 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 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 : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.06 % Allowed : 4.94 % Favored : 94.00 % 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: 2.29 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 70 HIS 0.002 0.000 HIS B 25 PHE 0.005 0.001 PHE B 269 TYR 0.008 0.001 TYR A 340 ARG 0.001 0.000 ARG B 58 *********************** 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 : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.7309 (tpt) cc_final: 0.7014 (tpp) REVERT: A 633 MET cc_start: 0.7954 (tpt) cc_final: 0.7561 (tpp) REVERT: A 669 ASP cc_start: 0.7836 (t0) cc_final: 0.7532 (t0) REVERT: B 357 MET cc_start: 0.7373 (tpt) cc_final: 0.7051 (tpp) REVERT: B 482 LEU cc_start: 0.9013 (mt) cc_final: 0.8790 (tt) REVERT: B 633 MET cc_start: 0.8036 (tpt) cc_final: 0.7537 (tpp) REVERT: B 669 ASP cc_start: 0.7739 (t0) cc_final: 0.7502 (t0) REVERT: B 719 LEU cc_start: 0.9397 (mt) cc_final: 0.9189 (mm) outliers start: 12 outliers final: 0 residues processed: 306 average time/residue: 0.2398 time to fit residues: 100.9659 Evaluate side-chains 144 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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: 0.0670 chunk 106 optimal weight: 50.0000 chunk 41 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 123 optimal weight: 0.2980 overall best weight: 1.6726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 722 GLN B 447 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10688 Z= 0.138 Angle : 0.523 8.320 14532 Z= 0.258 Chirality : 0.042 0.147 1728 Planarity : 0.004 0.030 1808 Dihedral : 2.909 12.521 1456 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: 2.26 (0.25), residues: 1352 helix: 2.29 (0.18), residues: 900 sheet: 3.39 (0.72), residues: 52 loop : -0.64 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 70 HIS 0.002 0.001 HIS A 25 PHE 0.009 0.001 PHE B 452 TYR 0.016 0.001 TYR A 123 ARG 0.003 0.000 ARG B 572 *********************** 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 181 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ILE cc_start: 0.8349 (pt) cc_final: 0.8119 (pt) REVERT: A 180 MET cc_start: 0.8541 (tpp) cc_final: 0.7936 (mmm) REVERT: A 357 MET cc_start: 0.7399 (tpt) cc_final: 0.7051 (tpp) REVERT: A 633 MET cc_start: 0.8003 (tpt) cc_final: 0.7643 (tpp) REVERT: B 63 MET cc_start: 0.8752 (ptp) cc_final: 0.8290 (ptm) REVERT: B 180 MET cc_start: 0.8626 (tpp) cc_final: 0.8231 (mmm) REVERT: B 299 MET cc_start: 0.8217 (mmp) cc_final: 0.7764 (tmm) REVERT: B 357 MET cc_start: 0.7425 (tpt) cc_final: 0.7045 (tpp) REVERT: B 482 LEU cc_start: 0.9031 (mt) cc_final: 0.8783 (tt) REVERT: B 633 MET cc_start: 0.8188 (tpt) cc_final: 0.7675 (tpp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1983 time to fit residues: 52.4523 Evaluate side-chains 140 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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: 30.0000 chunk 102 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 42 optimal weight: 30.0000 chunk 99 optimal weight: 8.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 454 GLN ** B 131 HIS ** 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: 0.7689 moved from start: 0.3160 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= 0.207 Angle : 0.537 6.539 14532 Z= 0.272 Chirality : 0.042 0.128 1728 Planarity : 0.004 0.034 1808 Dihedral : 3.246 14.400 1456 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.26 % Allowed : 3.09 % Favored : 96.65 % 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: 2.14 (0.25), residues: 1352 helix: 2.15 (0.18), residues: 906 sheet: 2.73 (0.74), residues: 52 loop : -0.53 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 699 HIS 0.005 0.001 HIS B 25 PHE 0.012 0.001 PHE A 703 TYR 0.017 0.001 TYR B 79 ARG 0.002 0.000 ARG A 130 *********************** 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 176 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ILE cc_start: 0.8435 (pt) cc_final: 0.8138 (pt) REVERT: A 180 MET cc_start: 0.8660 (tpp) cc_final: 0.8076 (mmm) REVERT: A 196 CYS cc_start: 0.8464 (p) cc_final: 0.8252 (p) REVERT: A 299 MET cc_start: 0.8232 (mmp) cc_final: 0.7700 (tmm) REVERT: A 357 MET cc_start: 0.7566 (tpt) cc_final: 0.7240 (tpp) REVERT: A 435 LEU cc_start: 0.8763 (mm) cc_final: 0.8462 (mm) REVERT: A 440 LEU cc_start: 0.9165 (mm) cc_final: 0.8505 (tp) REVERT: A 633 MET cc_start: 0.8338 (tpt) cc_final: 0.7859 (tpp) REVERT: B 121 ILE cc_start: 0.9199 (pt) cc_final: 0.8963 (mm) REVERT: B 180 MET cc_start: 0.8678 (tpp) cc_final: 0.8180 (mmm) REVERT: B 283 LYS cc_start: 0.9276 (mmpt) cc_final: 0.9070 (mmmt) REVERT: B 299 MET cc_start: 0.8296 (mmp) cc_final: 0.7833 (tmm) REVERT: B 397 LEU cc_start: 0.8317 (mt) cc_final: 0.8072 (mt) REVERT: B 435 LEU cc_start: 0.8758 (mm) cc_final: 0.8457 (mm) REVERT: B 482 LEU cc_start: 0.9009 (mt) cc_final: 0.8805 (tt) REVERT: B 633 MET cc_start: 0.8455 (tpt) cc_final: 0.7839 (tpp) outliers start: 3 outliers final: 2 residues processed: 176 average time/residue: 0.1968 time to fit residues: 51.1138 Evaluate side-chains 127 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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: 8.9990 chunk 93 optimal weight: 50.0000 chunk 64 optimal weight: 8.9990 chunk 13 optimal weight: 30.0000 chunk 59 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 131 optimal weight: 20.0000 chunk 117 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10688 Z= 0.211 Angle : 0.553 7.421 14532 Z= 0.273 Chirality : 0.043 0.144 1728 Planarity : 0.004 0.034 1808 Dihedral : 3.320 15.146 1456 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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: 2.10 (0.24), residues: 1352 helix: 2.09 (0.18), residues: 908 sheet: 2.57 (0.75), residues: 52 loop : -0.43 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 70 HIS 0.006 0.001 HIS B 25 PHE 0.014 0.001 PHE A 76 TYR 0.013 0.001 TYR A 552 ARG 0.002 0.000 ARG B 716 *********************** 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 167 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ILE cc_start: 0.8452 (pt) cc_final: 0.8193 (pt) REVERT: A 180 MET cc_start: 0.8670 (tpp) cc_final: 0.8061 (mmm) REVERT: A 196 CYS cc_start: 0.8473 (p) cc_final: 0.8257 (p) REVERT: A 228 TYR cc_start: 0.7133 (m-80) cc_final: 0.6651 (m-10) REVERT: A 299 MET cc_start: 0.8219 (mmp) cc_final: 0.7737 (tmm) REVERT: A 357 MET cc_start: 0.7646 (tpt) cc_final: 0.7272 (tpp) REVERT: A 435 LEU cc_start: 0.8827 (mm) cc_final: 0.8579 (mm) REVERT: A 452 PHE cc_start: 0.8364 (m-10) cc_final: 0.8035 (t80) REVERT: A 633 MET cc_start: 0.8326 (tpt) cc_final: 0.7849 (tpp) REVERT: B 121 ILE cc_start: 0.9204 (pt) cc_final: 0.8946 (mm) REVERT: B 180 MET cc_start: 0.8819 (tpp) cc_final: 0.8435 (mmm) REVERT: B 196 CYS cc_start: 0.8603 (p) cc_final: 0.8399 (p) REVERT: B 299 MET cc_start: 0.8328 (mmp) cc_final: 0.7842 (tmm) REVERT: B 397 LEU cc_start: 0.8742 (mt) cc_final: 0.8531 (mt) REVERT: B 435 LEU cc_start: 0.8790 (mm) cc_final: 0.8554 (mm) REVERT: B 452 PHE cc_start: 0.8410 (m-10) cc_final: 0.8063 (t80) REVERT: B 482 LEU cc_start: 0.9113 (mt) cc_final: 0.8840 (tt) REVERT: B 633 MET cc_start: 0.8453 (tpt) cc_final: 0.7817 (tpp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2033 time to fit residues: 49.9626 Evaluate side-chains 134 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.7715 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10688 Z= 0.162 Angle : 0.526 7.080 14532 Z= 0.258 Chirality : 0.042 0.144 1728 Planarity : 0.004 0.039 1808 Dihedral : 3.361 18.026 1456 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: 2.11 (0.24), residues: 1352 helix: 2.06 (0.18), residues: 908 sheet: 3.22 (0.90), residues: 38 loop : -0.28 (0.34), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 70 HIS 0.005 0.001 HIS A 25 PHE 0.021 0.001 PHE B 351 TYR 0.017 0.001 TYR A 552 ARG 0.002 0.000 ARG B 716 *********************** 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 169 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8625 (ppp) cc_final: 0.8258 (ppp) REVERT: A 132 ILE cc_start: 0.8485 (pt) cc_final: 0.8109 (pt) REVERT: A 180 MET cc_start: 0.8656 (tpp) cc_final: 0.8298 (mmm) REVERT: A 299 MET cc_start: 0.8223 (mmp) cc_final: 0.7766 (tmm) REVERT: A 357 MET cc_start: 0.7597 (tpt) cc_final: 0.7190 (tpp) REVERT: A 435 LEU cc_start: 0.8774 (mm) cc_final: 0.8514 (mm) REVERT: A 452 PHE cc_start: 0.8473 (m-10) cc_final: 0.8010 (t80) REVERT: A 633 MET cc_start: 0.8332 (tpt) cc_final: 0.7842 (tpp) REVERT: B 121 ILE cc_start: 0.9204 (pt) cc_final: 0.8958 (mm) REVERT: B 180 MET cc_start: 0.8779 (tpp) cc_final: 0.8467 (mmm) REVERT: B 196 CYS cc_start: 0.8567 (p) cc_final: 0.8321 (p) REVERT: B 228 TYR cc_start: 0.6968 (m-80) cc_final: 0.6699 (m-10) REVERT: B 299 MET cc_start: 0.8316 (mmp) cc_final: 0.7876 (tmm) REVERT: B 435 LEU cc_start: 0.8778 (mm) cc_final: 0.8549 (mm) REVERT: B 451 MET cc_start: 0.7792 (tpp) cc_final: 0.7240 (tpp) REVERT: B 482 LEU cc_start: 0.9083 (mt) cc_final: 0.8839 (tt) REVERT: B 633 MET cc_start: 0.8419 (tpt) cc_final: 0.8011 (tpp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2100 time to fit residues: 52.4400 Evaluate side-chains 125 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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: 8.9990 chunk 77 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 40.0000 chunk 60 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN B 33 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10688 Z= 0.230 Angle : 0.576 6.894 14532 Z= 0.284 Chirality : 0.044 0.175 1728 Planarity : 0.004 0.036 1808 Dihedral : 3.508 17.747 1456 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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 (0.25), residues: 1352 helix: 1.96 (0.18), residues: 920 sheet: 2.83 (0.90), residues: 38 loop : -0.52 (0.34), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 70 HIS 0.007 0.001 HIS A 25 PHE 0.018 0.001 PHE B 452 TYR 0.019 0.002 TYR B 79 ARG 0.002 0.000 ARG B 716 *********************** 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 158 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ILE cc_start: 0.8460 (pt) cc_final: 0.8194 (pt) REVERT: A 180 MET cc_start: 0.8638 (tpp) cc_final: 0.8326 (mmm) REVERT: A 299 MET cc_start: 0.8268 (mmp) cc_final: 0.7804 (tmm) REVERT: A 357 MET cc_start: 0.7725 (tpt) cc_final: 0.7341 (tpp) REVERT: A 435 LEU cc_start: 0.8836 (mm) cc_final: 0.8620 (mm) REVERT: A 440 LEU cc_start: 0.9004 (mm) cc_final: 0.8421 (tp) REVERT: A 452 PHE cc_start: 0.8577 (m-10) cc_final: 0.8015 (m-80) REVERT: A 633 MET cc_start: 0.8352 (tpt) cc_final: 0.7841 (tpp) REVERT: B 132 ILE cc_start: 0.8606 (pt) cc_final: 0.8370 (pt) REVERT: B 180 MET cc_start: 0.8749 (tpp) cc_final: 0.8450 (mmm) REVERT: B 196 CYS cc_start: 0.8622 (p) cc_final: 0.8406 (p) REVERT: B 228 TYR cc_start: 0.6696 (m-80) cc_final: 0.6481 (m-10) REVERT: B 299 MET cc_start: 0.8337 (mmp) cc_final: 0.7948 (tmm) REVERT: B 451 MET cc_start: 0.7748 (tpp) cc_final: 0.7545 (tpp) REVERT: B 452 PHE cc_start: 0.8586 (m-10) cc_final: 0.8158 (m-80) REVERT: B 633 MET cc_start: 0.8434 (tpt) cc_final: 0.8031 (tpp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1972 time to fit residues: 45.6188 Evaluate side-chains 121 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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: 0.0170 chunk 96 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- 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: 0.7734 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10688 Z= 0.147 Angle : 0.533 7.019 14532 Z= 0.262 Chirality : 0.043 0.159 1728 Planarity : 0.004 0.039 1808 Dihedral : 3.460 17.712 1456 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: 2.08 (0.25), residues: 1352 helix: 2.05 (0.18), residues: 906 sheet: 2.96 (0.90), residues: 38 loop : -0.27 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 699 HIS 0.004 0.001 HIS B 25 PHE 0.011 0.001 PHE A 269 TYR 0.030 0.001 TYR A 79 ARG 0.004 0.000 ARG A 236 *********************** 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 163 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8472 (ppp) cc_final: 0.8249 (ppp) REVERT: A 132 ILE cc_start: 0.8487 (pt) cc_final: 0.8047 (pt) REVERT: A 180 MET cc_start: 0.8598 (tpp) cc_final: 0.8306 (mmm) REVERT: A 299 MET cc_start: 0.8256 (mmp) cc_final: 0.7836 (tmm) REVERT: A 452 PHE cc_start: 0.8333 (m-10) cc_final: 0.8059 (t80) REVERT: A 484 LEU cc_start: 0.8817 (mt) cc_final: 0.7976 (tt) REVERT: A 633 MET cc_start: 0.8286 (tpt) cc_final: 0.7834 (tpp) REVERT: B 132 ILE cc_start: 0.8513 (pt) cc_final: 0.8279 (pt) REVERT: B 180 MET cc_start: 0.8708 (tpp) cc_final: 0.8426 (mmm) REVERT: B 196 CYS cc_start: 0.8635 (p) cc_final: 0.8416 (p) REVERT: B 299 MET cc_start: 0.8347 (mmp) cc_final: 0.7967 (tmm) REVERT: B 448 LEU cc_start: 0.9378 (tp) cc_final: 0.8759 (tp) REVERT: B 452 PHE cc_start: 0.8558 (m-10) cc_final: 0.7980 (m-80) REVERT: B 633 MET cc_start: 0.8354 (tpt) cc_final: 0.7987 (tpp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1845 time to fit residues: 44.7967 Evaluate side-chains 126 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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: 20.0000 chunk 39 optimal weight: 50.0000 chunk 25 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 119 optimal weight: 0.0000 chunk 125 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10688 Z= 0.141 Angle : 0.547 7.252 14532 Z= 0.266 Chirality : 0.043 0.151 1728 Planarity : 0.004 0.038 1808 Dihedral : 3.407 17.390 1456 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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 (0.25), residues: 1352 helix: 1.98 (0.18), residues: 918 sheet: 2.98 (0.90), residues: 38 loop : -0.49 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 70 HIS 0.004 0.001 HIS A 25 PHE 0.023 0.001 PHE A 117 TYR 0.026 0.001 TYR A 79 ARG 0.006 0.000 ARG B 572 *********************** 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 163 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8468 (ppp) cc_final: 0.8217 (ppp) REVERT: A 132 ILE cc_start: 0.8354 (pt) cc_final: 0.8042 (pt) REVERT: A 180 MET cc_start: 0.8563 (tpp) cc_final: 0.8249 (mmm) REVERT: A 299 MET cc_start: 0.8249 (mmp) cc_final: 0.7843 (tmm) REVERT: A 452 PHE cc_start: 0.8338 (m-10) cc_final: 0.8030 (t80) REVERT: A 484 LEU cc_start: 0.8766 (mt) cc_final: 0.8061 (tt) REVERT: A 633 MET cc_start: 0.8276 (tpt) cc_final: 0.7817 (tpp) REVERT: B 180 MET cc_start: 0.8685 (tpp) cc_final: 0.8427 (mmm) REVERT: B 196 CYS cc_start: 0.8657 (p) cc_final: 0.8409 (p) REVERT: B 276 LYS cc_start: 0.8057 (tttt) cc_final: 0.7739 (ptmt) REVERT: B 299 MET cc_start: 0.8337 (mmp) cc_final: 0.7949 (tmm) REVERT: B 445 ILE cc_start: 0.8807 (mm) cc_final: 0.8595 (mm) REVERT: B 488 LEU cc_start: 0.9134 (tt) cc_final: 0.8869 (tp) REVERT: B 633 MET cc_start: 0.8354 (tpt) cc_final: 0.7991 (tpp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1856 time to fit residues: 45.3233 Evaluate side-chains 127 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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: 7.9990 chunk 125 optimal weight: 0.1980 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4608 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= 0.184 Angle : 0.560 7.086 14532 Z= 0.275 Chirality : 0.043 0.146 1728 Planarity : 0.004 0.037 1808 Dihedral : 3.495 17.355 1456 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: 1.87 (0.25), residues: 1352 helix: 1.96 (0.18), residues: 914 sheet: 2.92 (0.89), residues: 38 loop : -0.61 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 70 HIS 0.006 0.001 HIS A 25 PHE 0.028 0.001 PHE B 351 TYR 0.024 0.001 TYR A 79 ARG 0.004 0.000 ARG B 572 *********************** 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 157 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8540 (ppp) cc_final: 0.8262 (ppp) REVERT: A 132 ILE cc_start: 0.8370 (pt) cc_final: 0.8020 (pt) REVERT: A 180 MET cc_start: 0.8559 (tpp) cc_final: 0.8270 (mmm) REVERT: A 299 MET cc_start: 0.8275 (mmp) cc_final: 0.7843 (tmm) REVERT: A 452 PHE cc_start: 0.8406 (m-10) cc_final: 0.8016 (t80) REVERT: A 484 LEU cc_start: 0.8807 (mt) cc_final: 0.8038 (tt) REVERT: A 633 MET cc_start: 0.8291 (tpt) cc_final: 0.7841 (tpp) REVERT: A 665 LYS cc_start: 0.8778 (tptp) cc_final: 0.8506 (tppt) REVERT: B 63 MET cc_start: 0.9106 (ptm) cc_final: 0.8904 (ptm) REVERT: B 180 MET cc_start: 0.8697 (tpp) cc_final: 0.8436 (mmm) REVERT: B 196 CYS cc_start: 0.8690 (p) cc_final: 0.8455 (p) REVERT: B 276 LYS cc_start: 0.8102 (tttt) cc_final: 0.7795 (ptmt) REVERT: B 299 MET cc_start: 0.8368 (mmp) cc_final: 0.7964 (tmm) REVERT: B 488 LEU cc_start: 0.9141 (tt) cc_final: 0.8915 (tp) REVERT: B 633 MET cc_start: 0.8383 (tpt) cc_final: 0.8015 (tpp) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1871 time to fit residues: 44.0896 Evaluate side-chains 122 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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: 10.0000 chunk 61 optimal weight: 9.9990 chunk 89 optimal weight: 30.0000 chunk 135 optimal weight: 0.6980 chunk 124 optimal weight: 9.9990 chunk 107 optimal weight: 40.0000 chunk 11 optimal weight: 40.0000 chunk 83 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 30.0000 chunk 114 optimal weight: 9.9990 overall best weight: 7.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN B 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10688 Z= 0.240 Angle : 0.597 7.589 14532 Z= 0.294 Chirality : 0.044 0.144 1728 Planarity : 0.004 0.038 1808 Dihedral : 3.667 17.835 1456 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 1.81 (0.25), residues: 1352 helix: 1.92 (0.18), residues: 912 sheet: 2.81 (0.89), residues: 38 loop : -0.62 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 699 HIS 0.005 0.001 HIS B 25 PHE 0.038 0.002 PHE B 351 TYR 0.025 0.001 TYR B 552 ARG 0.004 0.000 ARG B 572 ********************** 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 152 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8611 (ppp) cc_final: 0.8345 (ppp) REVERT: A 132 ILE cc_start: 0.8436 (pt) cc_final: 0.8129 (pt) REVERT: A 299 MET cc_start: 0.8310 (mmp) cc_final: 0.7872 (tmm) REVERT: A 452 PHE cc_start: 0.8485 (m-10) cc_final: 0.8024 (t80) REVERT: A 484 LEU cc_start: 0.8780 (mt) cc_final: 0.8124 (tt) REVERT: A 633 MET cc_start: 0.8298 (tpt) cc_final: 0.7862 (tpp) REVERT: B 63 MET cc_start: 0.9169 (ptm) cc_final: 0.8956 (ptm) REVERT: B 180 MET cc_start: 0.8652 (tpp) cc_final: 0.8430 (mmm) REVERT: B 299 MET cc_start: 0.8391 (mmp) cc_final: 0.7987 (tmm) REVERT: B 445 ILE cc_start: 0.8858 (mm) cc_final: 0.8640 (mm) REVERT: B 488 LEU cc_start: 0.9162 (tt) cc_final: 0.8713 (tp) REVERT: B 633 MET cc_start: 0.8429 (tpt) cc_final: 0.8049 (tpp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1913 time to fit residues: 43.3224 Evaluate side-chains 117 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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: 0.0570 chunk 15 optimal weight: 0.0980 chunk 29 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 94 optimal weight: 30.0000 chunk 6 optimal weight: 3.9990 overall best weight: 3.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 504 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.078751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.056113 restraints weight = 50819.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.058030 restraints weight = 26890.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.059285 restraints weight = 17820.156| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10688 Z= 0.153 Angle : 0.571 9.298 14532 Z= 0.277 Chirality : 0.044 0.190 1728 Planarity : 0.004 0.037 1808 Dihedral : 3.599 19.305 1456 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 1.82 (0.24), residues: 1352 helix: 1.92 (0.18), residues: 910 sheet: 2.89 (0.88), residues: 38 loop : -0.62 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 699 HIS 0.009 0.001 HIS B 25 PHE 0.048 0.001 PHE B 351 TYR 0.024 0.001 TYR A 79 ARG 0.008 0.000 ARG B 691 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.66 seconds wall clock time: 38 minutes 49.17 seconds (2329.17 seconds total)