Starting phenix.real_space_refine on Mon Dec 30 03:26:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2b_42904/12_2024/8v2b_42904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2b_42904/12_2024/8v2b_42904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v2b_42904/12_2024/8v2b_42904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2b_42904/12_2024/8v2b_42904.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2b_42904/12_2024/8v2b_42904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2b_42904/12_2024/8v2b_42904.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 49 5.16 5 C 7622 2.51 5 N 2005 2.21 5 O 2373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12049 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1343 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain breaks: 1 Chain: "B" Number of atoms: 4599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4599 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 545} Chain: "C" Number of atoms: 5701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5701 Classifications: {'peptide': 703} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 666} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 NAG E 2 " occ=0.50 ... (12 atoms not shown) pdb=" O7 NAG E 2 " occ=0.50 Time building chain proxies: 8.51, per 1000 atoms: 0.71 Number of scatterers: 12049 At special positions: 0 Unit cell: (135.02, 154.8, 196.94, 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 49 16.00 O 2373 8.00 N 2005 7.00 C 7622 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 456 " - pdb=" SG CYS B 464 " distance=2.03 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 252 " distance=2.03 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 282 " distance=2.03 Simple disulfide: pdb=" SG CYS C 363 " - pdb=" SG CYS C 403 " distance=2.03 Simple disulfide: pdb=" SG CYS C 559 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 668 " - pdb=" SG CYS C 684 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG B 701 " - " ASN B 225 " " NAG B 702 " - " ASN B 157 " " NAG B 703 " - " ASN B 388 " " NAG C 801 " - " ASN C 97 " " NAG C 802 " - " ASN C 130 " " NAG C 803 " - " ASN C 239 " " NAG C 804 " - " ASN C 377 " " NAG D 1 " - " ASN B 83 " " NAG E 1 " - " ASN B 551 " " NAG F 1 " - " ASN B 43 " " NAG G 1 " - " ASN B 131 " " NAG H 1 " - " ASN B 61 " " NAG I 1 " - " ASN C 74 " " NAG J 1 " - " ASN C 162 " " NAG K 1 " - " ASN C 271 " " NAG L 1 " - " ASN C 304 " " NAG M 1 " - " ASN C 323 " " NAG N 1 " - " ASN C 347 " Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 29 sheets defined 11.4% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 88 through 115 removed outlier: 3.572A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 Processing helix chain 'A' and resid 169 through 201 Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.694A pdb=" N GLY B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.749A pdb=" N MET B 276 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 removed outlier: 4.179A pdb=" N ASN B 546 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.571A pdb=" N ALA B 46 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 89 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS B 48 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER B 87 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 38 removed outlier: 5.526A pdb=" N ASN B 114 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 105 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR B 116 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN B 104 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 180 through 181 removed outlier: 3.564A pdb=" N CYS B 144 " --> pdb=" O CYS B 180 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP B 147 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN B 131 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N LYS B 219 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 136 " --> pdb=" O LYS B 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=AA6, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.814A pdb=" N ASN B 225 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL B 243 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 268 through 269 Processing sheet with id=AA8, first strand: chain 'B' and resid 330 through 334 Processing sheet with id=AA9, first strand: chain 'B' and resid 376 through 380 removed outlier: 3.678A pdb=" N VAL B 366 " --> pdb=" O TYR B 378 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP B 363 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 365 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 396 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 426 through 433 removed outlier: 6.339A pdb=" N ASN B 427 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR B 442 " --> pdb=" O ASN B 427 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 467 through 472 removed outlier: 3.934A pdb=" N ASP B 467 " --> pdb=" O TRP B 455 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS B 450 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 490 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 510 " --> pdb=" O TYR B 490 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 494 " --> pdb=" O GLU B 506 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU B 506 " --> pdb=" O VAL B 494 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 523 through 524 Processing sheet with id=AB4, first strand: chain 'B' and resid 564 through 569 removed outlier: 4.309A pdb=" N ASN B 551 " --> pdb=" O TYR B 593 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR B 593 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR B 586 " --> pdb=" O THR B 605 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR B 605 " --> pdb=" O TYR B 586 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 588 " --> pdb=" O GLU B 603 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU B 603 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N MET B 590 " --> pdb=" O GLY B 601 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 42 removed outlier: 7.345A pdb=" N GLU C 51 " --> pdb=" O HIS C 37 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL C 39 " --> pdb=" O ASN C 49 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN C 49 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE C 41 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU C 47 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP C 98 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 78 through 89 removed outlier: 6.468A pdb=" N THR C 78 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG C 72 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP C 80 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET C 64 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 111 " --> pdb=" O LYS C 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AB8, first strand: chain 'C' and resid 156 through 158 removed outlier: 3.533A pdb=" N THR C 226 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 177 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASN C 175 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 249 through 253 Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 274 removed outlier: 3.861A pdb=" N TYR C 303 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE C 322 " --> pdb=" O TYR C 303 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 334 through 340 removed outlier: 4.353A pdb=" N VAL C 336 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR C 349 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU C 338 " --> pdb=" O ASN C 347 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASN C 347 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 372 through 375 Processing sheet with id=AC4, first strand: chain 'C' and resid 372 through 375 Processing sheet with id=AC5, first strand: chain 'C' and resid 433 through 440 removed outlier: 3.650A pdb=" N THR C 490 " --> pdb=" O LEU C 448 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 478 through 484 removed outlier: 3.695A pdb=" N MET C 517 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE C 503 " --> pdb=" O SER C 515 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 530 through 534 removed outlier: 4.164A pdb=" N TYR C 616 " --> pdb=" O ILE C 533 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 607 " --> pdb=" O SER C 602 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER C 602 " --> pdb=" O ALA C 607 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU C 609 " --> pdb=" O GLU C 600 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU C 600 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 611 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 615 " --> pdb=" O TYR C 594 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG C 593 " --> pdb=" O HIS C 561 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 530 through 534 removed outlier: 4.164A pdb=" N TYR C 616 " --> pdb=" O ILE C 533 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 607 " --> pdb=" O SER C 602 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER C 602 " --> pdb=" O ALA C 607 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU C 609 " --> pdb=" O GLU C 600 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU C 600 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 611 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 615 " --> pdb=" O TYR C 594 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY C 553 " --> pdb=" O ARG C 601 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 556 " --> pdb=" O LYS C 572 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 572 " --> pdb=" O VAL C 556 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRP C 558 " --> pdb=" O GLN C 570 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C 570 " --> pdb=" O TRP C 558 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 542 through 543 removed outlier: 4.138A pdb=" N ILE C 542 " --> pdb=" O THR C 581 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 581 " --> pdb=" O ILE C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 638 through 641 removed outlier: 3.920A pdb=" N PHE C 638 " --> pdb=" O VAL C 698 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 698 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 673 through 677 removed outlier: 4.082A pdb=" N LEU C 677 " --> pdb=" O SER C 681 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER C 681 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 682 " --> pdb=" O SER C 663 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 663 " --> pdb=" O VAL C 682 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS C 684 " --> pdb=" O VAL C 661 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 661 " --> pdb=" O CYS C 684 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY C 656 " --> pdb=" O TYR C 714 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR C 714 " --> pdb=" O GLY C 656 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 712 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER C 705 " --> pdb=" O THR C 730 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR C 730 " --> pdb=" O SER C 705 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR C 707 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 728 " --> pdb=" O TYR C 707 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE C 709 " --> pdb=" O THR C 726 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1092 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: 4.55 Time building geometry restraints manager: 3.61 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: 3818 1.34 - 1.46: 3022 1.46 - 1.58: 5440 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 12348 Sorted by residual: bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.86e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 ... (remaining 12343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 16248 1.24 - 2.48: 447 2.48 - 3.72: 115 3.72 - 4.95: 8 4.95 - 6.19: 4 Bond angle restraints: 16822 Sorted by residual: angle pdb=" N VAL B 560 " pdb=" CA VAL B 560 " pdb=" C VAL B 560 " ideal model delta sigma weight residual 113.20 110.49 2.71 9.60e-01 1.09e+00 7.97e+00 angle pdb=" C ARG C 72 " pdb=" N LEU C 73 " pdb=" CA LEU C 73 " ideal model delta sigma weight residual 121.54 125.16 -3.62 1.91e+00 2.74e-01 3.60e+00 angle pdb=" N THR A 117 " pdb=" CA THR A 117 " pdb=" C THR A 117 " ideal model delta sigma weight residual 109.81 113.80 -3.99 2.21e+00 2.05e-01 3.26e+00 angle pdb=" N ASN B 83 " pdb=" CA ASN B 83 " pdb=" C ASN B 83 " ideal model delta sigma weight residual 108.34 110.63 -2.29 1.31e+00 5.83e-01 3.05e+00 angle pdb=" N CYS C 282 " pdb=" CA CYS C 282 " pdb=" C CYS C 282 " ideal model delta sigma weight residual 108.46 111.01 -2.55 1.51e+00 4.39e-01 2.85e+00 ... (remaining 16817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 7180 22.77 - 45.54: 320 45.54 - 68.30: 135 68.30 - 91.07: 41 91.07 - 113.84: 120 Dihedral angle restraints: 7796 sinusoidal: 3509 harmonic: 4287 Sorted by residual: dihedral pdb=" CB CYS C 275 " pdb=" SG CYS C 275 " pdb=" SG CYS C 282 " pdb=" CB CYS C 282 " ideal model delta sinusoidal sigma weight residual -86.00 -35.63 -50.37 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS B 28 " pdb=" SG CYS B 28 " pdb=" SG CYS B 54 " pdb=" CB CYS B 54 " ideal model delta sinusoidal sigma weight residual 93.00 140.16 -47.16 1 1.00e+01 1.00e-02 3.07e+01 dihedral pdb=" CB CYS C 559 " pdb=" SG CYS C 559 " pdb=" SG CYS C 567 " pdb=" CB CYS C 567 " ideal model delta sinusoidal sigma weight residual 93.00 47.30 45.70 1 1.00e+01 1.00e-02 2.90e+01 ... (remaining 7793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1743 0.075 - 0.150: 211 0.150 - 0.225: 2 0.225 - 0.300: 1 0.300 - 0.375: 2 Chirality restraints: 1959 Sorted by residual: chirality pdb=" C1 NAG C 803 " pdb=" ND2 ASN C 239 " pdb=" C2 NAG C 803 " pdb=" O5 NAG C 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C 74 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1956 not shown) Planarity restraints: 2125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO C 55 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 183 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO C 184 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 184 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 184 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 64 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO A 65 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " -0.015 5.00e-02 4.00e+02 ... (remaining 2122 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1457 2.76 - 3.29: 10710 3.29 - 3.83: 18702 3.83 - 4.36: 20558 4.36 - 4.90: 36530 Nonbonded interactions: 87957 Sorted by model distance: nonbonded pdb=" OE2 GLU C 255 " pdb=" O3 NAG C 803 " model vdw 2.223 3.040 nonbonded pdb=" O LEU B 50 " pdb=" OG1 THR B 85 " model vdw 2.242 3.040 nonbonded pdb=" OE2 GLU C 283 " pdb=" OH TYR C 291 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR C 306 " pdb=" O6 NAG L 1 " model vdw 2.303 3.040 nonbonded pdb=" O SER B 581 " pdb=" OG1 THR B 584 " model vdw 2.307 3.040 ... (remaining 87952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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=0.00 max=1.00 mean=0.99 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 31.750 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 : 0.003 0.063 12348 Z= 0.180 Angle : 0.483 6.192 16822 Z= 0.243 Chirality : 0.043 0.375 1959 Planarity : 0.003 0.031 2107 Dihedral : 21.988 113.841 4976 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 (0.19), residues: 1447 helix: 1.78 (0.44), residues: 137 sheet: -1.36 (0.19), residues: 560 loop : -2.27 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 438 HIS 0.001 0.000 HIS C 561 PHE 0.014 0.001 PHE A 120 TYR 0.004 0.000 TYR A 97 ARG 0.001 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.385 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 25 ASN cc_start: 0.8142 (t0) cc_final: 0.7835 (t0) REVERT: A 108 ASP cc_start: 0.7942 (t0) cc_final: 0.7654 (t0) REVERT: B 330 PHE cc_start: 0.6308 (t80) cc_final: 0.5385 (t80) REVERT: B 343 ARG cc_start: 0.5063 (ptt180) cc_final: 0.3505 (ttm170) REVERT: B 347 LEU cc_start: 0.8021 (mt) cc_final: 0.7443 (tp) REVERT: B 350 LYS cc_start: 0.8680 (mttt) cc_final: 0.7837 (mttt) REVERT: B 415 PRO cc_start: 0.7178 (Cg_endo) cc_final: 0.6023 (Cg_exo) REVERT: C 98 TRP cc_start: 0.8670 (t60) cc_final: 0.7989 (t60) REVERT: C 418 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8668 (tttm) REVERT: C 457 GLN cc_start: 0.7964 (mp10) cc_final: 0.7757 (mp10) REVERT: C 540 PHE cc_start: 0.6728 (m-80) cc_final: 0.6378 (m-80) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3101 time to fit residues: 66.4931 Evaluate side-chains 90 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 130 optimal weight: 20.0000 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 40 GLN A 112 GLN B 56 GLN B 57 HIS C 42 GLN C 46 GLN C 49 ASN C 171 GLN C 193 HIS C 300 GLN C 353 HIS C 376 HIS C 408 HIS C 466 ASN C 561 HIS C 565 GLN C 573 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12348 Z= 0.414 Angle : 0.723 8.861 16822 Z= 0.349 Chirality : 0.051 0.363 1959 Planarity : 0.005 0.050 2107 Dihedral : 22.544 100.931 2180 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.36 % Allowed : 9.83 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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: -1.67 (0.20), residues: 1447 helix: 2.37 (0.45), residues: 137 sheet: -0.94 (0.20), residues: 560 loop : -1.94 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 349 HIS 0.007 0.001 HIS C 408 PHE 0.023 0.002 PHE B 330 TYR 0.022 0.002 TYR A 183 ARG 0.004 0.001 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9208 (mm) REVERT: A 108 ASP cc_start: 0.8222 (t0) cc_final: 0.7857 (t0) REVERT: B 30 TYR cc_start: 0.5306 (p90) cc_final: 0.4861 (p90) REVERT: B 322 ASP cc_start: 0.7320 (t0) cc_final: 0.7071 (t0) REVERT: B 343 ARG cc_start: 0.5550 (ptt180) cc_final: 0.3831 (ttm170) REVERT: B 350 LYS cc_start: 0.8566 (mttt) cc_final: 0.7750 (mttt) REVERT: B 415 PRO cc_start: 0.7245 (Cg_endo) cc_final: 0.6239 (Cg_exo) REVERT: B 594 THR cc_start: 0.6860 (OUTLIER) cc_final: 0.6270 (t) REVERT: C 174 TYR cc_start: 0.6696 (m-80) cc_final: 0.6442 (m-80) REVERT: C 418 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8526 (tttm) REVERT: C 540 PHE cc_start: 0.6947 (m-80) cc_final: 0.6243 (m-80) outliers start: 18 outliers final: 11 residues processed: 109 average time/residue: 0.2487 time to fit residues: 39.7230 Evaluate side-chains 93 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 336 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 0.4980 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 129 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 181 GLN ** C 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12348 Z= 0.298 Angle : 0.704 10.394 16822 Z= 0.327 Chirality : 0.050 0.394 1959 Planarity : 0.004 0.048 2107 Dihedral : 17.050 97.041 2180 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.59 % Allowed : 13.16 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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: -1.29 (0.21), residues: 1447 helix: 2.75 (0.46), residues: 137 sheet: -0.66 (0.21), residues: 568 loop : -1.74 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 349 HIS 0.008 0.001 HIS C 59 PHE 0.017 0.002 PHE A 114 TYR 0.016 0.002 TYR B 32 ARG 0.004 0.000 ARG C 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8467 (t0) cc_final: 0.8207 (t0) REVERT: A 100 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9226 (mm) REVERT: B 322 ASP cc_start: 0.7367 (t0) cc_final: 0.6983 (t0) REVERT: B 343 ARG cc_start: 0.5666 (ptt180) cc_final: 0.3843 (ttm170) REVERT: B 350 LYS cc_start: 0.8363 (mttt) cc_final: 0.7575 (ptpt) REVERT: B 365 GLU cc_start: 0.7362 (mp0) cc_final: 0.6990 (mp0) REVERT: B 438 TRP cc_start: 0.7541 (m100) cc_final: 0.7267 (m100) REVERT: B 450 LYS cc_start: 0.7674 (pttt) cc_final: 0.7204 (mptt) REVERT: B 468 TRP cc_start: 0.7180 (p-90) cc_final: 0.6359 (p-90) REVERT: B 469 GLN cc_start: 0.5920 (pt0) cc_final: 0.5690 (pt0) REVERT: C 98 TRP cc_start: 0.8621 (t60) cc_final: 0.7804 (t60) REVERT: C 348 MET cc_start: 0.8006 (tpt) cc_final: 0.7672 (ttt) REVERT: C 418 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8488 (tttm) REVERT: C 540 PHE cc_start: 0.6841 (m-80) cc_final: 0.5932 (m-80) outliers start: 21 outliers final: 15 residues processed: 102 average time/residue: 0.2302 time to fit residues: 35.9221 Evaluate side-chains 90 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 GLN C 42 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12348 Z= 0.362 Angle : 0.749 12.708 16822 Z= 0.351 Chirality : 0.051 0.488 1959 Planarity : 0.005 0.044 2107 Dihedral : 14.354 96.967 2180 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.34 % Allowed : 15.89 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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: -1.19 (0.21), residues: 1447 helix: 2.67 (0.45), residues: 137 sheet: -0.57 (0.21), residues: 578 loop : -1.67 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 349 HIS 0.006 0.001 HIS C 376 PHE 0.019 0.002 PHE A 114 TYR 0.022 0.002 TYR B 307 ARG 0.006 0.001 ARG C 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9228 (mm) REVERT: B 322 ASP cc_start: 0.7523 (t0) cc_final: 0.7109 (t0) REVERT: B 343 ARG cc_start: 0.5449 (ptt180) cc_final: 0.3717 (ttm170) REVERT: B 350 LYS cc_start: 0.8470 (mttt) cc_final: 0.8165 (mttt) REVERT: B 365 GLU cc_start: 0.7444 (mp0) cc_final: 0.7148 (mp0) REVERT: B 415 PRO cc_start: 0.7353 (Cg_endo) cc_final: 0.6395 (Cg_exo) REVERT: B 450 LYS cc_start: 0.7619 (pttt) cc_final: 0.7176 (mptt) REVERT: C 64 MET cc_start: 0.6642 (mmm) cc_final: 0.6376 (mmm) REVERT: C 348 MET cc_start: 0.8014 (tpt) cc_final: 0.7787 (ttt) REVERT: C 418 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8494 (tttm) REVERT: C 509 MET cc_start: 0.8304 (mmt) cc_final: 0.7820 (mpp) REVERT: C 540 PHE cc_start: 0.6621 (m-80) cc_final: 0.6154 (m-80) outliers start: 31 outliers final: 20 residues processed: 103 average time/residue: 0.2079 time to fit residues: 33.8694 Evaluate side-chains 92 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 124 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 112 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN ** C 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12348 Z= 0.262 Angle : 0.683 11.167 16822 Z= 0.315 Chirality : 0.049 0.497 1959 Planarity : 0.004 0.046 2107 Dihedral : 13.032 96.047 2180 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.19 % Allowed : 17.10 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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: -1.03 (0.22), residues: 1447 helix: 2.77 (0.45), residues: 139 sheet: -0.48 (0.21), residues: 579 loop : -1.55 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 96 HIS 0.004 0.001 HIS C 374 PHE 0.020 0.002 PHE B 330 TYR 0.014 0.001 TYR C 594 ARG 0.003 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8534 (t0) cc_final: 0.8252 (t0) REVERT: A 100 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9214 (mm) REVERT: A 149 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7291 (mp0) REVERT: B 322 ASP cc_start: 0.7503 (t0) cc_final: 0.7066 (t0) REVERT: B 343 ARG cc_start: 0.5445 (ptt180) cc_final: 0.3665 (ttm170) REVERT: B 349 TRP cc_start: 0.7716 (p90) cc_final: 0.7466 (p90) REVERT: B 350 LYS cc_start: 0.8439 (mttt) cc_final: 0.8208 (mttt) REVERT: B 365 GLU cc_start: 0.7315 (mp0) cc_final: 0.7008 (mp0) REVERT: B 415 PRO cc_start: 0.7404 (Cg_endo) cc_final: 0.6446 (Cg_exo) REVERT: B 438 TRP cc_start: 0.7558 (m100) cc_final: 0.7257 (m100) REVERT: B 450 LYS cc_start: 0.7591 (pttt) cc_final: 0.7155 (mptt) REVERT: C 418 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8518 (tttm) REVERT: C 502 ARG cc_start: 0.8145 (mmt180) cc_final: 0.7620 (mmm160) REVERT: C 509 MET cc_start: 0.8232 (mmt) cc_final: 0.7747 (mpp) REVERT: C 540 PHE cc_start: 0.6654 (m-80) cc_final: 0.6058 (m-80) outliers start: 29 outliers final: 20 residues processed: 99 average time/residue: 0.2204 time to fit residues: 34.0128 Evaluate side-chains 88 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 446 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.0470 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12348 Z= 0.172 Angle : 0.621 9.516 16822 Z= 0.287 Chirality : 0.047 0.386 1959 Planarity : 0.004 0.044 2107 Dihedral : 11.805 95.877 2180 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.97 % Allowed : 17.32 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1447 helix: 3.10 (0.45), residues: 139 sheet: -0.34 (0.21), residues: 575 loop : -1.34 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 96 HIS 0.004 0.001 HIS C 408 PHE 0.014 0.001 PHE B 330 TYR 0.019 0.001 TYR A 105 ARG 0.002 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8407 (t0) cc_final: 0.8018 (t0) REVERT: A 100 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9198 (mm) REVERT: A 108 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8129 (t0) REVERT: B 322 ASP cc_start: 0.7490 (t0) cc_final: 0.7017 (t0) REVERT: B 343 ARG cc_start: 0.5336 (ptt180) cc_final: 0.3822 (ttm170) REVERT: B 349 TRP cc_start: 0.7622 (p90) cc_final: 0.7347 (p90) REVERT: B 365 GLU cc_start: 0.7144 (mp0) cc_final: 0.6836 (mp0) REVERT: B 450 LYS cc_start: 0.7608 (pttt) cc_final: 0.7155 (mptt) REVERT: B 593 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.6708 (t80) REVERT: C 418 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8673 (ttpp) REVERT: C 509 MET cc_start: 0.8169 (mmt) cc_final: 0.7679 (mpp) REVERT: C 540 PHE cc_start: 0.6760 (m-80) cc_final: 0.6047 (m-80) REVERT: C 552 MET cc_start: 0.2242 (mtt) cc_final: 0.1890 (mmm) outliers start: 26 outliers final: 16 residues processed: 90 average time/residue: 0.2369 time to fit residues: 33.4261 Evaluate side-chains 83 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 446 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12348 Z= 0.236 Angle : 0.636 11.597 16822 Z= 0.296 Chirality : 0.047 0.460 1959 Planarity : 0.004 0.042 2107 Dihedral : 10.943 93.890 2180 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.27 % Allowed : 17.47 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.22), residues: 1447 helix: 2.97 (0.45), residues: 139 sheet: -0.35 (0.21), residues: 583 loop : -1.28 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 96 HIS 0.004 0.001 HIS C 408 PHE 0.018 0.002 PHE B 330 TYR 0.011 0.001 TYR A 183 ARG 0.004 0.000 ARG C 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8430 (t0) cc_final: 0.8130 (t0) REVERT: A 100 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9207 (mm) REVERT: A 112 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: A 187 MET cc_start: 0.8971 (tpp) cc_final: 0.8760 (mmm) REVERT: B 322 ASP cc_start: 0.7523 (t0) cc_final: 0.7064 (t0) REVERT: B 343 ARG cc_start: 0.5331 (ptt180) cc_final: 0.3894 (ttm170) REVERT: B 349 TRP cc_start: 0.7702 (p90) cc_final: 0.7284 (p90) REVERT: B 350 LYS cc_start: 0.8451 (mttt) cc_final: 0.7955 (mttt) REVERT: B 365 GLU cc_start: 0.7290 (mp0) cc_final: 0.6963 (mp0) REVERT: B 415 PRO cc_start: 0.7279 (Cg_endo) cc_final: 0.6250 (Cg_exo) REVERT: B 450 LYS cc_start: 0.7601 (pttt) cc_final: 0.7264 (mmtp) REVERT: B 593 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.6800 (t80) REVERT: C 381 HIS cc_start: 0.6997 (OUTLIER) cc_final: 0.6774 (m-70) REVERT: C 418 LYS cc_start: 0.9076 (mmtt) cc_final: 0.8763 (ttpp) REVERT: C 509 MET cc_start: 0.8163 (mmt) cc_final: 0.7682 (mpp) REVERT: C 540 PHE cc_start: 0.6678 (m-80) cc_final: 0.6033 (m-80) outliers start: 30 outliers final: 21 residues processed: 95 average time/residue: 0.2001 time to fit residues: 30.1724 Evaluate side-chains 93 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 446 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 0.0870 chunk 109 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12348 Z= 0.234 Angle : 0.620 10.483 16822 Z= 0.292 Chirality : 0.047 0.454 1959 Planarity : 0.004 0.043 2107 Dihedral : 10.617 95.782 2180 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.34 % Allowed : 17.85 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1447 helix: 2.94 (0.45), residues: 139 sheet: -0.33 (0.21), residues: 582 loop : -1.28 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 96 HIS 0.004 0.001 HIS C 408 PHE 0.018 0.001 PHE B 330 TYR 0.019 0.001 TYR A 105 ARG 0.007 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8380 (t0) cc_final: 0.8133 (t0) REVERT: A 100 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9208 (mm) REVERT: A 112 GLN cc_start: 0.8180 (tm130) cc_final: 0.7712 (tm-30) REVERT: A 187 MET cc_start: 0.8938 (tpp) cc_final: 0.8731 (mmm) REVERT: B 322 ASP cc_start: 0.7537 (t0) cc_final: 0.7082 (t0) REVERT: B 343 ARG cc_start: 0.5279 (ptt180) cc_final: 0.3848 (ttm170) REVERT: B 349 TRP cc_start: 0.7695 (p90) cc_final: 0.7214 (p90) REVERT: B 350 LYS cc_start: 0.8475 (mttt) cc_final: 0.7866 (mttt) REVERT: B 365 GLU cc_start: 0.7268 (mp0) cc_final: 0.6931 (mp0) REVERT: B 450 LYS cc_start: 0.7592 (pttt) cc_final: 0.7168 (mptt) REVERT: B 593 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.6881 (t80) REVERT: C 381 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6210 (m-70) REVERT: C 418 LYS cc_start: 0.9086 (mmtt) cc_final: 0.8762 (ttpp) REVERT: C 509 MET cc_start: 0.8109 (mmt) cc_final: 0.7661 (mpp) REVERT: C 540 PHE cc_start: 0.6686 (m-80) cc_final: 0.6058 (m-80) outliers start: 31 outliers final: 23 residues processed: 96 average time/residue: 0.2276 time to fit residues: 34.0724 Evaluate side-chains 93 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 446 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.5074 > 50: distance: 30 - 63: 19.118 distance: 33 - 60: 24.988 distance: 47 - 52: 22.161 distance: 52 - 53: 31.734 distance: 52 - 185: 22.825 distance: 53 - 54: 35.735 distance: 53 - 56: 12.878 distance: 54 - 55: 40.103 distance: 54 - 60: 50.966 distance: 56 - 57: 45.305 distance: 57 - 58: 37.119 distance: 57 - 59: 29.172 distance: 60 - 61: 37.042 distance: 61 - 62: 19.517 distance: 61 - 64: 7.706 distance: 62 - 63: 13.727 distance: 62 - 71: 29.812 distance: 64 - 65: 11.197 distance: 65 - 66: 15.234 distance: 65 - 67: 8.225 distance: 66 - 68: 16.754 distance: 67 - 69: 10.792 distance: 68 - 70: 12.817 distance: 69 - 70: 6.764 distance: 71 - 72: 8.905 distance: 72 - 73: 29.387 distance: 72 - 75: 26.491 distance: 73 - 74: 21.800 distance: 73 - 85: 23.784 distance: 75 - 76: 20.532 distance: 76 - 77: 8.293 distance: 76 - 78: 6.159 distance: 77 - 79: 23.416 distance: 78 - 80: 13.817 distance: 78 - 81: 7.169 distance: 79 - 80: 4.473 distance: 80 - 82: 12.309 distance: 81 - 83: 13.577 distance: 82 - 84: 4.915 distance: 83 - 84: 13.370 distance: 85 - 86: 11.238 distance: 86 - 87: 17.357 distance: 86 - 89: 24.158 distance: 87 - 88: 21.035 distance: 87 - 94: 9.500 distance: 89 - 90: 24.655 distance: 90 - 91: 20.756 distance: 91 - 92: 15.768 distance: 92 - 93: 27.423 distance: 94 - 95: 32.303 distance: 94 - 100: 16.197 distance: 95 - 96: 27.602 distance: 95 - 98: 22.358 distance: 96 - 97: 41.520 distance: 96 - 101: 49.008 distance: 98 - 99: 20.766 distance: 99 - 100: 25.300 distance: 101 - 102: 28.173 distance: 102 - 103: 31.034 distance: 102 - 105: 40.832 distance: 103 - 104: 32.393 distance: 103 - 109: 15.547 distance: 105 - 106: 39.066 distance: 106 - 107: 4.320 distance: 106 - 108: 44.742 distance: 109 - 110: 22.715 distance: 110 - 111: 10.817 distance: 110 - 113: 8.591 distance: 111 - 112: 10.829 distance: 111 - 117: 4.469 distance: 112 - 141: 9.826 distance: 113 - 114: 17.688 distance: 114 - 115: 19.826 distance: 114 - 116: 16.314 distance: 117 - 118: 7.132 distance: 118 - 119: 9.871 distance: 118 - 121: 3.429 distance: 119 - 120: 6.358 distance: 119 - 126: 16.486 distance: 120 - 146: 5.348 distance: 121 - 122: 4.331 distance: 122 - 123: 6.833 distance: 123 - 124: 5.344 distance: 126 - 127: 19.903 distance: 127 - 128: 6.404 distance: 127 - 130: 23.856 distance: 128 - 129: 33.170 distance: 128 - 132: 24.876 distance: 130 - 131: 41.901 distance: 132 - 133: 34.081 distance: 133 - 134: 23.782 distance: 133 - 136: 43.927 distance: 134 - 135: 17.671 distance: 134 - 141: 14.112 distance: 136 - 137: 26.391 distance: 137 - 138: 21.345 distance: 138 - 139: 24.730 distance: 138 - 140: 8.885