Starting phenix.real_space_refine on Fri Jan 19 20:58:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw5_33491/01_2024/7xw5_33491_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw5_33491/01_2024/7xw5_33491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw5_33491/01_2024/7xw5_33491.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw5_33491/01_2024/7xw5_33491.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw5_33491/01_2024/7xw5_33491_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw5_33491/01_2024/7xw5_33491_neut_updated.pdb" } resolution = 2.96 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= -0.002 sd= 0.093 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 95 5.16 5 C 8177 2.51 5 N 2059 2.21 5 O 2287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G ARG 27": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N ARG 19": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N ARG 72": "NH1" <-> "NH2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N ARG 105": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ARG 46": "NH1" <-> "NH2" Residue "R ARG 65": "NH1" <-> "NH2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "R ARG 109": "NH1" <-> "NH2" Residue "R ARG 112": "NH1" <-> "NH2" Residue "R ARG 255": "NH1" <-> "NH2" Residue "R ARG 274": "NH1" <-> "NH2" Residue "R ARG 418": "NH1" <-> "NH2" Residue "R ARG 450": "NH1" <-> "NH2" Residue "R ARG 519": "NH1" <-> "NH2" Residue "R ARG 528": "NH1" <-> "NH2" Residue "R ARG 531": "NH1" <-> "NH2" Residue "R ARG 534": "NH1" <-> "NH2" Residue "R ARG 536": "NH1" <-> "NH2" Residue "R ARG 609": "NH1" <-> "NH2" Residue "R ARG 625": "NH1" <-> "NH2" Residue "R ARG 687": "NH1" <-> "NH2" Residue "X ARG 35": "NH1" <-> "NH2" Residue "X ARG 42": "NH1" <-> "NH2" Residue "X ARG 67": "NH1" <-> "NH2" Residue "Y ARG 33": "NH1" <-> "NH2" Residue "Y ARG 34": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 75": "NH1" <-> "NH2" Residue "Y ARG 80": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12618 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1964 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 4517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4517 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 545} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 35 Chain: "X" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 670 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "Y" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 838 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "R" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 577 Unusual residues: {'CLR': 14, 'HOI': 1, 'NAG': 4, 'PLM': 5} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" 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: "Y" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.23, per 1000 atoms: 0.57 Number of scatterers: 12618 At special positions: 0 Unit cell: (80.325, 101.745, 192.78, 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 95 16.00 O 2287 8.00 N 2059 7.00 C 8177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 31 " - pdb=" SG CYS R 41 " distance=2.04 Simple disulfide: pdb=" SG CYS R 283 " - pdb=" SG CYS R 398 " distance=2.05 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 408 " distance=2.04 Simple disulfide: pdb=" SG CYS R 494 " - pdb=" SG CYS R 569 " distance=2.03 Simple disulfide: pdb=" SG CYS X 7 " - pdb=" SG CYS X 31 " distance=2.03 Simple disulfide: pdb=" SG CYS X 10 " - pdb=" SG CYS X 60 " distance=2.05 Simple disulfide: pdb=" SG CYS X 28 " - pdb=" SG CYS X 82 " distance=2.03 Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS X 84 " distance=2.02 Simple disulfide: pdb=" SG CYS X 59 " - pdb=" SG CYS X 87 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 72 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 36 " - pdb=" SG CYS Y 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 39 " - pdb=" SG CYS Y 125 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 47 " - pdb=" SG CYS Y 103 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 51 " - pdb=" SG CYS Y 105 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 108 " - pdb=" SG CYS Y 115 " distance=2.04 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 Links applied NAG-ASN " NAG R 801 " - " ASN R 198 " " NAG R 802 " - " ASN R 177 " " NAG R 803 " - " ASN R 99 " " NAG R 804 " - " ASN R 77 " " NAG X 201 " - " ASN X 78 " " NAG X 202 " - " ASN X 52 " " NAG Y 201 " - " ASN Y 43 " Time building additional restraints: 5.11 Conformation dependent library (CDL) restraints added in 2.0 seconds 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2890 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 17 sheets defined 28.4% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 11 through 37 removed outlier: 3.705A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (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 63 removed outlier: 4.626A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 322 through 341 removed outlier: 3.676A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 380 removed outlier: 4.126A pdb=" N ALA A 362 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 364 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 365 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 367 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 370 " --> pdb=" O ASN A 367 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 373 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 379 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.614A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 266 through 269 Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'R' and resid 383 through 388 Processing helix chain 'R' and resid 415 through 441 removed outlier: 4.421A pdb=" N TRP R 422 " --> pdb=" O ARG R 418 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE R 423 " --> pdb=" O ILE R 419 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN R 432 " --> pdb=" O ALA R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 448 through 477 Processing helix chain 'R' and resid 481 through 483 No H-bonds generated for 'chain 'R' and resid 481 through 483' Processing helix chain 'R' and resid 485 through 490 Processing helix chain 'R' and resid 492 through 524 Processing helix chain 'R' and resid 529 through 531 No H-bonds generated for 'chain 'R' and resid 529 through 531' Processing helix chain 'R' and resid 535 through 558 removed outlier: 4.111A pdb=" N CYS R 548 " --> pdb=" O GLY R 544 " (cutoff:3.500A) Proline residue: R 556 - end of helix Processing helix chain 'R' and resid 577 through 608 removed outlier: 3.630A pdb=" N PHE R 594 " --> pdb=" O ASN R 590 " (cutoff:3.500A) Processing helix chain 'R' and resid 618 through 648 removed outlier: 3.757A pdb=" N ALA R 623 " --> pdb=" O ASP R 619 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL R 628 " --> pdb=" O LYS R 624 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU R 629 " --> pdb=" O ARG R 625 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS R 636 " --> pdb=" O THR R 632 " (cutoff:3.500A) Proline residue: R 639 - end of helix Processing helix chain 'R' and resid 656 through 665 removed outlier: 3.545A pdb=" N LYS R 660 " --> pdb=" O VAL R 656 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE R 661 " --> pdb=" O SER R 657 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU R 662 " --> pdb=" O ASN R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 669 through 678 Proline residue: R 675 - end of helix Processing helix chain 'R' and resid 683 through 696 removed outlier: 3.704A pdb=" N PHE R 696 " --> pdb=" O LEU R 692 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 46 removed outlier: 3.753A pdb=" N LYS X 45 " --> pdb=" O LEU X 41 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR X 46 " --> pdb=" O ARG X 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 41 through 46' Processing sheet with id= A, first strand: chain 'A' and resid 349 through 353 removed outlier: 7.104A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.901A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 93 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.881A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.624A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.842A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.689A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 306 through 308 removed outlier: 3.697A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.712A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 8 Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.522A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 33 through 35 removed outlier: 6.350A pdb=" N THR R 56 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N CYS R 41 " --> pdb=" O THR R 56 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS R 58 " --> pdb=" O CYS R 41 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG R 80 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU R 59 " --> pdb=" O ARG R 80 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR R 82 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS R 105 " --> pdb=" O ILE R 81 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL R 83 " --> pdb=" O HIS R 105 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU R 107 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE R 85 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG R 109 " --> pdb=" O ILE R 85 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE R 130 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE R 108 " --> pdb=" O PHE R 130 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLY R 132 " --> pdb=" O ILE R 108 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE R 155 " --> pdb=" O LEU R 131 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE R 133 " --> pdb=" O ILE R 155 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU R 157 " --> pdb=" O ILE R 133 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU R 182 " --> pdb=" O ASP R 203 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL R 205 " --> pdb=" O LEU R 182 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU R 230 " --> pdb=" O VAL R 205 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU R 251 " --> pdb=" O LEU R 231 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG R 274 " --> pdb=" O LEU R 252 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL R 397 " --> pdb=" O ALA R 275 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'X' and resid 11 through 14 Processing sheet with id= M, first strand: chain 'X' and resid 65 through 70 Processing sheet with id= N, first strand: chain 'X' and resid 59 through 64 removed outlier: 6.336A pdb=" N ALA X 81 " --> pdb=" O LYS X 63 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'Y' and resid 23 through 31 Processing sheet with id= P, first strand: chain 'Y' and resid 77 through 83 Processing sheet with id= Q, first strand: chain 'Y' and resid 71 through 76 removed outlier: 6.153A pdb=" N SER Y 102 " --> pdb=" O ARG Y 75 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 5.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1960 1.27 - 1.41: 3186 1.41 - 1.55: 7380 1.55 - 1.69: 264 1.69 - 1.83: 126 Bond restraints: 12916 Sorted by residual: bond pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 1.520 1.339 0.182 1.31e-02 5.83e+03 1.92e+02 bond pdb=" CA ALA B 104 " pdb=" CB ALA B 104 " ideal model delta sigma weight residual 1.535 1.403 0.132 1.32e-02 5.74e+03 1.00e+02 bond pdb=" CA PHE B 292 " pdb=" C PHE B 292 " ideal model delta sigma weight residual 1.522 1.396 0.126 1.33e-02 5.65e+03 9.00e+01 bond pdb=" C ALA B 104 " pdb=" O ALA B 104 " ideal model delta sigma weight residual 1.235 1.128 0.107 1.14e-02 7.69e+03 8.84e+01 bond pdb=" CA ALA B 106 " pdb=" C ALA B 106 " ideal model delta sigma weight residual 1.526 1.416 0.109 1.25e-02 6.40e+03 7.67e+01 ... (remaining 12911 not shown) Histogram of bond angle deviations from ideal: 91.24 - 99.93: 10 99.93 - 108.62: 1377 108.62 - 117.31: 7708 117.31 - 126.00: 8150 126.00 - 134.68: 323 Bond angle restraints: 17568 Sorted by residual: angle pdb=" N TYR B 105 " pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 108.46 91.24 17.22 1.51e+00 4.39e-01 1.30e+02 angle pdb=" N PHE B 292 " pdb=" CA PHE B 292 " pdb=" C PHE B 292 " ideal model delta sigma weight residual 113.56 122.99 -9.43 1.39e+00 5.18e-01 4.60e+01 angle pdb=" C TYR B 105 " pdb=" CA TYR B 105 " pdb=" CB TYR B 105 " ideal model delta sigma weight residual 109.72 98.98 10.74 1.61e+00 3.86e-01 4.45e+01 angle pdb=" CA ASP N 50 " pdb=" CB ASP N 50 " pdb=" CG ASP N 50 " ideal model delta sigma weight residual 112.60 119.01 -6.41 1.00e+00 1.00e+00 4.11e+01 angle pdb=" N LYS A 25 " pdb=" CA LYS A 25 " pdb=" C LYS A 25 " ideal model delta sigma weight residual 111.14 104.30 6.84 1.08e+00 8.57e-01 4.01e+01 ... (remaining 17563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.95: 8192 23.95 - 47.91: 312 47.91 - 71.86: 32 71.86 - 95.82: 13 95.82 - 119.77: 1 Dihedral angle restraints: 8550 sinusoidal: 4084 harmonic: 4466 Sorted by residual: dihedral pdb=" C TYR B 105 " pdb=" N TYR B 105 " pdb=" CA TYR B 105 " pdb=" CB TYR B 105 " ideal model delta harmonic sigma weight residual -122.60 -100.77 -21.83 0 2.50e+00 1.60e-01 7.62e+01 dihedral pdb=" CB CYS X 10 " pdb=" SG CYS X 10 " pdb=" SG CYS X 60 " pdb=" CB CYS X 60 " ideal model delta sinusoidal sigma weight residual 93.00 166.18 -73.18 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CB CYS R 284 " pdb=" SG CYS R 284 " pdb=" SG CYS R 408 " pdb=" CB CYS R 408 " ideal model delta sinusoidal sigma weight residual -86.00 -145.94 59.94 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 8547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 1875 0.177 - 0.354: 156 0.354 - 0.531: 7 0.531 - 0.707: 0 0.707 - 0.884: 1 Chirality restraints: 2039 Sorted by residual: chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" CA THR B 87 " pdb=" N THR B 87 " pdb=" C THR B 87 " pdb=" CB THR B 87 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 2036 not shown) Planarity restraints: 2139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 HOI R 805 " 0.048 2.00e-02 2.50e+03 1.40e-01 4.42e+02 pdb=" C11 HOI R 805 " -0.000 2.00e-02 2.50e+03 pdb=" C12 HOI R 805 " 0.119 2.00e-02 2.50e+03 pdb=" C13 HOI R 805 " 0.167 2.00e-02 2.50e+03 pdb=" C14 HOI R 805 " 0.029 2.00e-02 2.50e+03 pdb=" C15 HOI R 805 " 0.003 2.00e-02 2.50e+03 pdb=" C16 HOI R 805 " -0.208 2.00e-02 2.50e+03 pdb=" C9 HOI R 805 " 0.116 2.00e-02 2.50e+03 pdb=" O5 HOI R 805 " -0.274 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 348 " -0.236 2.00e-02 2.50e+03 1.28e-01 3.29e+02 pdb=" CG TYR A 348 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR A 348 " 0.115 2.00e-02 2.50e+03 pdb=" CD2 TYR A 348 " 0.102 2.00e-02 2.50e+03 pdb=" CE1 TYR A 348 " 0.066 2.00e-02 2.50e+03 pdb=" CE2 TYR A 348 " 0.073 2.00e-02 2.50e+03 pdb=" CZ TYR A 348 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 348 " -0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " -0.178 2.00e-02 2.50e+03 9.20e-02 2.12e+02 pdb=" CG TRP B 99 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " 0.088 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " 0.121 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " -0.117 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " -0.095 2.00e-02 2.50e+03 ... (remaining 2136 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 96 2.68 - 3.23: 11528 3.23 - 3.79: 18930 3.79 - 4.34: 27184 4.34 - 4.90: 43941 Nonbonded interactions: 101679 Sorted by model distance: nonbonded pdb=" N TYR B 105 " pdb=" O TYR B 105 " model vdw 2.119 2.496 nonbonded pdb=" O TRP B 339 " pdb=" OD1 ASN B 340 " model vdw 2.197 3.040 nonbonded pdb=" CG2 THR A 40 " pdb=" OD1 ASN A 218 " model vdw 2.461 3.460 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.539 2.440 nonbonded pdb=" OE2 GLU R 506 " pdb=" CG1 VAL R 586 " model vdw 2.539 3.460 ... (remaining 101674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 6.390 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 36.110 Find NCS groups from input model: 0.330 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 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 : 0.014 0.182 12916 Z= 0.906 Angle : 1.875 17.215 17568 Z= 1.232 Chirality : 0.105 0.884 2039 Planarity : 0.016 0.166 2132 Dihedral : 12.541 119.769 5609 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.53 % Allowed : 4.53 % Favored : 94.94 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.98 (0.20), residues: 1502 helix: -0.91 (0.21), residues: 404 sheet: -0.47 (0.30), residues: 280 loop : -0.45 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.178 0.031 TRP B 99 HIS 0.017 0.004 HIS A 347 PHE 0.067 0.016 PHE R 269 TYR 0.236 0.019 TYR A 348 ARG 0.010 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 269 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7170 (mm-40) cc_final: 0.6749 (mm110) REVERT: A 35 GLN cc_start: 0.7711 (tt0) cc_final: 0.7058 (mm-40) REVERT: A 58 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7514 (ttpp) REVERT: A 236 GLN cc_start: 0.8410 (mt0) cc_final: 0.8196 (pt0) REVERT: A 346 ARG cc_start: 0.6783 (mtp180) cc_final: 0.6484 (mtm-85) REVERT: B 57 LYS cc_start: 0.8541 (pttm) cc_final: 0.8295 (pttt) REVERT: B 263 THR cc_start: 0.8521 (t) cc_final: 0.8255 (m) REVERT: B 303 ASP cc_start: 0.6724 (t0) cc_final: 0.6244 (m-30) REVERT: N 83 MET cc_start: 0.6648 (ttm) cc_final: 0.6444 (ttp) REVERT: R 32 HIS cc_start: 0.7084 (m90) cc_final: 0.6860 (m-70) REVERT: R 57 LEU cc_start: 0.8659 (mp) cc_final: 0.8331 (tp) REVERT: R 140 MET cc_start: 0.7151 (ptm) cc_final: 0.6780 (ptm) REVERT: R 191 SER cc_start: 0.8897 (t) cc_final: 0.8667 (p) REVERT: R 248 HIS cc_start: 0.6975 (m-70) cc_final: 0.6566 (m-70) REVERT: R 434 PHE cc_start: 0.8063 (t80) cc_final: 0.7791 (t80) REVERT: R 539 CYS cc_start: 0.7962 (t) cc_final: 0.7615 (m) REVERT: R 610 ASN cc_start: 0.7001 (p0) cc_final: 0.6777 (p0) REVERT: R 651 LYS cc_start: 0.7064 (mttt) cc_final: 0.6819 (tppt) REVERT: R 683 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7346 (pttt) REVERT: X 44 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.7005 (mttp) REVERT: X 91 LYS cc_start: 0.7539 (mttp) cc_final: 0.7211 (mtmt) REVERT: Y 52 MET cc_start: 0.7878 (tpp) cc_final: 0.7280 (tmm) outliers start: 7 outliers final: 2 residues processed: 274 average time/residue: 1.0387 time to fit residues: 314.1262 Evaluate side-chains 168 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain X residue 44 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN G 18 GLN N 13 GLN R 33 GLN R 105 HIS R 170 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12916 Z= 0.244 Angle : 0.679 9.700 17568 Z= 0.352 Chirality : 0.045 0.207 2039 Planarity : 0.005 0.060 2132 Dihedral : 7.717 59.349 2820 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.93 % Allowed : 12.08 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.09 (0.21), residues: 1502 helix: 0.85 (0.24), residues: 417 sheet: -0.34 (0.28), residues: 330 loop : -0.07 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 297 HIS 0.008 0.001 HIS A 347 PHE 0.025 0.002 PHE R 434 TYR 0.015 0.002 TYR A 348 ARG 0.005 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 197 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6624 (mm-40) cc_final: 0.6366 (mm110) REVERT: A 35 GLN cc_start: 0.7570 (tt0) cc_final: 0.6821 (mm-40) REVERT: A 59 GLN cc_start: 0.7848 (tp40) cc_final: 0.7506 (mm110) REVERT: A 239 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7786 (p0) REVERT: A 285 ASP cc_start: 0.7195 (p0) cc_final: 0.6924 (p0) REVERT: A 289 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: A 301 TYR cc_start: 0.8324 (m-80) cc_final: 0.8099 (m-80) REVERT: A 346 ARG cc_start: 0.6801 (mtp180) cc_final: 0.6335 (mtm-85) REVERT: B 98 SER cc_start: 0.8546 (m) cc_final: 0.8015 (t) REVERT: B 226 GLU cc_start: 0.7256 (pt0) cc_final: 0.7040 (pt0) REVERT: B 263 THR cc_start: 0.8557 (t) cc_final: 0.8280 (m) REVERT: B 283 ARG cc_start: 0.8071 (tpt-90) cc_final: 0.7709 (tpt-90) REVERT: G 29 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7734 (mtpp) REVERT: N 83 MET cc_start: 0.6674 (ttm) cc_final: 0.6348 (ttm) REVERT: R 57 LEU cc_start: 0.8430 (mp) cc_final: 0.8188 (tp) REVERT: R 115 THR cc_start: 0.8552 (m) cc_final: 0.8225 (m) REVERT: R 140 MET cc_start: 0.7214 (ptm) cc_final: 0.6770 (pmm) REVERT: R 191 SER cc_start: 0.8872 (t) cc_final: 0.8638 (p) REVERT: R 434 PHE cc_start: 0.7847 (t80) cc_final: 0.7543 (t80) REVERT: R 534 ARG cc_start: 0.5592 (ttp80) cc_final: 0.5066 (mmm160) REVERT: R 651 LYS cc_start: 0.7197 (mttt) cc_final: 0.6819 (tppt) REVERT: X 91 LYS cc_start: 0.7633 (mttp) cc_final: 0.7297 (mtmt) REVERT: Y 25 THR cc_start: 0.7413 (m) cc_final: 0.7202 (m) REVERT: Y 70 ASP cc_start: 0.8542 (m-30) cc_final: 0.8192 (t0) outliers start: 52 outliers final: 19 residues processed: 222 average time/residue: 0.9997 time to fit residues: 246.1960 Evaluate side-chains 184 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 439 LEU Chi-restraints excluded: chain R residue 554 LEU Chi-restraints excluded: chain R residue 576 THR Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 115 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 91 optimal weight: 0.0270 chunk 37 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 176 GLN N 3 GLN R 484 HIS X 13 GLN X 15 ASN ** X 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 30 HIS ** Y 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12916 Z= 0.197 Angle : 0.596 10.304 17568 Z= 0.308 Chirality : 0.044 0.205 2039 Planarity : 0.004 0.045 2132 Dihedral : 7.141 59.695 2814 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.55 % Allowed : 15.18 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.49 (0.22), residues: 1502 helix: 1.53 (0.26), residues: 402 sheet: -0.27 (0.28), residues: 330 loop : 0.06 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 36 HIS 0.012 0.001 HIS X 83 PHE 0.044 0.002 PHE R 153 TYR 0.015 0.001 TYR B 111 ARG 0.006 0.000 ARG Y 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 175 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6638 (mm-40) cc_final: 0.6354 (mm110) REVERT: A 35 GLN cc_start: 0.7726 (tt0) cc_final: 0.6965 (mm-40) REVERT: A 58 LYS cc_start: 0.8065 (ttmm) cc_final: 0.7063 (tptt) REVERT: A 59 GLN cc_start: 0.7900 (tp40) cc_final: 0.7604 (mm110) REVERT: A 285 ASP cc_start: 0.6895 (p0) cc_final: 0.6455 (p0) REVERT: A 289 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: A 301 TYR cc_start: 0.8289 (m-80) cc_final: 0.7928 (m-80) REVERT: A 346 ARG cc_start: 0.6831 (mtp180) cc_final: 0.6344 (mtm-85) REVERT: B 98 SER cc_start: 0.8469 (m) cc_final: 0.8005 (t) REVERT: B 175 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7456 (tp40) REVERT: B 303 ASP cc_start: 0.6691 (t0) cc_final: 0.6249 (m-30) REVERT: G 51 LEU cc_start: 0.8197 (mt) cc_final: 0.7818 (mt) REVERT: N 83 MET cc_start: 0.6416 (ttm) cc_final: 0.6151 (ttm) REVERT: R 57 LEU cc_start: 0.8394 (mp) cc_final: 0.8041 (tp) REVERT: R 396 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7415 (pp-130) REVERT: R 453 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.6407 (mtp) REVERT: R 534 ARG cc_start: 0.5548 (ttp80) cc_final: 0.5205 (mtp85) REVERT: R 651 LYS cc_start: 0.7240 (mttt) cc_final: 0.6770 (tppt) REVERT: X 45 LYS cc_start: 0.8519 (ptpp) cc_final: 0.8226 (pttp) REVERT: Y 57 ASN cc_start: 0.7463 (OUTLIER) cc_final: 0.7022 (m110) REVERT: Y 70 ASP cc_start: 0.8555 (m-30) cc_final: 0.8089 (t0) outliers start: 47 outliers final: 24 residues processed: 202 average time/residue: 0.9327 time to fit residues: 210.9952 Evaluate side-chains 186 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 396 MET Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 453 MET Chi-restraints excluded: chain R residue 554 LEU Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain Y residue 30 HIS Chi-restraints excluded: chain Y residue 57 ASN Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 103 CYS Chi-restraints excluded: chain Y residue 115 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 HIS R 489 GLN ** Y 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12916 Z= 0.292 Angle : 0.626 10.305 17568 Z= 0.319 Chirality : 0.045 0.212 2039 Planarity : 0.004 0.053 2132 Dihedral : 7.353 59.533 2814 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.29 % Allowed : 15.33 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.38 (0.22), residues: 1502 helix: 1.46 (0.26), residues: 402 sheet: -0.29 (0.27), residues: 332 loop : -0.04 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 36 HIS 0.016 0.002 HIS Y 30 PHE 0.021 0.002 PHE X 74 TYR 0.016 0.002 TYR X 89 ARG 0.005 0.000 ARG Y 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 167 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6676 (mm-40) cc_final: 0.6374 (mm110) REVERT: A 35 GLN cc_start: 0.7721 (tt0) cc_final: 0.6971 (mm-40) REVERT: A 58 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7088 (tptt) REVERT: A 59 GLN cc_start: 0.7886 (tp40) cc_final: 0.7544 (mm110) REVERT: A 239 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7799 (t0) REVERT: A 301 TYR cc_start: 0.8382 (m-80) cc_final: 0.8110 (m-80) REVERT: A 346 ARG cc_start: 0.6905 (mtp180) cc_final: 0.6355 (mtm-85) REVERT: B 98 SER cc_start: 0.8528 (m) cc_final: 0.8059 (t) REVERT: B 233 CYS cc_start: 0.8355 (t) cc_final: 0.7427 (p) REVERT: B 303 ASP cc_start: 0.6757 (t0) cc_final: 0.6234 (m-30) REVERT: G 29 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7840 (mtpp) REVERT: G 51 LEU cc_start: 0.8284 (mt) cc_final: 0.7863 (mt) REVERT: N 83 MET cc_start: 0.6499 (ttm) cc_final: 0.6209 (ttm) REVERT: R 57 LEU cc_start: 0.8524 (mp) cc_final: 0.8107 (tp) REVERT: R 453 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6341 (mtp) REVERT: R 534 ARG cc_start: 0.5583 (ttp80) cc_final: 0.5371 (ttp80) REVERT: R 535 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8508 (tt) REVERT: R 565 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8719 (mmtm) REVERT: R 651 LYS cc_start: 0.7317 (mttt) cc_final: 0.6880 (tppt) REVERT: R 683 LYS cc_start: 0.7627 (mtpp) cc_final: 0.7257 (pttt) REVERT: X 45 LYS cc_start: 0.8545 (ptpp) cc_final: 0.8230 (pttp) REVERT: X 50 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7997 (mm110) REVERT: Y 57 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7319 (m110) REVERT: Y 70 ASP cc_start: 0.8563 (m-30) cc_final: 0.8061 (t0) outliers start: 70 outliers final: 35 residues processed: 211 average time/residue: 0.9975 time to fit residues: 235.1647 Evaluate side-chains 196 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 91 GLN Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 153 PHE Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 257 THR Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 439 LEU Chi-restraints excluded: chain R residue 453 MET Chi-restraints excluded: chain R residue 535 LEU Chi-restraints excluded: chain R residue 554 LEU Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain R residue 565 LYS Chi-restraints excluded: chain R residue 576 THR Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 52 ASN Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain Y residue 57 ASN Chi-restraints excluded: chain Y residue 103 CYS Chi-restraints excluded: chain Y residue 115 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN R 271 HIS ** Y 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12916 Z= 0.174 Angle : 0.564 8.249 17568 Z= 0.290 Chirality : 0.043 0.224 2039 Planarity : 0.004 0.044 2132 Dihedral : 6.992 59.232 2814 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.15 % Allowed : 17.30 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.39 (0.22), residues: 1502 helix: 1.46 (0.26), residues: 414 sheet: -0.25 (0.27), residues: 324 loop : -0.08 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 36 HIS 0.009 0.001 HIS X 83 PHE 0.023 0.001 PHE R 153 TYR 0.010 0.001 TYR R 667 ARG 0.005 0.000 ARG Y 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 159 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6650 (mm-40) cc_final: 0.6358 (mm110) REVERT: A 35 GLN cc_start: 0.7760 (tt0) cc_final: 0.7019 (mm-40) REVERT: A 58 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7064 (tptt) REVERT: A 59 GLN cc_start: 0.7967 (tp40) cc_final: 0.7721 (mm110) REVERT: A 239 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7846 (t0) REVERT: A 301 TYR cc_start: 0.8407 (m-80) cc_final: 0.8145 (m-80) REVERT: A 346 ARG cc_start: 0.6811 (mtp180) cc_final: 0.6310 (mtm-85) REVERT: B 23 LYS cc_start: 0.9106 (tptp) cc_final: 0.8767 (mtmt) REVERT: B 98 SER cc_start: 0.8522 (m) cc_final: 0.8090 (t) REVERT: B 127 LYS cc_start: 0.6536 (mmmm) cc_final: 0.6305 (mmmt) REVERT: B 214 ARG cc_start: 0.7485 (mmt-90) cc_final: 0.6709 (mmt-90) REVERT: B 217 MET cc_start: 0.7502 (pmm) cc_final: 0.7129 (mmp) REVERT: B 303 ASP cc_start: 0.6720 (t0) cc_final: 0.6280 (m-30) REVERT: G 51 LEU cc_start: 0.8251 (mt) cc_final: 0.7810 (mt) REVERT: N 83 MET cc_start: 0.6545 (ttm) cc_final: 0.6255 (ttm) REVERT: R 57 LEU cc_start: 0.8426 (mp) cc_final: 0.8130 (tp) REVERT: R 144 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8113 (mt) REVERT: R 453 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6364 (mtp) REVERT: R 651 LYS cc_start: 0.7269 (mttt) cc_final: 0.6836 (tppt) REVERT: R 683 LYS cc_start: 0.7566 (mtpp) cc_final: 0.7234 (pttt) REVERT: X 45 LYS cc_start: 0.8526 (ptpp) cc_final: 0.8227 (pttp) REVERT: Y 33 ARG cc_start: 0.7775 (mmm-85) cc_final: 0.7506 (mmm-85) REVERT: Y 57 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7479 (m110) REVERT: Y 70 ASP cc_start: 0.8548 (m-30) cc_final: 0.8034 (t0) REVERT: Y 120 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7271 (pt) outliers start: 55 outliers final: 33 residues processed: 195 average time/residue: 1.0424 time to fit residues: 225.3079 Evaluate side-chains 182 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 143 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 91 GLN Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 257 THR Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 453 MET Chi-restraints excluded: chain R residue 494 CYS Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 52 ASN Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain Y residue 57 ASN Chi-restraints excluded: chain Y residue 115 CYS Chi-restraints excluded: chain Y residue 120 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 118 optimal weight: 0.1980 chunk 66 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 HIS ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 GLN ** Y 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12916 Z= 0.308 Angle : 0.637 10.750 17568 Z= 0.325 Chirality : 0.045 0.248 2039 Planarity : 0.004 0.052 2132 Dihedral : 7.292 59.605 2814 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.91 % Allowed : 16.39 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.15 (0.22), residues: 1502 helix: 1.13 (0.25), residues: 426 sheet: -0.30 (0.28), residues: 332 loop : -0.21 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.008 0.001 HIS X 83 PHE 0.042 0.002 PHE R 153 TYR 0.015 0.002 TYR A 348 ARG 0.003 0.000 ARG Y 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 160 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6688 (mm-40) cc_final: 0.6368 (mm110) REVERT: A 35 GLN cc_start: 0.7787 (tt0) cc_final: 0.7039 (mm-40) REVERT: A 58 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7111 (tptt) REVERT: A 59 GLN cc_start: 0.8014 (tp40) cc_final: 0.7702 (mm110) REVERT: A 208 PHE cc_start: 0.7865 (m-10) cc_final: 0.7664 (m-10) REVERT: A 239 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7822 (t0) REVERT: A 301 TYR cc_start: 0.8446 (m-80) cc_final: 0.8236 (m-80) REVERT: A 346 ARG cc_start: 0.6926 (mtp180) cc_final: 0.6372 (mtm-85) REVERT: B 98 SER cc_start: 0.8569 (m) cc_final: 0.8125 (t) REVERT: B 233 CYS cc_start: 0.8353 (t) cc_final: 0.7433 (p) REVERT: B 303 ASP cc_start: 0.6720 (t0) cc_final: 0.6245 (m-30) REVERT: G 29 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7743 (mtpp) REVERT: G 51 LEU cc_start: 0.8349 (mt) cc_final: 0.7886 (mt) REVERT: N 83 MET cc_start: 0.6501 (ttm) cc_final: 0.6134 (ttm) REVERT: R 57 LEU cc_start: 0.8520 (mp) cc_final: 0.8280 (tp) REVERT: R 144 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7991 (mt) REVERT: R 403 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7298 (t0) REVERT: R 453 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.5916 (tpt) REVERT: R 534 ARG cc_start: 0.5609 (ttp80) cc_final: 0.5386 (ttp80) REVERT: R 651 LYS cc_start: 0.7321 (mttt) cc_final: 0.6910 (tppt) REVERT: R 683 LYS cc_start: 0.7591 (mtpp) cc_final: 0.7255 (pttt) REVERT: X 45 LYS cc_start: 0.8560 (ptpp) cc_final: 0.8285 (pttp) REVERT: X 71 MET cc_start: 0.4600 (pmm) cc_final: 0.4346 (pmm) REVERT: Y 70 ASP cc_start: 0.8488 (m-30) cc_final: 0.7928 (t0) REVERT: Y 120 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7337 (pt) outliers start: 65 outliers final: 38 residues processed: 201 average time/residue: 0.9835 time to fit residues: 219.2992 Evaluate side-chains 191 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 257 THR Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 403 ASP Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain R residue 439 LEU Chi-restraints excluded: chain R residue 453 MET Chi-restraints excluded: chain R residue 494 CYS Chi-restraints excluded: chain R residue 554 LEU Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain R residue 576 THR Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain Y residue 29 MET Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 120 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 7.9990 chunk 16 optimal weight: 0.0070 chunk 81 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN R 271 HIS X 13 GLN X 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12916 Z= 0.177 Angle : 0.579 11.548 17568 Z= 0.293 Chirality : 0.042 0.203 2039 Planarity : 0.004 0.046 2132 Dihedral : 6.776 59.354 2814 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.15 % Allowed : 17.52 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.26 (0.22), residues: 1502 helix: 1.34 (0.26), residues: 426 sheet: -0.27 (0.28), residues: 332 loop : -0.21 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.007 0.001 HIS X 83 PHE 0.014 0.001 PHE X 74 TYR 0.010 0.001 TYR R 667 ARG 0.004 0.000 ARG R 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 152 time to evaluate : 1.453 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6643 (mm-40) cc_final: 0.6340 (mm110) REVERT: A 35 GLN cc_start: 0.7782 (tt0) cc_final: 0.7040 (mm-40) REVERT: A 58 LYS cc_start: 0.7976 (ttmm) cc_final: 0.6952 (tptt) REVERT: A 59 GLN cc_start: 0.7942 (tp40) cc_final: 0.7715 (mm110) REVERT: A 208 PHE cc_start: 0.7820 (m-10) cc_final: 0.7597 (m-10) REVERT: A 239 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7889 (t0) REVERT: A 301 TYR cc_start: 0.8477 (m-80) cc_final: 0.8230 (m-80) REVERT: A 346 ARG cc_start: 0.6849 (mtp180) cc_final: 0.6307 (mtm-85) REVERT: B 23 LYS cc_start: 0.9107 (tptp) cc_final: 0.8802 (mtmt) REVERT: B 98 SER cc_start: 0.8547 (m) cc_final: 0.8140 (t) REVERT: B 214 ARG cc_start: 0.7584 (mmt-90) cc_final: 0.6894 (mmt-90) REVERT: B 233 CYS cc_start: 0.8228 (t) cc_final: 0.7449 (p) REVERT: B 303 ASP cc_start: 0.6719 (t0) cc_final: 0.6219 (m-30) REVERT: G 51 LEU cc_start: 0.8369 (mt) cc_final: 0.7943 (mt) REVERT: N 83 MET cc_start: 0.6438 (ttm) cc_final: 0.6128 (ttm) REVERT: R 144 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8068 (mt) REVERT: R 453 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.5921 (tpt) REVERT: R 535 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8372 (tt) REVERT: R 651 LYS cc_start: 0.7241 (mttt) cc_final: 0.6867 (tppt) REVERT: R 683 LYS cc_start: 0.7690 (mtpp) cc_final: 0.7302 (pttt) REVERT: X 45 LYS cc_start: 0.8584 (ptpp) cc_final: 0.8314 (pttp) REVERT: X 71 MET cc_start: 0.5073 (pmm) cc_final: 0.4766 (pmm) REVERT: Y 70 ASP cc_start: 0.8381 (m-30) cc_final: 0.7799 (t0) REVERT: Y 120 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7336 (pt) outliers start: 55 outliers final: 35 residues processed: 191 average time/residue: 0.9998 time to fit residues: 212.5525 Evaluate side-chains 186 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 146 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 257 THR Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 453 MET Chi-restraints excluded: chain R residue 494 CYS Chi-restraints excluded: chain R residue 535 LEU Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 52 ASN Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain Y residue 29 MET Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 115 CYS Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Y residue 123 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.4685 > 50: distance: 92 - 106: 14.332 distance: 102 - 106: 16.988 distance: 106 - 107: 8.632 distance: 107 - 108: 26.022 distance: 107 - 110: 20.421 distance: 108 - 109: 25.654 distance: 108 - 117: 26.047 distance: 110 - 111: 16.277 distance: 111 - 112: 23.197 distance: 111 - 113: 13.764 distance: 112 - 114: 20.623 distance: 113 - 115: 17.547 distance: 114 - 116: 11.778 distance: 115 - 116: 15.798 distance: 117 - 118: 21.104 distance: 118 - 119: 11.215 distance: 118 - 121: 7.050 distance: 119 - 120: 28.275 distance: 119 - 125: 24.270 distance: 121 - 122: 23.538 distance: 122 - 123: 7.008 distance: 122 - 124: 29.014 distance: 125 - 126: 10.446 distance: 126 - 127: 3.816 distance: 126 - 129: 9.841 distance: 127 - 128: 7.060 distance: 127 - 135: 13.164 distance: 129 - 130: 36.930 distance: 130 - 131: 36.994 distance: 130 - 132: 35.233 distance: 131 - 133: 30.823 distance: 132 - 134: 16.058 distance: 133 - 134: 18.962 distance: 135 - 136: 14.550 distance: 136 - 137: 25.979 distance: 136 - 139: 16.474 distance: 137 - 138: 36.525 distance: 137 - 143: 28.387 distance: 139 - 140: 36.377 distance: 140 - 141: 29.831 distance: 140 - 142: 29.823 distance: 143 - 144: 18.065 distance: 144 - 145: 24.694 distance: 144 - 147: 29.285 distance: 145 - 146: 38.909 distance: 145 - 150: 39.048 distance: 147 - 148: 21.547 distance: 147 - 149: 18.375 distance: 150 - 151: 24.520 distance: 151 - 152: 23.596 distance: 151 - 154: 36.576 distance: 152 - 153: 42.977 distance: 152 - 161: 40.420 distance: 154 - 155: 32.788 distance: 155 - 156: 23.552 distance: 156 - 157: 24.235 distance: 157 - 158: 14.415 distance: 158 - 159: 18.487 distance: 158 - 160: 19.779 distance: 161 - 162: 43.909 distance: 162 - 163: 53.710 distance: 162 - 165: 55.164 distance: 163 - 164: 58.838 distance: 163 - 166: 24.115 distance: 166 - 167: 29.682 distance: 167 - 168: 43.098 distance: 167 - 170: 63.478 distance: 168 - 169: 37.837 distance: 168 - 174: 14.118 distance: 170 - 171: 55.092 distance: 171 - 172: 19.685 distance: 171 - 173: 29.730 distance: 174 - 175: 38.763 distance: 175 - 176: 28.141 distance: 175 - 178: 49.984 distance: 176 - 177: 48.221 distance: 176 - 182: 16.490 distance: 178 - 179: 62.701 distance: 179 - 180: 41.233 distance: 179 - 181: 31.831 distance: 182 - 183: 8.748 distance: 183 - 184: 26.807 distance: 183 - 186: 32.871 distance: 184 - 185: 51.054 distance: 184 - 188: 26.103 distance: 186 - 187: 54.246