Starting phenix.real_space_refine on Mon Aug 5 03:27:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqa_40700/08_2024/8sqa_40700.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqa_40700/08_2024/8sqa_40700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqa_40700/08_2024/8sqa_40700.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqa_40700/08_2024/8sqa_40700.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqa_40700/08_2024/8sqa_40700.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqa_40700/08_2024/8sqa_40700.cif" } resolution = 4.2 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= 0.005 sd= 0.057 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 34 5.16 5 C 7662 2.51 5 N 2079 2.21 5 O 2381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "F ARG 1269": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12156 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6052 Classifications: {'peptide': 765} Link IDs: {'CIS': 2, 'PTRANS': 28, 'TRANS': 734} Chain breaks: 4 Chain: "B" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2776 Classifications: {'peptide': 369} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 355} Chain breaks: 1 Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 437 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1740 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 668 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "F" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 483 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 7.01, per 1000 atoms: 0.58 Number of scatterers: 12156 At special positions: 0 Unit cell: (100.44, 139.32, 128.52, 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 34 16.00 O 2381 8.00 N 2079 7.00 C 7662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS F1208 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.72 Conformation dependent library (CDL) restraints added in 2.1 seconds 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2852 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 22 sheets defined 22.5% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 158 through 162 removed outlier: 3.801A pdb=" N ARG A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.606A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 removed outlier: 4.075A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 297 through 316 removed outlier: 3.861A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.973A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.634A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 removed outlier: 4.175A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 removed outlier: 4.136A pdb=" N ALA D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.945A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.721A pdb=" N GLY D 129 " --> pdb=" O GLY D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.953A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 203 Processing helix chain 'D' and resid 208 through 225 removed outlier: 4.209A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 240 removed outlier: 3.543A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.718A pdb=" N SER E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 removed outlier: 3.626A pdb=" N VAL E 55 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 154 removed outlier: 3.571A pdb=" N LYS A 152 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 168 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 183 removed outlier: 6.976A pdb=" N GLU A 176 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N VAL A 256 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLN A 178 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 12.830A pdb=" N VAL A 258 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N ILE A 180 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.059A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP A 342 " --> pdb=" O ARG A 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.059A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.764A pdb=" N ALA A 375 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 401 removed outlier: 3.930A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 415 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 426 Processing sheet with id=AA8, first strand: chain 'A' and resid 429 through 432 Processing sheet with id=AA9, first strand: chain 'A' and resid 455 through 458 removed outlier: 3.530A pdb=" N GLY A 457 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 473 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY A 516 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 486 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 525 through 526 removed outlier: 4.029A pdb=" N ARG A 526 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 618 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 614 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR A 596 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A 610 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET A 711 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 716 " --> pdb=" O TRP A 739 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 718 " --> pdb=" O PHE A 737 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 737 " --> pdb=" O PHE A 718 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 736 " --> pdb=" O ALA A 773 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 773 " --> pdb=" O SER A 736 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 772 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 743 through 744 removed outlier: 3.936A pdb=" N LEU A 716 " --> pdb=" O TRP A 739 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 718 " --> pdb=" O PHE A 737 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 737 " --> pdb=" O PHE A 718 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 736 " --> pdb=" O ALA A 773 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 773 " --> pdb=" O SER A 736 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 772 " --> pdb=" O TYR A 787 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 784 " --> pdb=" O ASN A 805 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 805 " --> pdb=" O VAL A 784 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.791A pdb=" N LYS B 82 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.723A pdb=" N THR B 116 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 123 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 132 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.650A pdb=" N LEU B 174 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 185 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 173 " --> pdb=" O TRP B 183 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 202 through 203 removed outlier: 3.720A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 253 through 254 removed outlier: 3.647A pdb=" N VAL B 254 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.935A pdb=" N ILE B 290 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR B 297 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 307 " --> pdb=" O TRP B 317 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.685A pdb=" N VAL B 331 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 338 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 372 through 373 Processing sheet with id=AC2, first strand: chain 'E' and resid 32 through 33 removed outlier: 3.812A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 1223 through 1226 removed outlier: 3.620A pdb=" N GLU F1277 " --> pdb=" O ASN F1293 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 1266 through 1267 383 hydrogen bonds defined for protein. 1044 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: 4.46 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4070 1.34 - 1.46: 2527 1.46 - 1.57: 5751 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 12413 Sorted by residual: bond pdb=" C ASP B 248 " pdb=" N THR B 249 " ideal model delta sigma weight residual 1.331 1.273 0.057 2.56e-02 1.53e+03 5.03e+00 bond pdb=" C THR A 722 " pdb=" N PRO A 723 " ideal model delta sigma weight residual 1.334 1.315 0.018 8.40e-03 1.42e+04 4.66e+00 bond pdb=" C TYR A 319 " pdb=" N PRO A 320 " ideal model delta sigma weight residual 1.326 1.299 0.027 1.44e-02 4.82e+03 3.50e+00 bond pdb=" CB VAL D 181 " pdb=" CG1 VAL D 181 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.21e+00 bond pdb=" N THR B 249 " pdb=" CA THR B 249 " ideal model delta sigma weight residual 1.460 1.426 0.034 2.12e-02 2.22e+03 2.60e+00 ... (remaining 12408 not shown) Histogram of bond angle deviations from ideal: 98.98 - 105.99: 256 105.99 - 113.00: 6636 113.00 - 120.02: 4168 120.02 - 127.03: 5673 127.03 - 134.04: 130 Bond angle restraints: 16863 Sorted by residual: angle pdb=" N ILE B 56 " pdb=" CA ILE B 56 " pdb=" C ILE B 56 " ideal model delta sigma weight residual 113.71 107.28 6.43 9.50e-01 1.11e+00 4.58e+01 angle pdb=" C ASP D 204 " pdb=" N TYR D 205 " pdb=" CA TYR D 205 " ideal model delta sigma weight residual 123.21 115.53 7.68 1.19e+00 7.06e-01 4.16e+01 angle pdb=" C TYR B 263 " pdb=" N ASN B 264 " pdb=" CA ASN B 264 " ideal model delta sigma weight residual 121.44 114.97 6.47 1.59e+00 3.96e-01 1.65e+01 angle pdb=" N ASP A 500 " pdb=" CA ASP A 500 " pdb=" C ASP A 500 " ideal model delta sigma weight residual 110.06 115.84 -5.78 1.43e+00 4.89e-01 1.63e+01 angle pdb=" C ALA A 499 " pdb=" N ASP A 500 " pdb=" CA ASP A 500 " ideal model delta sigma weight residual 122.62 116.66 5.96 1.63e+00 3.76e-01 1.34e+01 ... (remaining 16858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 6519 17.65 - 35.30: 678 35.30 - 52.95: 96 52.95 - 70.61: 15 70.61 - 88.26: 13 Dihedral angle restraints: 7321 sinusoidal: 2842 harmonic: 4479 Sorted by residual: dihedral pdb=" CA ILE B 227 " pdb=" C ILE B 227 " pdb=" N TRP B 228 " pdb=" CA TRP B 228 " ideal model delta harmonic sigma weight residual 180.00 133.96 46.04 0 5.00e+00 4.00e-02 8.48e+01 dihedral pdb=" CA SER B 285 " pdb=" C SER B 285 " pdb=" N VAL B 286 " pdb=" CA VAL B 286 " ideal model delta harmonic sigma weight residual -180.00 -143.28 -36.72 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA LEU A 158 " pdb=" C LEU A 158 " pdb=" N PRO A 159 " pdb=" CA PRO A 159 " ideal model delta harmonic sigma weight residual 180.00 -147.55 -32.45 0 5.00e+00 4.00e-02 4.21e+01 ... (remaining 7318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1269 0.044 - 0.088: 437 0.088 - 0.132: 116 0.132 - 0.175: 18 0.175 - 0.219: 6 Chirality restraints: 1846 Sorted by residual: chirality pdb=" CA TRP D 191 " pdb=" N TRP D 191 " pdb=" C TRP D 191 " pdb=" CB TRP D 191 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CG LEU B 35 " pdb=" CB LEU B 35 " pdb=" CD1 LEU B 35 " pdb=" CD2 LEU B 35 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE B 227 " pdb=" CA ILE B 227 " pdb=" CG1 ILE B 227 " pdb=" CG2 ILE B 227 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1843 not shown) Planarity restraints: 2219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 199 " -0.036 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO B 200 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 540 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A 541 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 541 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 541 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 520 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C ASN A 520 " 0.030 2.00e-02 2.50e+03 pdb=" O ASN A 520 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 521 " -0.010 2.00e-02 2.50e+03 ... (remaining 2216 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 391 2.63 - 3.19: 12811 3.19 - 3.76: 18599 3.76 - 4.33: 24626 4.33 - 4.90: 37947 Nonbonded interactions: 94374 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASN B 264 " model vdw 2.058 3.040 nonbonded pdb=" OH TYR C 41 " pdb=" OD1 ASP D 162 " model vdw 2.141 3.040 nonbonded pdb=" O LEU A 501 " pdb=" OH TYR A 674 " model vdw 2.145 3.040 nonbonded pdb=" O ASN E 41 " pdb=" OG SER E 44 " model vdw 2.146 3.040 nonbonded pdb=" OD2 ASP B 363 " pdb=" OH TYR B 388 " model vdw 2.148 3.040 ... (remaining 94369 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 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 35.600 Find NCS groups from input model: 0.130 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 : 0.007 0.083 12413 Z= 0.463 Angle : 0.807 14.424 16863 Z= 0.444 Chirality : 0.048 0.219 1846 Planarity : 0.004 0.053 2219 Dihedral : 14.346 88.257 4466 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 26.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 18.78 % Favored : 81.16 % Rotamer: Outliers : 0.39 % Allowed : 11.92 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.27 % 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: -5.75 (0.16), residues: 1539 helix: -2.13 (0.23), residues: 304 sheet: -4.09 (0.20), residues: 411 loop : -4.47 (0.16), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 191 HIS 0.007 0.002 HIS E 83 PHE 0.023 0.002 PHE A 197 TYR 0.021 0.002 TYR D 205 ARG 0.005 0.001 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9484 (ttp) cc_final: 0.9172 (ttm) REVERT: A 372 MET cc_start: 0.9308 (mmm) cc_final: 0.9034 (mmp) REVERT: A 477 TYR cc_start: 0.9132 (m-80) cc_final: 0.8899 (m-80) REVERT: A 512 ASP cc_start: 0.8824 (p0) cc_final: 0.8589 (p0) REVERT: B 226 MET cc_start: 0.8758 (ppp) cc_final: 0.8445 (pmm) REVERT: B 278 MET cc_start: 0.9126 (mmt) cc_final: 0.8712 (mmm) REVERT: B 289 PHE cc_start: 0.9247 (p90) cc_final: 0.8860 (p90) REVERT: D 93 ASP cc_start: 0.8716 (t70) cc_final: 0.8460 (t70) REVERT: D 199 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8280 (tm-30) REVERT: E 52 GLN cc_start: 0.9246 (mt0) cc_final: 0.8931 (mt0) REVERT: E 63 LEU cc_start: 0.9715 (tp) cc_final: 0.9505 (tp) REVERT: F 1297 ARG cc_start: 0.8887 (ttt90) cc_final: 0.8650 (tpp80) REVERT: F 1298 TYR cc_start: 0.8596 (t80) cc_final: 0.8369 (t80) outliers start: 5 outliers final: 5 residues processed: 124 average time/residue: 0.2417 time to fit residues: 44.0946 Evaluate side-chains 92 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 538 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 359 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN E 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12413 Z= 0.248 Angle : 0.701 10.431 16863 Z= 0.369 Chirality : 0.047 0.197 1846 Planarity : 0.005 0.046 2219 Dihedral : 6.044 46.227 1703 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.18), residues: 1539 helix: -0.17 (0.28), residues: 307 sheet: -3.41 (0.22), residues: 399 loop : -3.82 (0.17), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 228 HIS 0.007 0.001 HIS E 83 PHE 0.016 0.001 PHE F1296 TYR 0.015 0.001 TYR C 31 ARG 0.005 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9471 (ttp) cc_final: 0.9164 (ttm) REVERT: A 430 ILE cc_start: 0.8595 (mt) cc_final: 0.8379 (mp) REVERT: A 480 VAL cc_start: 0.9318 (m) cc_final: 0.8907 (p) REVERT: A 545 MET cc_start: 0.9033 (mtp) cc_final: 0.8044 (mtm) REVERT: B 80 LEU cc_start: 0.9161 (pt) cc_final: 0.8952 (pp) REVERT: B 221 MET cc_start: 0.8047 (ttt) cc_final: 0.7767 (ttt) REVERT: B 278 MET cc_start: 0.9014 (mmt) cc_final: 0.8734 (mmm) REVERT: B 289 PHE cc_start: 0.9099 (p90) cc_final: 0.8700 (p90) REVERT: B 319 GLN cc_start: 0.8097 (tm130) cc_final: 0.7567 (tm130) REVERT: D 93 ASP cc_start: 0.8855 (t70) cc_final: 0.8645 (t0) REVERT: D 109 MET cc_start: 0.8905 (mmm) cc_final: 0.8115 (tpp) REVERT: D 199 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8355 (tm-30) REVERT: E 52 GLN cc_start: 0.9252 (mt0) cc_final: 0.8818 (mt0) REVERT: F 1296 PHE cc_start: 0.8346 (m-10) cc_final: 0.7864 (m-80) REVERT: F 1297 ARG cc_start: 0.8866 (ttt90) cc_final: 0.8602 (tpp80) REVERT: F 1298 TYR cc_start: 0.8593 (t80) cc_final: 0.8301 (t80) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2115 time to fit residues: 44.2453 Evaluate side-chains 105 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 139 optimal weight: 0.4980 chunk 150 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 111 optimal weight: 0.3980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 466 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN B 264 ASN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN E 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12413 Z= 0.167 Angle : 0.639 8.759 16863 Z= 0.335 Chirality : 0.045 0.193 1846 Planarity : 0.004 0.065 2219 Dihedral : 5.511 44.202 1703 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.19), residues: 1539 helix: 0.82 (0.29), residues: 307 sheet: -2.98 (0.22), residues: 407 loop : -3.40 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 228 HIS 0.005 0.001 HIS E 83 PHE 0.011 0.001 PHE A 738 TYR 0.023 0.001 TYR A 477 ARG 0.006 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9461 (ttp) cc_final: 0.9160 (ttm) REVERT: A 539 MET cc_start: 0.8551 (mmm) cc_final: 0.8255 (mmt) REVERT: A 545 MET cc_start: 0.8931 (mtp) cc_final: 0.8204 (mtp) REVERT: A 552 MET cc_start: 0.8736 (mmm) cc_final: 0.8509 (mtp) REVERT: A 777 MET cc_start: 0.8817 (tpp) cc_final: 0.8607 (tpp) REVERT: B 80 LEU cc_start: 0.9034 (pt) cc_final: 0.8798 (pp) REVERT: B 267 LEU cc_start: 0.8734 (tt) cc_final: 0.8381 (mp) REVERT: B 306 MET cc_start: 0.8551 (ppp) cc_final: 0.8207 (ppp) REVERT: B 317 TRP cc_start: 0.8479 (p-90) cc_final: 0.8067 (p-90) REVERT: B 370 GLU cc_start: 0.9218 (pt0) cc_final: 0.8974 (pm20) REVERT: D 93 ASP cc_start: 0.8858 (t70) cc_final: 0.8612 (t0) REVERT: D 187 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8198 (tm-30) REVERT: D 199 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8268 (tm-30) REVERT: E 52 GLN cc_start: 0.9231 (mt0) cc_final: 0.8825 (mt0) REVERT: E 80 GLN cc_start: 0.8439 (tm-30) cc_final: 0.7863 (tm-30) REVERT: E 104 ILE cc_start: 0.9354 (pt) cc_final: 0.9103 (mp) REVERT: F 1297 ARG cc_start: 0.8803 (ttt90) cc_final: 0.8600 (tpp80) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.2125 time to fit residues: 52.1363 Evaluate side-chains 115 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 139 optimal weight: 0.0370 chunk 147 optimal weight: 40.0000 chunk 132 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 123 optimal weight: 0.7980 overall best weight: 3.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 466 GLN ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 12413 Z= 0.316 Angle : 0.703 11.440 16863 Z= 0.366 Chirality : 0.046 0.211 1846 Planarity : 0.004 0.047 2219 Dihedral : 5.759 46.216 1703 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.20), residues: 1539 helix: 0.92 (0.30), residues: 306 sheet: -2.77 (0.23), residues: 395 loop : -3.33 (0.18), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 191 HIS 0.004 0.001 HIS E 83 PHE 0.023 0.002 PHE B 289 TYR 0.018 0.002 TYR A 477 ARG 0.005 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9432 (ttp) cc_final: 0.9137 (ttm) REVERT: A 545 MET cc_start: 0.8874 (mtp) cc_final: 0.8136 (mtm) REVERT: A 552 MET cc_start: 0.8777 (mmm) cc_final: 0.8503 (mtp) REVERT: B 80 LEU cc_start: 0.9082 (pt) cc_final: 0.8850 (pp) REVERT: B 221 MET cc_start: 0.8262 (ttt) cc_final: 0.8027 (ttt) REVERT: B 267 LEU cc_start: 0.8716 (tt) cc_final: 0.8422 (mp) REVERT: B 289 PHE cc_start: 0.9069 (p90) cc_final: 0.8596 (p90) REVERT: B 381 GLN cc_start: 0.9248 (tt0) cc_final: 0.8805 (mt0) REVERT: C 67 ILE cc_start: 0.8927 (tp) cc_final: 0.8550 (tp) REVERT: D 93 ASP cc_start: 0.8944 (t70) cc_final: 0.8627 (t70) REVERT: D 199 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8370 (tm-30) REVERT: E 52 GLN cc_start: 0.9279 (mt0) cc_final: 0.8835 (mt0) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2007 time to fit residues: 38.8410 Evaluate side-chains 100 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 319 GLN D 70 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12413 Z= 0.214 Angle : 0.656 11.134 16863 Z= 0.342 Chirality : 0.045 0.207 1846 Planarity : 0.004 0.054 2219 Dihedral : 5.519 44.714 1703 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.20), residues: 1539 helix: 1.10 (0.30), residues: 305 sheet: -2.54 (0.23), residues: 396 loop : -3.14 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 228 HIS 0.005 0.001 HIS E 83 PHE 0.018 0.001 PHE B 289 TYR 0.017 0.001 TYR C 31 ARG 0.004 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8539 (tp) cc_final: 0.8315 (tp) REVERT: A 304 MET cc_start: 0.9439 (ttp) cc_final: 0.9130 (ttm) REVERT: A 545 MET cc_start: 0.8831 (mtp) cc_final: 0.8252 (mtm) REVERT: A 552 MET cc_start: 0.8765 (mmm) cc_final: 0.8525 (mtp) REVERT: B 80 LEU cc_start: 0.9033 (pt) cc_final: 0.8789 (pp) REVERT: B 221 MET cc_start: 0.8181 (ttt) cc_final: 0.7945 (ttt) REVERT: B 267 LEU cc_start: 0.8750 (tt) cc_final: 0.8413 (mp) REVERT: B 306 MET cc_start: 0.8590 (ppp) cc_final: 0.8248 (ppp) REVERT: B 381 GLN cc_start: 0.9206 (tt0) cc_final: 0.8843 (mt0) REVERT: D 93 ASP cc_start: 0.8887 (t70) cc_final: 0.8558 (t0) REVERT: D 187 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8359 (tm-30) REVERT: D 199 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8376 (tm-30) REVERT: D 232 GLU cc_start: 0.8586 (pm20) cc_final: 0.8379 (pm20) REVERT: E 52 GLN cc_start: 0.9246 (mt0) cc_final: 0.8800 (mt0) REVERT: E 80 GLN cc_start: 0.8504 (tm-30) cc_final: 0.7982 (tm-30) REVERT: E 104 ILE cc_start: 0.9362 (pt) cc_final: 0.9116 (mp) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2088 time to fit residues: 45.4719 Evaluate side-chains 112 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12413 Z= 0.237 Angle : 0.665 10.546 16863 Z= 0.344 Chirality : 0.045 0.169 1846 Planarity : 0.004 0.060 2219 Dihedral : 5.515 47.010 1703 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % 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: -2.92 (0.20), residues: 1539 helix: 1.21 (0.30), residues: 306 sheet: -2.36 (0.23), residues: 396 loop : -3.07 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 228 HIS 0.004 0.001 HIS E 83 PHE 0.019 0.001 PHE B 289 TYR 0.017 0.001 TYR D 185 ARG 0.005 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9441 (ttp) cc_final: 0.9208 (ttm) REVERT: A 539 MET cc_start: 0.8461 (tpp) cc_final: 0.8229 (mmt) REVERT: A 545 MET cc_start: 0.8752 (mtp) cc_final: 0.8431 (mtp) REVERT: A 552 MET cc_start: 0.8783 (mmm) cc_final: 0.8520 (mtp) REVERT: B 80 LEU cc_start: 0.9034 (pt) cc_final: 0.8789 (pp) REVERT: B 221 MET cc_start: 0.8371 (ttt) cc_final: 0.8142 (ttt) REVERT: B 267 LEU cc_start: 0.8686 (tt) cc_final: 0.8400 (mp) REVERT: B 306 MET cc_start: 0.8702 (ppp) cc_final: 0.8441 (ppp) REVERT: B 381 GLN cc_start: 0.9176 (tt0) cc_final: 0.8550 (mt0) REVERT: D 93 ASP cc_start: 0.8885 (t70) cc_final: 0.8551 (t70) REVERT: D 187 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8367 (tm-30) REVERT: D 199 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8386 (tm-30) REVERT: E 52 GLN cc_start: 0.9278 (mt0) cc_final: 0.8837 (mt0) REVERT: E 80 GLN cc_start: 0.8496 (tm-30) cc_final: 0.7947 (tm-30) REVERT: E 104 ILE cc_start: 0.9352 (pt) cc_final: 0.9098 (mp) REVERT: F 1268 ILE cc_start: 0.8459 (tt) cc_final: 0.7843 (tt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2061 time to fit residues: 42.6195 Evaluate side-chains 110 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 0.0670 chunk 108 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12413 Z= 0.154 Angle : 0.637 8.032 16863 Z= 0.329 Chirality : 0.045 0.175 1846 Planarity : 0.004 0.061 2219 Dihedral : 5.240 45.971 1703 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % 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: -2.62 (0.21), residues: 1539 helix: 1.41 (0.30), residues: 307 sheet: -2.15 (0.24), residues: 393 loop : -2.87 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 228 HIS 0.004 0.000 HIS E 83 PHE 0.016 0.001 PHE B 289 TYR 0.012 0.001 TYR A 504 ARG 0.007 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8623 (tp) cc_final: 0.8304 (tt) REVERT: A 304 MET cc_start: 0.9446 (ttp) cc_final: 0.9200 (ttm) REVERT: A 545 MET cc_start: 0.8816 (mtp) cc_final: 0.8581 (mtm) REVERT: A 550 TYR cc_start: 0.8346 (m-10) cc_final: 0.8137 (m-80) REVERT: A 552 MET cc_start: 0.8756 (mmm) cc_final: 0.8529 (mtp) REVERT: A 711 MET cc_start: 0.8402 (tmm) cc_final: 0.7586 (tmm) REVERT: B 221 MET cc_start: 0.8280 (ttt) cc_final: 0.8053 (ttt) REVERT: B 267 LEU cc_start: 0.8648 (tt) cc_final: 0.8356 (mp) REVERT: B 306 MET cc_start: 0.8663 (ppp) cc_final: 0.8355 (ppp) REVERT: B 317 TRP cc_start: 0.8351 (p-90) cc_final: 0.8070 (p-90) REVERT: B 370 GLU cc_start: 0.9239 (pt0) cc_final: 0.8651 (pm20) REVERT: B 380 ILE cc_start: 0.9421 (tt) cc_final: 0.9137 (tt) REVERT: C 56 MET cc_start: 0.8671 (pmm) cc_final: 0.8435 (pmm) REVERT: C 67 ILE cc_start: 0.8742 (tp) cc_final: 0.8486 (tp) REVERT: D 93 ASP cc_start: 0.8898 (t70) cc_final: 0.8580 (t0) REVERT: D 187 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8402 (tm-30) REVERT: D 199 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8208 (tm-30) REVERT: D 218 MET cc_start: 0.8938 (tpp) cc_final: 0.8633 (tpp) REVERT: E 52 GLN cc_start: 0.9249 (mt0) cc_final: 0.8809 (mt0) REVERT: E 80 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8036 (tm-30) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2060 time to fit residues: 46.6688 Evaluate side-chains 117 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 207 ASN ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 GLN A 805 ASN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN D 54 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12413 Z= 0.198 Angle : 0.652 9.898 16863 Z= 0.338 Chirality : 0.045 0.190 1846 Planarity : 0.004 0.058 2219 Dihedral : 5.216 46.241 1703 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.55 (0.21), residues: 1539 helix: 1.28 (0.30), residues: 306 sheet: -2.06 (0.23), residues: 416 loop : -2.77 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 228 HIS 0.003 0.001 HIS E 83 PHE 0.016 0.001 PHE B 289 TYR 0.024 0.001 TYR D 79 ARG 0.007 0.000 ARG F1273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8614 (tp) cc_final: 0.8309 (tt) REVERT: A 140 PHE cc_start: 0.8994 (t80) cc_final: 0.8769 (t80) REVERT: A 304 MET cc_start: 0.9449 (ttp) cc_final: 0.9215 (ttm) REVERT: A 325 MET cc_start: 0.8884 (pmm) cc_final: 0.8678 (pmm) REVERT: A 550 TYR cc_start: 0.8355 (m-10) cc_final: 0.8152 (m-80) REVERT: A 552 MET cc_start: 0.8801 (mmm) cc_final: 0.8544 (mtp) REVERT: A 711 MET cc_start: 0.8465 (tmm) cc_final: 0.7665 (tmm) REVERT: B 221 MET cc_start: 0.8330 (ttt) cc_final: 0.8088 (ttt) REVERT: B 259 PHE cc_start: 0.8748 (m-80) cc_final: 0.8411 (m-80) REVERT: B 267 LEU cc_start: 0.8651 (tt) cc_final: 0.8335 (mp) REVERT: B 306 MET cc_start: 0.8622 (ppp) cc_final: 0.8305 (ppp) REVERT: B 317 TRP cc_start: 0.8466 (p-90) cc_final: 0.8165 (p-90) REVERT: B 370 GLU cc_start: 0.9254 (pt0) cc_final: 0.8699 (pm20) REVERT: C 56 MET cc_start: 0.8558 (pmm) cc_final: 0.8334 (pmm) REVERT: D 187 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8325 (tm-30) REVERT: D 199 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8125 (tm-30) REVERT: D 218 MET cc_start: 0.8901 (tpp) cc_final: 0.8446 (tpp) REVERT: E 52 GLN cc_start: 0.9265 (mt0) cc_final: 0.8835 (mt0) REVERT: E 80 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8082 (tm-30) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1903 time to fit residues: 42.4030 Evaluate side-chains 114 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12413 Z= 0.174 Angle : 0.645 9.213 16863 Z= 0.332 Chirality : 0.045 0.246 1846 Planarity : 0.004 0.058 2219 Dihedral : 5.093 45.991 1703 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.08 % Allowed : 0.62 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.37 (0.21), residues: 1539 helix: 1.42 (0.31), residues: 306 sheet: -1.99 (0.24), residues: 415 loop : -2.61 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 228 HIS 0.003 0.000 HIS E 83 PHE 0.012 0.001 PHE F1274 TYR 0.022 0.001 TYR D 185 ARG 0.004 0.000 ARG F1273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: A 304 MET cc_start: 0.9438 (ttp) cc_final: 0.9200 (ttm) REVERT: A 552 MET cc_start: 0.8773 (mmm) cc_final: 0.8531 (mtp) REVERT: B 221 MET cc_start: 0.8337 (ttt) cc_final: 0.8099 (ttt) REVERT: B 259 PHE cc_start: 0.8722 (m-80) cc_final: 0.8432 (m-80) REVERT: B 267 LEU cc_start: 0.8595 (tt) cc_final: 0.8331 (mp) REVERT: B 306 MET cc_start: 0.8653 (ppp) cc_final: 0.8361 (ppp) REVERT: B 317 TRP cc_start: 0.8406 (p-90) cc_final: 0.8113 (p-90) REVERT: B 370 GLU cc_start: 0.9246 (pt0) cc_final: 0.8710 (pm20) REVERT: B 380 ILE cc_start: 0.9363 (tt) cc_final: 0.9154 (tt) REVERT: D 178 GLU cc_start: 0.8408 (pp20) cc_final: 0.8183 (pp20) REVERT: D 187 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8426 (tm-30) REVERT: D 199 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8027 (tm-30) REVERT: E 52 GLN cc_start: 0.9258 (mt0) cc_final: 0.8831 (mt0) REVERT: E 75 TYR cc_start: 0.8804 (m-80) cc_final: 0.8552 (m-10) REVERT: E 80 GLN cc_start: 0.8456 (tm-30) cc_final: 0.7973 (tm-30) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.1834 time to fit residues: 42.5448 Evaluate side-chains 119 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-dev-5409/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-dev-5409/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: 70.1691 > 50: distance: 76 - 80: 21.723 distance: 80 - 81: 9.224 distance: 81 - 82: 28.120 distance: 81 - 84: 23.308 distance: 82 - 83: 12.376 distance: 82 - 88: 16.080 distance: 84 - 85: 16.346 distance: 84 - 86: 17.852 distance: 85 - 87: 8.715 distance: 88 - 89: 29.211 distance: 89 - 90: 32.172 distance: 89 - 92: 23.485 distance: 90 - 91: 16.855 distance: 90 - 94: 13.722 distance: 92 - 93: 27.441 distance: 94 - 95: 18.669 distance: 95 - 96: 12.342 distance: 95 - 98: 6.035 distance: 96 - 97: 16.946 distance: 96 - 102: 8.263 distance: 98 - 99: 18.643 distance: 99 - 100: 17.236 distance: 99 - 101: 31.578 distance: 102 - 103: 14.609 distance: 103 - 104: 11.680 distance: 103 - 106: 19.392 distance: 104 - 105: 15.646 distance: 104 - 111: 21.816 distance: 106 - 107: 25.654 distance: 107 - 108: 13.746 distance: 108 - 109: 22.957 distance: 109 - 110: 19.301 distance: 111 - 112: 8.026 distance: 112 - 113: 23.283 distance: 113 - 114: 13.283 distance: 113 - 123: 17.173 distance: 115 - 116: 15.127 distance: 116 - 117: 9.109 distance: 116 - 118: 8.053 distance: 117 - 119: 17.312 distance: 118 - 120: 13.846 distance: 119 - 121: 11.474 distance: 120 - 121: 9.866 distance: 121 - 122: 15.416 distance: 123 - 124: 60.457 distance: 124 - 125: 8.679 distance: 124 - 127: 13.145 distance: 125 - 126: 46.568 distance: 125 - 128: 44.734 distance: 128 - 129: 5.538 distance: 129 - 130: 20.887 distance: 129 - 132: 30.992 distance: 130 - 131: 31.439 distance: 130 - 136: 3.490 distance: 132 - 133: 26.230 distance: 133 - 134: 14.309 distance: 133 - 135: 11.586 distance: 136 - 137: 23.724 distance: 137 - 138: 6.353 distance: 137 - 140: 24.180 distance: 138 - 139: 16.474 distance: 138 - 142: 8.261 distance: 140 - 141: 40.200 distance: 142 - 143: 29.735 distance: 143 - 144: 22.745 distance: 143 - 146: 14.531 distance: 144 - 145: 33.477 distance: 144 - 149: 25.025 distance: 146 - 147: 9.134 distance: 146 - 148: 26.174 distance: 149 - 150: 12.187 distance: 150 - 151: 11.304 distance: 150 - 153: 15.221 distance: 151 - 152: 25.084 distance: 151 - 160: 28.968 distance: 153 - 154: 9.248 distance: 154 - 155: 30.075 distance: 155 - 156: 16.166 distance: 156 - 157: 9.601 distance: 157 - 158: 4.476 distance: 157 - 159: 11.201