Starting phenix.real_space_refine on Fri Jan 19 11:40:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5m_14331/01_2024/7r5m_14331.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5m_14331/01_2024/7r5m_14331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5m_14331/01_2024/7r5m_14331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5m_14331/01_2024/7r5m_14331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5m_14331/01_2024/7r5m_14331.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5m_14331/01_2024/7r5m_14331.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 24 5.16 5 C 7203 2.51 5 N 1920 2.21 5 O 2148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "F GLU 322": "OE1" <-> "OE2" Residue "F ASP 331": "OD1" <-> "OD2" Residue "G GLU 245": "OE1" <-> "OE2" Residue "G ASP 276": "OD1" <-> "OD2" Residue "G PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 420": "OD1" <-> "OD2" Residue "G GLU 445": "OE1" <-> "OE2" Residue "J GLU 322": "OE1" <-> "OE2" Residue "L GLU 350": "OE1" <-> "OE2" Residue "M GLU 322": "OE1" <-> "OE2" 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: 11295 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "B" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "F" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 110} Chain breaks: 1 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: "G" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "H" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1076 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 5 Chain: "J" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 110} Chain breaks: 1 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: "K" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1076 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 5 Chain: "L" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1076 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 5 Chain: "M" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 110} Chain breaks: 1 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 Time building chain proxies: 6.39, per 1000 atoms: 0.57 Number of scatterers: 11295 At special positions: 0 Unit cell: (116.96, 126.42, 115.24, 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 24 16.00 O 2148 8.00 N 1920 7.00 C 7203 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.18 Conformation dependent library (CDL) restraints added in 2.0 seconds 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2796 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 24 sheets defined 44.9% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.733A pdb=" N LYS A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 239 " --> pdb=" O MET A 235 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 282 through 298 removed outlier: 3.844A pdb=" N PHE A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.848A pdb=" N GLN A 366 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 452 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'B' and resid 233 through 250 removed outlier: 3.734A pdb=" N LYS B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 Processing helix chain 'B' and resid 282 through 298 removed outlier: 3.844A pdb=" N PHE B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 340 through 358 Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.848A pdb=" N GLN B 366 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 452 Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'F' and resid 275 through 289 Processing helix chain 'F' and resid 294 through 307 removed outlier: 4.199A pdb=" N PHE F 298 " --> pdb=" O PRO F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 329 Processing helix chain 'F' and resid 399 through 419 removed outlier: 4.561A pdb=" N LYS F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ARG F 404 " --> pdb=" O SER F 400 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 407 " --> pdb=" O LYS F 403 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE F 408 " --> pdb=" O ARG F 404 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 250 removed outlier: 3.733A pdb=" N LYS G 237 " --> pdb=" O SER G 233 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR G 238 " --> pdb=" O GLY G 234 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG G 242 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 272 Processing helix chain 'G' and resid 282 through 298 removed outlier: 3.844A pdb=" N PHE G 286 " --> pdb=" O SER G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 301 No H-bonds generated for 'chain 'G' and resid 299 through 301' Processing helix chain 'G' and resid 340 through 358 Processing helix chain 'G' and resid 361 through 366 removed outlier: 3.848A pdb=" N GLN G 366 " --> pdb=" O GLU G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 452 Processing helix chain 'G' and resid 453 through 457 Processing helix chain 'H' and resid 261 through 272 Processing helix chain 'H' and resid 282 through 298 removed outlier: 3.738A pdb=" N PHE H 286 " --> pdb=" O SER H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 355 removed outlier: 3.502A pdb=" N ALA H 352 " --> pdb=" O VAL H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 452 Processing helix chain 'H' and resid 453 through 457 Processing helix chain 'J' and resid 275 through 289 Processing helix chain 'J' and resid 294 through 307 removed outlier: 4.199A pdb=" N PHE J 298 " --> pdb=" O PRO J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 329 Processing helix chain 'J' and resid 399 through 419 removed outlier: 4.561A pdb=" N LYS J 403 " --> pdb=" O LYS J 399 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG J 404 " --> pdb=" O SER J 400 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA J 407 " --> pdb=" O LYS J 403 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE J 408 " --> pdb=" O ARG J 404 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU J 417 " --> pdb=" O LYS J 413 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 272 Processing helix chain 'K' and resid 282 through 298 removed outlier: 3.738A pdb=" N PHE K 286 " --> pdb=" O SER K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 355 removed outlier: 3.502A pdb=" N ALA K 352 " --> pdb=" O VAL K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 439 through 452 Processing helix chain 'K' and resid 453 through 457 Processing helix chain 'L' and resid 261 through 272 Processing helix chain 'L' and resid 282 through 298 removed outlier: 3.738A pdb=" N PHE L 286 " --> pdb=" O SER L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 355 removed outlier: 3.502A pdb=" N ALA L 352 " --> pdb=" O VAL L 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 452 Processing helix chain 'L' and resid 453 through 457 Processing helix chain 'M' and resid 275 through 289 Processing helix chain 'M' and resid 294 through 307 removed outlier: 4.199A pdb=" N PHE M 298 " --> pdb=" O PRO M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 329 Processing helix chain 'M' and resid 399 through 419 removed outlier: 4.561A pdb=" N LYS M 403 " --> pdb=" O LYS M 399 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ARG M 404 " --> pdb=" O SER M 400 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA M 407 " --> pdb=" O LYS M 403 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE M 408 " --> pdb=" O ARG M 404 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU M 417 " --> pdb=" O LYS M 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 231 removed outlier: 3.512A pdb=" N VAL A 230 " --> pdb=" O ILE B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 332 through 333 removed outlier: 6.509A pdb=" N SER A 319 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN A 374 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER A 371 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL A 398 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER A 373 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333 removed outlier: 6.509A pdb=" N SER A 319 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN A 374 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER A 371 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL A 398 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER A 373 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER G 383 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 305 removed outlier: 3.546A pdb=" N ILE A 310 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL G 230 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 324 Processing sheet with id=AA6, first strand: chain 'A' and resid 383 through 384 removed outlier: 3.777A pdb=" N SER A 383 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER B 371 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL B 398 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER B 373 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER B 319 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ASN B 374 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 383 through 384 removed outlier: 3.777A pdb=" N SER A 383 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 228 through 231 Processing sheet with id=AA9, first strand: chain 'B' and resid 322 through 324 removed outlier: 3.882A pdb=" N VAL B 322 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 383 through 384 removed outlier: 3.845A pdb=" N SER B 383 " --> pdb=" O SER G 256 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER G 371 " --> pdb=" O LEU G 396 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL G 398 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER G 373 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER G 319 " --> pdb=" O ILE G 372 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ASN G 374 " --> pdb=" O SER G 319 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 383 through 384 removed outlier: 3.845A pdb=" N SER B 383 " --> pdb=" O SER G 256 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR G 414 " --> pdb=" O ASN G 410 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 266 through 271 Processing sheet with id=AB4, first strand: chain 'G' and resid 322 through 324 removed outlier: 3.891A pdb=" N VAL G 322 " --> pdb=" O ILE G 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 257 through 260 removed outlier: 7.015A pdb=" N SER H 373 " --> pdb=" O VAL H 398 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 257 through 260 removed outlier: 3.850A pdb=" N THR H 414 " --> pdb=" O ASN H 410 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 317 through 319 Processing sheet with id=AB8, first strand: chain 'J' and resid 266 through 271 Processing sheet with id=AB9, first strand: chain 'K' and resid 257 through 260 removed outlier: 7.015A pdb=" N SER K 373 " --> pdb=" O VAL K 398 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 257 through 260 removed outlier: 3.850A pdb=" N THR K 414 " --> pdb=" O ASN K 410 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 317 through 319 Processing sheet with id=AC3, first strand: chain 'L' and resid 257 through 260 removed outlier: 7.014A pdb=" N SER L 373 " --> pdb=" O VAL L 398 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 257 through 260 removed outlier: 3.850A pdb=" N THR L 414 " --> pdb=" O ASN L 410 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 317 through 319 Processing sheet with id=AC6, first strand: chain 'M' and resid 266 through 271 632 hydrogen bonds defined for protein. 1758 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: 3.10 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2388 1.33 - 1.45: 2130 1.45 - 1.57: 6885 1.57 - 1.69: 3 1.69 - 1.81: 48 Bond restraints: 11454 Sorted by residual: bond pdb=" N VAL F 327 " pdb=" CA VAL F 327 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.35e+00 bond pdb=" N VAL M 327 " pdb=" CA VAL M 327 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.12e+00 bond pdb=" N VAL J 327 " pdb=" CA VAL J 327 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.24e-02 6.50e+03 7.10e+00 bond pdb=" CB GLN G 366 " pdb=" CG GLN G 366 " ideal model delta sigma weight residual 1.520 1.600 -0.080 3.00e-02 1.11e+03 7.05e+00 bond pdb=" CB GLN A 366 " pdb=" CG GLN A 366 " ideal model delta sigma weight residual 1.520 1.600 -0.080 3.00e-02 1.11e+03 7.04e+00 ... (remaining 11449 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.07: 291 106.07 - 113.04: 6355 113.04 - 120.02: 3877 120.02 - 126.99: 4861 126.99 - 133.96: 123 Bond angle restraints: 15507 Sorted by residual: angle pdb=" CA MET A 291 " pdb=" C MET A 291 " pdb=" O MET A 291 " ideal model delta sigma weight residual 120.55 116.55 4.00 1.06e+00 8.90e-01 1.42e+01 angle pdb=" CA MET B 291 " pdb=" C MET B 291 " pdb=" O MET B 291 " ideal model delta sigma weight residual 120.55 116.58 3.97 1.06e+00 8.90e-01 1.41e+01 angle pdb=" CA MET G 291 " pdb=" C MET G 291 " pdb=" O MET G 291 " ideal model delta sigma weight residual 120.55 116.61 3.94 1.06e+00 8.90e-01 1.38e+01 angle pdb=" CB GLN B 366 " pdb=" CG GLN B 366 " pdb=" CD GLN B 366 " ideal model delta sigma weight residual 112.60 118.70 -6.10 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CB GLN G 366 " pdb=" CG GLN G 366 " pdb=" CD GLN G 366 " ideal model delta sigma weight residual 112.60 118.68 -6.08 1.70e+00 3.46e-01 1.28e+01 ... (remaining 15502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6479 17.88 - 35.75: 426 35.75 - 53.63: 116 53.63 - 71.50: 41 71.50 - 89.38: 15 Dihedral angle restraints: 7077 sinusoidal: 2799 harmonic: 4278 Sorted by residual: dihedral pdb=" CB GLU B 445 " pdb=" CG GLU B 445 " pdb=" CD GLU B 445 " pdb=" OE1 GLU B 445 " ideal model delta sinusoidal sigma weight residual 0.00 89.38 -89.38 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 445 " pdb=" CG GLU A 445 " pdb=" CD GLU A 445 " pdb=" OE1 GLU A 445 " ideal model delta sinusoidal sigma weight residual 0.00 89.37 -89.37 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU G 445 " pdb=" CG GLU G 445 " pdb=" CD GLU G 445 " pdb=" OE1 GLU G 445 " ideal model delta sinusoidal sigma weight residual 0.00 89.37 -89.37 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 7074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1414 0.058 - 0.117: 344 0.117 - 0.175: 120 0.175 - 0.233: 3 0.233 - 0.292: 6 Chirality restraints: 1887 Sorted by residual: chirality pdb=" CB THR J 345 " pdb=" CA THR J 345 " pdb=" OG1 THR J 345 " pdb=" CG2 THR J 345 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB THR F 345 " pdb=" CA THR F 345 " pdb=" OG1 THR F 345 " pdb=" CG2 THR F 345 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB THR M 345 " pdb=" CA THR M 345 " pdb=" OG1 THR M 345 " pdb=" CG2 THR M 345 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1884 not shown) Planarity restraints: 1959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 348 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C VAL B 348 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL B 348 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS B 349 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 348 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.54e+00 pdb=" C VAL A 348 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL A 348 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 349 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 348 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C VAL G 348 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL G 348 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS G 349 " 0.014 2.00e-02 2.50e+03 ... (remaining 1956 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 4064 2.91 - 3.41: 10428 3.41 - 3.90: 16167 3.90 - 4.40: 17071 4.40 - 4.90: 30845 Nonbonded interactions: 78575 Sorted by model distance: nonbonded pdb=" OD1 ASP L 420 " pdb=" N GLU L 421 " model vdw 2.411 2.520 nonbonded pdb=" OD1 ASP K 420 " pdb=" N GLU K 421 " model vdw 2.412 2.520 nonbonded pdb=" OD1 ASP H 420 " pdb=" N GLU H 421 " model vdw 2.412 2.520 nonbonded pdb=" CE LYS M 413 " pdb=" OE2 GLU M 417 " model vdw 2.423 3.440 nonbonded pdb=" O GLU J 337 " pdb=" OG SER J 338 " model vdw 2.481 2.440 ... (remaining 78570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.100 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 32.270 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 : 0.006 0.080 11454 Z= 0.412 Angle : 0.945 7.085 15507 Z= 0.534 Chirality : 0.057 0.292 1887 Planarity : 0.004 0.033 1959 Dihedral : 14.644 89.377 4281 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.80 % Allowed : 2.15 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.22), residues: 1437 helix: 0.79 (0.22), residues: 588 sheet: -0.38 (0.35), residues: 192 loop : -1.83 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 442 HIS 0.006 0.001 HIS B 252 PHE 0.017 0.002 PHE F 408 TYR 0.021 0.003 TYR F 316 ARG 0.005 0.001 ARG H 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 256 time to evaluate : 1.338 Fit side-chains REVERT: M 322 GLU cc_start: 0.5810 (tt0) cc_final: 0.5587 (tt0) outliers start: 10 outliers final: 1 residues processed: 261 average time/residue: 0.2405 time to fit residues: 86.7180 Evaluate side-chains 197 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 332 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 85 optimal weight: 0.0670 chunk 133 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN F 308 GLN F 325 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11454 Z= 0.145 Angle : 0.506 6.062 15507 Z= 0.262 Chirality : 0.043 0.158 1887 Planarity : 0.004 0.039 1959 Dihedral : 3.770 38.834 1537 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.83 % Allowed : 7.48 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1437 helix: 2.30 (0.22), residues: 597 sheet: -0.06 (0.33), residues: 192 loop : -1.34 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 305 HIS 0.001 0.000 HIS B 252 PHE 0.010 0.001 PHE G 384 TYR 0.013 0.001 TYR B 365 ARG 0.004 0.000 ARG M 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 213 time to evaluate : 1.436 Fit side-chains REVERT: A 329 ILE cc_start: 0.7567 (mm) cc_final: 0.7303 (mm) REVERT: B 329 ILE cc_start: 0.7488 (mm) cc_final: 0.7216 (mm) REVERT: B 444 ARG cc_start: 0.7480 (ttp-170) cc_final: 0.7253 (ttp-170) REVERT: B 451 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7126 (mm-30) REVERT: G 329 ILE cc_start: 0.7464 (mm) cc_final: 0.7251 (mm) REVERT: J 293 LEU cc_start: 0.7780 (pp) cc_final: 0.7428 (pp) REVERT: J 307 ASN cc_start: 0.7853 (m110) cc_final: 0.7631 (m-40) REVERT: L 258 ASN cc_start: 0.7341 (p0) cc_final: 0.7090 (p0) outliers start: 23 outliers final: 22 residues processed: 229 average time/residue: 0.2546 time to fit residues: 80.3004 Evaluate side-chains 210 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain J residue 274 SER Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain M residue 291 VAL Chi-restraints excluded: chain M residue 414 LEU Chi-restraints excluded: chain M residue 415 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 111 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 269 GLN ** F 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 ASN F 325 ASN ** M 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 307 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11454 Z= 0.172 Angle : 0.492 5.957 15507 Z= 0.251 Chirality : 0.043 0.139 1887 Planarity : 0.004 0.038 1959 Dihedral : 3.752 38.467 1537 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.70 % Allowed : 9.47 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.23), residues: 1437 helix: 2.53 (0.21), residues: 615 sheet: 0.35 (0.32), residues: 222 loop : -1.12 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 442 HIS 0.002 0.001 HIS F 286 PHE 0.011 0.001 PHE B 253 TYR 0.011 0.001 TYR A 365 ARG 0.005 0.000 ARG H 297 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 210 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: A 329 ILE cc_start: 0.7571 (mm) cc_final: 0.7306 (tp) REVERT: B 329 ILE cc_start: 0.7456 (mm) cc_final: 0.7185 (mm) REVERT: G 329 ILE cc_start: 0.7558 (mm) cc_final: 0.7299 (mm) REVERT: H 351 LEU cc_start: 0.8003 (mt) cc_final: 0.7761 (mm) REVERT: H 451 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5367 (mp0) REVERT: J 293 LEU cc_start: 0.7876 (pp) cc_final: 0.7467 (pp) REVERT: J 339 ARG cc_start: 0.7946 (mtp180) cc_final: 0.7613 (mtp180) REVERT: K 451 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.5352 (mp0) REVERT: L 278 ARG cc_start: 0.7297 (mtm180) cc_final: 0.7023 (mtp85) REVERT: L 451 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.5279 (mp0) outliers start: 34 outliers final: 25 residues processed: 231 average time/residue: 0.2647 time to fit residues: 84.0334 Evaluate side-chains 220 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 283 ASN Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain H residue 424 ILE Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain J residue 274 SER Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 451 GLU Chi-restraints excluded: chain M residue 291 VAL Chi-restraints excluded: chain M residue 414 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 9.9990 chunk 100 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 134 optimal weight: 0.3980 chunk 142 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 127 optimal weight: 0.0370 chunk 38 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS A 269 GLN B 269 GLN ** F 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN ** M 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 326 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11454 Z= 0.124 Angle : 0.446 5.844 15507 Z= 0.225 Chirality : 0.041 0.132 1887 Planarity : 0.004 0.038 1959 Dihedral : 3.489 37.220 1537 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.83 % Allowed : 11.46 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.23), residues: 1437 helix: 3.00 (0.21), residues: 609 sheet: 0.49 (0.30), residues: 234 loop : -0.94 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 442 HIS 0.002 0.001 HIS B 252 PHE 0.011 0.001 PHE B 253 TYR 0.011 0.001 TYR B 365 ARG 0.007 0.000 ARG L 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 208 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 329 ILE cc_start: 0.7435 (mm) cc_final: 0.7180 (tp) REVERT: B 359 LYS cc_start: 0.7572 (ptpp) cc_final: 0.7275 (ptpt) REVERT: B 451 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6834 (mt-10) REVERT: F 284 LYS cc_start: 0.8184 (tttm) cc_final: 0.7982 (tttm) REVERT: H 451 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.5623 (mp0) REVERT: J 293 LEU cc_start: 0.7809 (pp) cc_final: 0.7377 (pp) REVERT: J 339 ARG cc_start: 0.7935 (mtp180) cc_final: 0.7617 (mtp180) REVERT: K 451 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.5290 (mp0) outliers start: 23 outliers final: 14 residues processed: 223 average time/residue: 0.2822 time to fit residues: 86.1592 Evaluate side-chains 200 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain J residue 274 SER Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 451 GLU Chi-restraints excluded: chain M residue 414 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS A 269 GLN B 269 GLN F 307 ASN G 269 GLN ** J 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 307 ASN ** M 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 326 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11454 Z= 0.300 Angle : 0.581 6.663 15507 Z= 0.299 Chirality : 0.045 0.162 1887 Planarity : 0.004 0.036 1959 Dihedral : 4.316 36.381 1537 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.26 % Allowed : 12.09 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.22), residues: 1437 helix: 2.65 (0.20), residues: 609 sheet: 0.79 (0.30), residues: 207 loop : -1.19 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 305 HIS 0.006 0.002 HIS B 252 PHE 0.016 0.002 PHE G 253 TYR 0.009 0.001 TYR B 365 ARG 0.007 0.001 ARG L 297 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 209 time to evaluate : 1.348 Fit side-chains REVERT: H 451 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.5697 (mp0) REVERT: J 293 LEU cc_start: 0.7758 (pp) cc_final: 0.7396 (pp) REVERT: K 451 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.5355 (mp0) outliers start: 41 outliers final: 32 residues processed: 236 average time/residue: 0.2602 time to fit residues: 84.0721 Evaluate side-chains 225 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain H residue 424 ILE Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 307 ASN Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain M residue 291 VAL Chi-restraints excluded: chain M residue 315 ASN Chi-restraints excluded: chain M residue 414 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 4.9990 chunk 127 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 269 GLN ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11454 Z= 0.205 Angle : 0.505 5.811 15507 Z= 0.261 Chirality : 0.043 0.140 1887 Planarity : 0.004 0.050 1959 Dihedral : 4.046 34.757 1537 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.50 % Allowed : 13.68 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.22), residues: 1437 helix: 2.83 (0.20), residues: 609 sheet: 0.75 (0.29), residues: 219 loop : -1.16 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 305 HIS 0.002 0.001 HIS A 431 PHE 0.016 0.002 PHE A 253 TYR 0.010 0.001 TYR B 365 ARG 0.007 0.000 ARG H 297 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 197 time to evaluate : 1.213 Fit side-chains REVERT: L 278 ARG cc_start: 0.7289 (mtp180) cc_final: 0.6876 (ttp-170) REVERT: M 283 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.7083 (m110) outliers start: 44 outliers final: 32 residues processed: 224 average time/residue: 0.2582 time to fit residues: 79.0569 Evaluate side-chains 215 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain H residue 424 ILE Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain M residue 283 ASN Chi-restraints excluded: chain M residue 315 ASN Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 414 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 269 GLN ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN J 307 ASN ** M 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11454 Z= 0.182 Angle : 0.489 5.767 15507 Z= 0.253 Chirality : 0.042 0.131 1887 Planarity : 0.004 0.038 1959 Dihedral : 3.903 33.990 1537 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.70 % Allowed : 14.88 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.22), residues: 1437 helix: 2.99 (0.20), residues: 606 sheet: 0.83 (0.29), residues: 219 loop : -1.18 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 305 HIS 0.001 0.001 HIS B 252 PHE 0.016 0.001 PHE J 393 TYR 0.010 0.001 TYR B 365 ARG 0.006 0.000 ARG H 297 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 198 time to evaluate : 1.387 Fit side-chains REVERT: L 278 ARG cc_start: 0.7265 (mtp180) cc_final: 0.6903 (ttp-170) REVERT: M 283 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.7085 (m110) outliers start: 34 outliers final: 28 residues processed: 222 average time/residue: 0.2611 time to fit residues: 78.6918 Evaluate side-chains 216 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 187 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain M residue 283 ASN Chi-restraints excluded: chain M residue 315 ASN Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 414 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 128 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN F 307 ASN ** J 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 307 ASN ** M 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11454 Z= 0.155 Angle : 0.463 5.746 15507 Z= 0.239 Chirality : 0.041 0.126 1887 Planarity : 0.004 0.038 1959 Dihedral : 3.736 33.222 1537 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.55 % Allowed : 15.35 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.22), residues: 1437 helix: 3.12 (0.21), residues: 606 sheet: 0.83 (0.28), residues: 219 loop : -1.12 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 442 HIS 0.001 0.000 HIS A 431 PHE 0.014 0.001 PHE B 253 TYR 0.009 0.001 TYR B 365 ARG 0.005 0.000 ARG H 297 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 1.890 Fit side-chains REVERT: B 451 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6923 (mt-10) REVERT: L 278 ARG cc_start: 0.7172 (mtp180) cc_final: 0.6889 (ttp-170) outliers start: 32 outliers final: 23 residues processed: 221 average time/residue: 0.2786 time to fit residues: 84.0230 Evaluate side-chains 210 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 187 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 307 ASN Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain M residue 315 ASN Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 414 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 56.1881 > 50: distance: 23 - 28: 5.925 distance: 24 - 55: 19.902 distance: 28 - 29: 5.350 distance: 29 - 30: 4.936 distance: 29 - 32: 4.383 distance: 30 - 31: 7.463 distance: 30 - 36: 7.144 distance: 31 - 63: 33.220 distance: 32 - 33: 5.998 distance: 33 - 34: 11.567 distance: 33 - 35: 15.351 distance: 37 - 38: 6.539 distance: 37 - 40: 9.853 distance: 38 - 39: 5.769 distance: 38 - 44: 4.049 distance: 39 - 71: 24.127 distance: 40 - 41: 9.113 distance: 41 - 42: 12.526 distance: 41 - 43: 11.953 distance: 45 - 46: 5.893 distance: 45 - 48: 3.143 distance: 46 - 55: 8.046 distance: 47 - 80: 12.434 distance: 49 - 51: 4.711 distance: 50 - 52: 4.050 distance: 51 - 53: 8.050 distance: 52 - 54: 4.885 distance: 53 - 54: 4.935 distance: 55 - 56: 8.212 distance: 56 - 57: 13.974 distance: 56 - 59: 4.833 distance: 57 - 58: 17.816 distance: 57 - 63: 28.482 distance: 58 - 85: 15.569 distance: 59 - 60: 16.392 distance: 60 - 61: 12.875 distance: 60 - 62: 16.973 distance: 63 - 64: 28.442 distance: 64 - 65: 5.310 distance: 64 - 67: 18.070 distance: 65 - 66: 6.531 distance: 65 - 71: 4.283 distance: 66 - 93: 21.155 distance: 67 - 68: 13.414 distance: 67 - 69: 18.932 distance: 68 - 70: 20.969 distance: 71 - 72: 5.982 distance: 72 - 73: 4.606 distance: 74 - 97: 8.777 distance: 75 - 76: 7.506 distance: 76 - 77: 8.356 distance: 77 - 78: 8.350 distance: 78 - 79: 12.651 distance: 80 - 81: 4.545 distance: 81 - 82: 3.504 distance: 81 - 84: 5.397 distance: 82 - 83: 3.147 distance: 82 - 85: 3.221 distance: 83 - 105: 8.424 distance: 85 - 86: 5.338 distance: 86 - 87: 5.990 distance: 86 - 89: 5.715 distance: 87 - 88: 13.909 distance: 88 - 110: 22.807 distance: 89 - 90: 10.988 distance: 90 - 91: 7.535 distance: 91 - 92: 18.917 distance: 94 - 95: 3.229 distance: 95 - 96: 3.023 distance: 96 - 116: 6.289 distance: 97 - 98: 3.821 distance: 98 - 99: 3.612 distance: 98 - 101: 4.072 distance: 99 - 100: 7.518 distance: 99 - 105: 3.014 distance: 100 - 122: 10.031 distance: 101 - 102: 5.055 distance: 101 - 103: 7.442 distance: 102 - 104: 4.688