Starting phenix.real_space_refine on Sat Dec 9 14:09:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5m_14331/12_2023/7r5m_14331.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5m_14331/12_2023/7r5m_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_14331/12_2023/7r5m_14331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5m_14331/12_2023/7r5m_14331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5m_14331/12_2023/7r5m_14331.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5m_14331/12_2023/7r5m_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-1.21rc1-5172/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: 6.28, per 1000 atoms: 0.56 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: 3.97 Conformation dependent library (CDL) restraints added in 2.1 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: 1.26 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: 3.20 Time building geometry restraints manager: 4.32 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: 0.800 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: 4.060 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.410 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.980 ------------------------------------------------------------------------------- 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 : 1.380 Fit side-chains outliers start: 10 outliers final: 1 residues processed: 261 average time/residue: 0.2511 time to fit residues: 90.1629 Evaluate side-chains 197 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.313 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4335 time to fit residues: 2.3165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 M 326 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 11454 Z= 0.145 Angle : 0.509 6.084 15507 Z= 0.263 Chirality : 0.043 0.158 1887 Planarity : 0.004 0.040 1959 Dihedral : 3.633 16.333 1533 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.75 % Allowed : 7.24 % Favored : 91.01 % 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: 0.63 (0.23), residues: 1437 helix: 2.34 (0.22), residues: 594 sheet: -0.07 (0.33), residues: 192 loop : -1.33 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 305 HIS 0.001 0.001 HIS B 252 PHE 0.010 0.001 PHE G 384 TYR 0.012 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 241 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 219 time to evaluate : 1.288 Fit side-chains outliers start: 22 outliers final: 22 residues processed: 232 average time/residue: 0.2528 time to fit residues: 80.3560 Evaluate side-chains 214 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.0983 time to fit residues: 5.8793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 G 269 GLN J 307 ASN ** M 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 307 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11454 Z= 0.229 Angle : 0.548 5.959 15507 Z= 0.280 Chirality : 0.044 0.151 1887 Planarity : 0.004 0.038 1959 Dihedral : 3.989 19.297 1533 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.27 % Allowed : 10.74 % Favored : 87.99 % 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: 0.95 (0.22), residues: 1437 helix: 2.45 (0.21), residues: 609 sheet: 0.53 (0.32), residues: 207 loop : -1.28 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 305 HIS 0.002 0.001 HIS M 286 PHE 0.011 0.002 PHE G 384 TYR 0.011 0.001 TYR A 365 ARG 0.005 0.000 ARG M 339 *********************** 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 233 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 217 time to evaluate : 1.234 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 225 average time/residue: 0.2651 time to fit residues: 81.0856 Evaluate side-chains 192 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 1.168 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0931 time to fit residues: 2.5493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 8.9990 chunk 100 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 0.3980 chunk 134 optimal weight: 0.2980 chunk 142 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 38 optimal weight: 0.2980 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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 G 269 GLN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11454 Z= 0.146 Angle : 0.472 5.917 15507 Z= 0.241 Chirality : 0.042 0.171 1887 Planarity : 0.004 0.038 1959 Dihedral : 3.636 17.283 1533 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.43 % Allowed : 12.09 % Favored : 86.48 % 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: 1.40 (0.23), residues: 1437 helix: 2.87 (0.21), residues: 609 sheet: 0.78 (0.30), residues: 219 loop : -1.13 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 442 HIS 0.001 0.000 HIS A 252 PHE 0.023 0.001 PHE J 393 TYR 0.010 0.001 TYR B 365 ARG 0.006 0.000 ARG H 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 219 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 1.300 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 211 average time/residue: 0.2673 time to fit residues: 76.8385 Evaluate side-chains 190 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 180 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0972 time to fit residues: 3.7328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 2 optimal weight: 0.3980 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 127 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 G 269 GLN J 307 ASN M 283 ASN ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11454 Z= 0.142 Angle : 0.454 5.851 15507 Z= 0.234 Chirality : 0.042 0.135 1887 Planarity : 0.004 0.039 1959 Dihedral : 3.553 17.176 1533 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.88 % Allowed : 13.52 % Favored : 85.60 % 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: 1.66 (0.23), residues: 1437 helix: 3.08 (0.21), residues: 609 sheet: 0.96 (0.29), residues: 219 loop : -1.01 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 442 HIS 0.001 0.000 HIS A 252 PHE 0.013 0.001 PHE B 253 TYR 0.010 0.001 TYR B 365 ARG 0.006 0.000 ARG H 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 210 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 1.319 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 201 average time/residue: 0.2573 time to fit residues: 70.4660 Evaluate side-chains 187 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 182 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1005 time to fit residues: 2.6640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11454 Z= 0.223 Angle : 0.513 5.833 15507 Z= 0.265 Chirality : 0.043 0.129 1887 Planarity : 0.004 0.038 1959 Dihedral : 3.917 19.044 1533 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.51 % Allowed : 14.80 % Favored : 83.69 % 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: 1.50 (0.22), residues: 1437 helix: 2.95 (0.20), residues: 609 sheet: 0.99 (0.28), residues: 219 loop : -1.15 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 305 HIS 0.002 0.001 HIS A 431 PHE 0.016 0.002 PHE J 393 TYR 0.009 0.001 TYR B 365 ARG 0.006 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 220 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 1.297 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 215 average time/residue: 0.2629 time to fit residues: 77.6834 Evaluate side-chains 190 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 182 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0990 time to fit residues: 3.3539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 103 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 86 optimal weight: 0.0870 chunk 65 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN J 307 ASN ** 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: 0.7930 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11454 Z= 0.135 Angle : 0.448 5.782 15507 Z= 0.233 Chirality : 0.041 0.126 1887 Planarity : 0.004 0.041 1959 Dihedral : 3.577 17.452 1533 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.80 % Allowed : 16.07 % Favored : 83.13 % 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: 1.68 (0.22), residues: 1437 helix: 3.13 (0.21), residues: 609 sheet: 0.97 (0.28), residues: 219 loop : -1.04 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 442 HIS 0.000 0.000 HIS A 431 PHE 0.015 0.001 PHE F 393 TYR 0.009 0.001 TYR B 365 ARG 0.004 0.000 ARG L 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 212 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 202 time to evaluate : 1.327 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 209 average time/residue: 0.2650 time to fit residues: 75.8834 Evaluate side-chains 189 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0976 time to fit residues: 2.8272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** 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: 0.7992 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11454 Z= 0.192 Angle : 0.484 5.786 15507 Z= 0.250 Chirality : 0.042 0.127 1887 Planarity : 0.004 0.040 1959 Dihedral : 3.747 18.528 1533 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.72 % Allowed : 16.95 % Favored : 82.34 % 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: 1.64 (0.22), residues: 1437 helix: 3.08 (0.21), residues: 609 sheet: 1.00 (0.28), residues: 219 loop : -1.07 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 305 HIS 0.002 0.001 HIS G 252 PHE 0.015 0.001 PHE A 253 TYR 0.008 0.001 TYR B 365 ARG 0.004 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 202 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 1.298 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 199 average time/residue: 0.2873 time to fit residues: 77.5433 Evaluate side-chains 191 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 183 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1024 time to fit residues: 3.5387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11454 Z= 0.155 Angle : 0.463 5.772 15507 Z= 0.240 Chirality : 0.041 0.125 1887 Planarity : 0.004 0.042 1959 Dihedral : 3.609 17.309 1533 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.56 % Allowed : 17.18 % Favored : 82.26 % 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: 1.69 (0.22), residues: 1437 helix: 3.13 (0.21), residues: 609 sheet: 1.02 (0.28), residues: 219 loop : -1.04 (0.24), residues: 609 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 0.013 0.001 PHE B 253 TYR 0.008 0.001 TYR B 365 ARG 0.004 0.000 ARG H 297 *********************** REFINEMENT MACRO_CYCLE 9 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 205 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 198 time to evaluate : 1.289 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 201 average time/residue: 0.2751 time to fit residues: 74.8822 Evaluate side-chains 194 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 189 time to evaluate : 1.383 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1037 time to fit residues: 2.9303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 392 GLN ** J 307 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: 0.7990 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11454 Z= 0.183 Angle : 0.485 5.784 15507 Z= 0.251 Chirality : 0.042 0.125 1887 Planarity : 0.004 0.042 1959 Dihedral : 3.704 18.115 1533 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.24 % Allowed : 17.66 % 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: 1.65 (0.22), residues: 1437 helix: 3.06 (0.21), residues: 609 sheet: 1.02 (0.28), residues: 219 loop : -1.02 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.002 0.001 HIS B 431 PHE 0.014 0.001 PHE B 253 TYR 0.009 0.001 TYR B 365 ARG 0.004 0.000 ARG H 297 ********************** REFINEMENT MACRO_CYCLE 10 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 192 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 1.316 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 191 average time/residue: 0.2809 time to fit residues: 72.8746 Evaluate side-chains 188 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 185 time to evaluate : 1.391 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1016 time to fit residues: 2.3899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 307 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.173791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.123623 restraints weight = 14043.749| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.29 r_work: 0.3135 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4138 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= 0.162 Angle : 0.467 5.765 15507 Z= 0.242 Chirality : 0.041 0.126 1887 Planarity : 0.004 0.043 1959 Dihedral : 3.595 17.193 1533 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.08 % Allowed : 18.14 % Favored : 81.78 % 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: 1.73 (0.22), residues: 1437 helix: 3.13 (0.21), residues: 609 sheet: 1.02 (0.28), residues: 219 loop : -0.97 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 442 HIS 0.001 0.001 HIS A 431 PHE 0.015 0.001 PHE M 298 TYR 0.009 0.001 TYR B 365 ARG 0.004 0.000 ARG H 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.35 seconds wall clock time: 48 minutes 9.40 seconds (2889.40 seconds total)