Starting phenix.real_space_refine on Thu Feb 15 14:48:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1z_31631/02_2024/7v1z_31631.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1z_31631/02_2024/7v1z_31631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1z_31631/02_2024/7v1z_31631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1z_31631/02_2024/7v1z_31631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1z_31631/02_2024/7v1z_31631.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1z_31631/02_2024/7v1z_31631.pdb" } resolution = 2.98 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 64 5.16 5 C 8088 2.51 5 N 2112 2.21 5 O 2324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 363": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B GLU 540": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C ASP 355": "OD1" <-> "OD2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "C GLU 363": "OE1" <-> "OE2" Residue "C GLU 451": "OE1" <-> "OE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D GLU 365": "OE1" <-> "OE2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12588 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3147 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3147 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3147 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3147 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 7.08, per 1000 atoms: 0.56 Number of scatterers: 12588 At special positions: 0 Unit cell: (115.132, 83.928, 152.792, 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 64 16.00 O 2324 8.00 N 2112 7.00 C 8088 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: 4.78 Conformation dependent library (CDL) restraints added in 2.4 seconds 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 15 sheets defined 42.0% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 104 through 123 Processing helix chain 'A' and resid 165 through 180 removed outlier: 3.627A pdb=" N LEU A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.625A pdb=" N SER A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 239 removed outlier: 3.742A pdb=" N VAL A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.798A pdb=" N LEU A 294 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 308 removed outlier: 3.612A pdb=" N LEU A 307 " --> pdb=" O SER A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 340 Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 394 through 399 removed outlier: 3.679A pdb=" N GLY A 399 " --> pdb=" O TRP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 425 removed outlier: 3.863A pdb=" N LEU A 407 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLY A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 444 removed outlier: 3.549A pdb=" N MET A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 511 removed outlier: 3.505A pdb=" N ASN A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 544 removed outlier: 3.518A pdb=" N LYS A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 123 removed outlier: 3.575A pdb=" N SER B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 180 removed outlier: 4.271A pdb=" N SER B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 226 through 239 Processing helix chain 'B' and resid 290 through 294 removed outlier: 3.571A pdb=" N LEU B 294 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 325 through 340 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 394 through 399 removed outlier: 3.619A pdb=" N GLY B 399 " --> pdb=" O TRP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 425 removed outlier: 3.815A pdb=" N LEU B 407 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 423 " --> pdb=" O GLN B 419 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN B 425 " --> pdb=" O GLY B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 444 Processing helix chain 'B' and resid 504 through 511 removed outlier: 3.515A pdb=" N ILE B 508 " --> pdb=" O ASP B 504 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B 509 " --> pdb=" O THR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 544 removed outlier: 4.094A pdb=" N ASP B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 123 removed outlier: 3.725A pdb=" N LEU C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 180 removed outlier: 3.864A pdb=" N SER C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 209 through 215 removed outlier: 3.887A pdb=" N SER C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 239 removed outlier: 3.628A pdb=" N GLU C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.709A pdb=" N LEU C 294 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 325 through 340 Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.543A pdb=" N TYR C 346 " --> pdb=" O LYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 395 removed outlier: 3.515A pdb=" N LYS C 394 " --> pdb=" O ASN C 391 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TRP C 395 " --> pdb=" O SER C 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 395' Processing helix chain 'C' and resid 403 through 425 removed outlier: 3.771A pdb=" N LEU C 407 " --> pdb=" O THR C 403 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU C 422 " --> pdb=" O TYR C 418 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 423 " --> pdb=" O GLN C 419 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN C 425 " --> pdb=" O GLY C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 444 Processing helix chain 'C' and resid 504 through 511 Processing helix chain 'C' and resid 530 through 544 removed outlier: 3.603A pdb=" N ASP C 544 " --> pdb=" O GLU C 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'D' and resid 164 through 180 removed outlier: 3.911A pdb=" N SER D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 209 through 215 removed outlier: 3.523A pdb=" N SER D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 239 Processing helix chain 'D' and resid 289 through 294 removed outlier: 3.717A pdb=" N LEU D 294 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 325 through 340 Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 394 through 399 removed outlier: 3.791A pdb=" N GLY D 399 " --> pdb=" O TRP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 424 removed outlier: 3.925A pdb=" N LEU D 407 " --> pdb=" O THR D 403 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLY D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU D 422 " --> pdb=" O TYR D 418 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE D 423 " --> pdb=" O GLN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 444 Processing helix chain 'D' and resid 504 through 511 removed outlier: 3.509A pdb=" N ILE D 508 " --> pdb=" O ASP D 504 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN D 509 " --> pdb=" O THR D 505 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN D 510 " --> pdb=" O GLU D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 544 removed outlier: 3.883A pdb=" N ASP D 544 " --> pdb=" O GLU D 540 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 5.318A pdb=" N GLU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 133 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP A 139 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 492 " --> pdb=" O ALA A 489 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 162 removed outlier: 4.211A pdb=" N PHE A 400 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 377 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.545A pdb=" N VAL B 152 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL B 133 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 492 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA7, first strand: chain 'B' and resid 375 through 377 Processing sheet with id=AA8, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.611A pdb=" N VAL C 152 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 133 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 492 " --> pdb=" O ALA C 489 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AB1, first strand: chain 'C' and resid 200 through 201 Processing sheet with id=AB2, first strand: chain 'C' and resid 375 through 377 Processing sheet with id=AB3, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.520A pdb=" N VAL D 152 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL D 133 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP D 139 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 160 through 161 Processing sheet with id=AB5, first strand: chain 'D' and resid 200 through 201 removed outlier: 3.607A pdb=" N TYR D 201 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 375 through 377 539 hydrogen bonds defined for protein. 1500 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: 3.97 Time building geometry restraints manager: 5.07 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: 3349 1.33 - 1.45: 2277 1.45 - 1.57: 7134 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 12868 Sorted by residual: bond pdb=" C ALA A 124 " pdb=" N PRO A 125 " ideal model delta sigma weight residual 1.336 1.368 -0.032 1.23e-02 6.61e+03 6.94e+00 bond pdb=" CA ALA A 124 " pdb=" C ALA A 124 " ideal model delta sigma weight residual 1.528 1.555 -0.027 1.13e-02 7.83e+03 5.83e+00 bond pdb=" C GLU B 365 " pdb=" N PRO B 366 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.34e-02 5.57e+03 5.27e+00 bond pdb=" CA LEU D 115 " pdb=" C LEU D 115 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.27e-02 6.20e+03 4.90e+00 bond pdb=" C LEU D 115 " pdb=" O LEU D 115 " ideal model delta sigma weight residual 1.236 1.213 0.023 1.15e-02 7.56e+03 4.09e+00 ... (remaining 12863 not shown) Histogram of bond angle deviations from ideal: 99.98 - 107.14: 373 107.14 - 114.29: 7357 114.29 - 121.44: 6618 121.44 - 128.59: 2967 128.59 - 135.75: 81 Bond angle restraints: 17396 Sorted by residual: angle pdb=" C GLU B 365 " pdb=" N PRO B 366 " pdb=" CA PRO B 366 " ideal model delta sigma weight residual 119.78 114.06 5.72 1.03e+00 9.43e-01 3.08e+01 angle pdb=" N ALA A 124 " pdb=" CA ALA A 124 " pdb=" C ALA A 124 " ideal model delta sigma weight residual 109.57 115.45 -5.88 1.23e+00 6.61e-01 2.29e+01 angle pdb=" N SER A 402 " pdb=" CA SER A 402 " pdb=" C SER A 402 " ideal model delta sigma weight residual 108.79 115.59 -6.80 1.53e+00 4.27e-01 1.97e+01 angle pdb=" N THR A 472 " pdb=" CA THR A 472 " pdb=" C THR A 472 " ideal model delta sigma weight residual 111.36 115.74 -4.38 1.09e+00 8.42e-01 1.61e+01 angle pdb=" N SER B 484 " pdb=" CA SER B 484 " pdb=" C SER B 484 " ideal model delta sigma weight residual 109.23 115.33 -6.10 1.55e+00 4.16e-01 1.55e+01 ... (remaining 17391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6972 17.70 - 35.39: 616 35.39 - 53.09: 114 53.09 - 70.79: 15 70.79 - 88.49: 11 Dihedral angle restraints: 7728 sinusoidal: 3108 harmonic: 4620 Sorted by residual: dihedral pdb=" CB GLU A 363 " pdb=" CG GLU A 363 " pdb=" CD GLU A 363 " pdb=" OE1 GLU A 363 " ideal model delta sinusoidal sigma weight residual 0.00 88.49 -88.49 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU C 291 " pdb=" CG GLU C 291 " pdb=" CD GLU C 291 " pdb=" OE1 GLU C 291 " ideal model delta sinusoidal sigma weight residual 0.00 86.36 -86.36 1 3.00e+01 1.11e-03 9.99e+00 dihedral pdb=" CB GLU A 540 " pdb=" CG GLU A 540 " pdb=" CD GLU A 540 " pdb=" OE1 GLU A 540 " ideal model delta sinusoidal sigma weight residual 0.00 85.72 -85.72 1 3.00e+01 1.11e-03 9.87e+00 ... (remaining 7725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1455 0.045 - 0.091: 307 0.091 - 0.136: 127 0.136 - 0.182: 11 0.182 - 0.227: 8 Chirality restraints: 1908 Sorted by residual: chirality pdb=" CA TYR B 369 " pdb=" N TYR B 369 " pdb=" C TYR B 369 " pdb=" CB TYR B 369 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN A 370 " pdb=" N ASN A 370 " pdb=" C ASN A 370 " pdb=" CB ASN A 370 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LYS A 381 " pdb=" N LYS A 381 " pdb=" C LYS A 381 " pdb=" CB LYS A 381 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1905 not shown) Planarity restraints: 2208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 124 " 0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO A 125 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 124 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO D 125 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 125 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 125 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 374 " 0.016 2.00e-02 2.50e+03 1.14e-02 2.26e+00 pdb=" CG PHE A 374 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 374 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 374 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 374 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 374 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 374 " 0.005 2.00e-02 2.50e+03 ... (remaining 2205 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1106 2.75 - 3.28: 11933 3.28 - 3.82: 19773 3.82 - 4.36: 24061 4.36 - 4.90: 42368 Nonbonded interactions: 99241 Sorted by model distance: nonbonded pdb=" OE2 GLU C 137 " pdb=" OG SER C 140 " model vdw 2.207 2.440 nonbonded pdb=" O VAL D 441 " pdb=" OG1 THR D 445 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR A 358 " pdb=" OD2 ASP A 406 " model vdw 2.275 2.440 nonbonded pdb=" OE2 GLU A 137 " pdb=" OG SER A 140 " model vdw 2.286 2.440 nonbonded pdb=" OD1 ASP B 542 " pdb=" NH2 ARG B 545 " model vdw 2.318 2.520 ... (remaining 99236 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 'C' selection = chain 'D' } 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: 1.370 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: 5.270 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 35.720 Find NCS groups from input model: 0.760 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: 0.000 Load rotamer database and sin/cos tables:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12868 Z= 0.177 Angle : 0.578 10.746 17396 Z= 0.346 Chirality : 0.045 0.227 1908 Planarity : 0.004 0.051 2208 Dihedral : 13.828 88.487 4776 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.22 % Allowed : 0.82 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), residues: 1576 helix: 1.90 (0.23), residues: 524 sheet: 1.29 (0.38), residues: 188 loop : 0.03 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 454 HIS 0.006 0.001 HIS B 191 PHE 0.024 0.001 PHE A 374 TYR 0.012 0.001 TYR C 328 ARG 0.003 0.000 ARG D 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 247 time to evaluate : 1.490 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.7639 (mtpt) cc_final: 0.7391 (mttm) REVERT: A 355 ASP cc_start: 0.7992 (t70) cc_final: 0.7518 (t0) REVERT: A 510 ASN cc_start: 0.7510 (m-40) cc_final: 0.7047 (m-40) REVERT: A 540 GLU cc_start: 0.8044 (tp30) cc_final: 0.7835 (tp30) REVERT: B 460 TYR cc_start: 0.8886 (t80) cc_final: 0.8600 (t80) REVERT: B 462 MET cc_start: 0.8043 (mmt) cc_final: 0.7767 (mmm) REVERT: C 120 ASP cc_start: 0.7950 (m-30) cc_final: 0.7679 (m-30) REVERT: C 224 GLU cc_start: 0.7348 (tp30) cc_final: 0.7144 (tm-30) REVERT: C 320 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7834 (tp40) REVERT: C 373 ARG cc_start: 0.7596 (mtp85) cc_final: 0.7266 (mmm160) REVERT: D 200 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6996 (mp0) outliers start: 3 outliers final: 0 residues processed: 250 average time/residue: 1.5358 time to fit residues: 409.6273 Evaluate side-chains 136 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 0.0070 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN A 425 ASN A 510 ASN B 370 ASN C 191 HIS C 216 HIS ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12868 Z= 0.162 Angle : 0.502 5.866 17396 Z= 0.267 Chirality : 0.041 0.137 1908 Planarity : 0.004 0.039 2208 Dihedral : 3.962 16.761 1740 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.63 % Allowed : 10.46 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.21), residues: 1576 helix: 2.17 (0.22), residues: 532 sheet: 1.34 (0.38), residues: 188 loop : 0.09 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 178 HIS 0.010 0.001 HIS C 191 PHE 0.012 0.001 PHE D 374 TYR 0.014 0.001 TYR A 328 ARG 0.003 0.000 ARG D 469 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8272 (mp) REVERT: A 225 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7518 (mttt) REVERT: A 228 LYS cc_start: 0.7267 (mtmp) cc_final: 0.6920 (mmmt) REVERT: A 355 ASP cc_start: 0.8143 (t70) cc_final: 0.7775 (t0) REVERT: A 442 MET cc_start: 0.8474 (ttp) cc_final: 0.8252 (tmm) REVERT: B 460 TYR cc_start: 0.8877 (t80) cc_final: 0.8615 (t80) REVERT: B 462 MET cc_start: 0.8130 (mmt) cc_final: 0.7855 (mmm) REVERT: C 120 ASP cc_start: 0.7935 (m-30) cc_final: 0.7609 (m-30) REVERT: C 224 GLU cc_start: 0.7496 (tp30) cc_final: 0.7121 (tm-30) REVERT: C 373 ARG cc_start: 0.7536 (mtp85) cc_final: 0.7274 (mmm160) REVERT: C 456 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7744 (mmmt) REVERT: C 508 ILE cc_start: 0.7816 (mt) cc_final: 0.7594 (mm) REVERT: C 542 ASP cc_start: 0.8095 (t0) cc_final: 0.7875 (t0) REVERT: D 232 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: D 525 MET cc_start: 0.8809 (tpt) cc_final: 0.8604 (tpp) outliers start: 22 outliers final: 11 residues processed: 162 average time/residue: 1.6475 time to fit residues: 285.5261 Evaluate side-chains 141 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 427 ASN A 481 HIS C 191 HIS C 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 12868 Z= 0.428 Angle : 0.673 7.609 17396 Z= 0.356 Chirality : 0.048 0.150 1908 Planarity : 0.005 0.042 2208 Dihedral : 4.609 18.790 1740 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.89 % Allowed : 12.69 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.85 (0.20), residues: 1576 helix: 1.83 (0.22), residues: 528 sheet: 1.37 (0.43), residues: 140 loop : -0.32 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 178 HIS 0.011 0.002 HIS C 191 PHE 0.022 0.002 PHE D 423 TYR 0.021 0.002 TYR A 328 ARG 0.004 0.001 ARG D 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 136 time to evaluate : 1.493 Fit side-chains REVERT: A 145 TYR cc_start: 0.8941 (m-80) cc_final: 0.8737 (m-80) REVERT: A 225 LYS cc_start: 0.8025 (mtpt) cc_final: 0.7661 (mttt) REVERT: A 228 LYS cc_start: 0.7580 (mtmp) cc_final: 0.7102 (mmmt) REVERT: A 355 ASP cc_start: 0.8307 (t70) cc_final: 0.7861 (t0) REVERT: A 373 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7668 (mtp180) REVERT: A 525 MET cc_start: 0.8797 (tpp) cc_final: 0.8556 (tpp) REVERT: B 460 TYR cc_start: 0.8910 (t80) cc_final: 0.8620 (t80) REVERT: B 462 MET cc_start: 0.8255 (mmt) cc_final: 0.8048 (mmm) REVERT: C 190 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7206 (mt0) REVERT: C 224 GLU cc_start: 0.7692 (tp30) cc_final: 0.7261 (tm-30) REVERT: C 233 GLU cc_start: 0.6367 (mp0) cc_final: 0.6094 (mp0) REVERT: C 362 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: C 373 ARG cc_start: 0.7518 (mtp85) cc_final: 0.7273 (mmm160) REVERT: D 117 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8136 (mtp180) REVERT: D 232 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6850 (tm-30) outliers start: 39 outliers final: 16 residues processed: 166 average time/residue: 1.5628 time to fit residues: 278.2190 Evaluate side-chains 138 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN A 427 ASN B 150 ASN C 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12868 Z= 0.192 Angle : 0.519 7.435 17396 Z= 0.275 Chirality : 0.042 0.143 1908 Planarity : 0.004 0.040 2208 Dihedral : 4.231 16.764 1740 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.74 % Allowed : 14.39 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.04 (0.21), residues: 1576 helix: 2.11 (0.22), residues: 528 sheet: 0.50 (0.40), residues: 188 loop : -0.12 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 178 HIS 0.011 0.001 HIS C 191 PHE 0.013 0.001 PHE D 374 TYR 0.016 0.001 TYR A 328 ARG 0.002 0.000 ARG D 545 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 127 time to evaluate : 1.704 Fit side-chains REVERT: A 225 LYS cc_start: 0.7858 (mtpt) cc_final: 0.7550 (mttt) REVERT: A 228 LYS cc_start: 0.7547 (mtmp) cc_final: 0.7122 (mmmt) REVERT: A 289 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6378 (mp10) REVERT: A 355 ASP cc_start: 0.8249 (t70) cc_final: 0.7952 (t0) REVERT: A 469 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7849 (ptt90) REVERT: A 485 HIS cc_start: 0.8963 (OUTLIER) cc_final: 0.8673 (t-170) REVERT: B 460 TYR cc_start: 0.8945 (t80) cc_final: 0.8704 (t80) REVERT: C 190 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7189 (mt0) REVERT: C 224 GLU cc_start: 0.7642 (tp30) cc_final: 0.7216 (tm-30) REVERT: C 233 GLU cc_start: 0.6421 (mp0) cc_final: 0.6152 (mp0) REVERT: C 348 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7601 (tm-30) REVERT: C 362 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: C 373 ARG cc_start: 0.7510 (mtp85) cc_final: 0.7284 (mmm160) REVERT: D 232 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6767 (tm-30) outliers start: 37 outliers final: 16 residues processed: 160 average time/residue: 1.5587 time to fit residues: 267.7900 Evaluate side-chains 138 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN A 427 ASN B 510 ASN C 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12868 Z= 0.311 Angle : 0.586 8.013 17396 Z= 0.308 Chirality : 0.044 0.145 1908 Planarity : 0.004 0.042 2208 Dihedral : 4.385 17.908 1740 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.12 % Allowed : 15.65 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.21), residues: 1576 helix: 2.03 (0.22), residues: 528 sheet: 1.16 (0.43), residues: 140 loop : -0.28 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 464 HIS 0.011 0.001 HIS C 191 PHE 0.016 0.002 PHE D 374 TYR 0.018 0.002 TYR A 328 ARG 0.003 0.000 ARG D 545 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 125 time to evaluate : 1.611 Fit side-chains REVERT: A 177 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8484 (mp) REVERT: A 225 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7602 (mttt) REVERT: A 228 LYS cc_start: 0.7578 (mtmp) cc_final: 0.7142 (mmmt) REVERT: A 355 ASP cc_start: 0.8292 (t70) cc_final: 0.7960 (t0) REVERT: A 469 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7880 (ptt90) REVERT: A 485 HIS cc_start: 0.8999 (OUTLIER) cc_final: 0.8743 (t-170) REVERT: B 460 TYR cc_start: 0.8929 (t80) cc_final: 0.8697 (t80) REVERT: C 190 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7060 (mt0) REVERT: C 191 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7053 (t-90) REVERT: C 200 GLU cc_start: 0.6910 (tt0) cc_final: 0.6587 (tt0) REVERT: C 224 GLU cc_start: 0.7663 (tp30) cc_final: 0.7199 (tm-30) REVERT: C 348 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: C 362 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7171 (tt0) REVERT: C 373 ARG cc_start: 0.7452 (mtp85) cc_final: 0.7210 (mmm160) REVERT: C 540 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7399 (mt-10) REVERT: D 232 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6790 (tm-30) outliers start: 42 outliers final: 20 residues processed: 159 average time/residue: 1.6202 time to fit residues: 275.6892 Evaluate side-chains 144 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 chunk 37 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN A 427 ASN C 190 GLN C 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12868 Z= 0.157 Angle : 0.500 9.366 17396 Z= 0.262 Chirality : 0.041 0.142 1908 Planarity : 0.003 0.040 2208 Dihedral : 4.099 16.156 1740 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.67 % Allowed : 16.62 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.21), residues: 1576 helix: 2.27 (0.22), residues: 528 sheet: 1.04 (0.44), residues: 148 loop : -0.12 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 178 HIS 0.020 0.001 HIS C 191 PHE 0.010 0.001 PHE D 374 TYR 0.015 0.001 TYR A 328 ARG 0.002 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 135 time to evaluate : 1.525 Fit side-chains REVERT: A 177 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8406 (mp) REVERT: A 190 GLN cc_start: 0.8241 (mp10) cc_final: 0.8007 (mm-40) REVERT: A 225 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7580 (mptt) REVERT: A 228 LYS cc_start: 0.7485 (mtmp) cc_final: 0.6733 (mmmt) REVERT: A 232 GLU cc_start: 0.7401 (pp20) cc_final: 0.7135 (mp0) REVERT: A 289 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6488 (mp10) REVERT: A 355 ASP cc_start: 0.8215 (t70) cc_final: 0.7971 (t0) REVERT: A 469 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7756 (ptt90) REVERT: B 362 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7375 (tt0) REVERT: C 190 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7198 (mt0) REVERT: C 200 GLU cc_start: 0.6891 (tt0) cc_final: 0.6573 (tt0) REVERT: C 224 GLU cc_start: 0.7635 (tp30) cc_final: 0.7185 (tm-30) REVERT: C 348 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7560 (tm-30) REVERT: C 373 ARG cc_start: 0.7390 (mtp85) cc_final: 0.7157 (mmm160) REVERT: C 540 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7232 (mt-10) REVERT: D 232 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6796 (tm-30) outliers start: 36 outliers final: 18 residues processed: 164 average time/residue: 1.5594 time to fit residues: 274.4399 Evaluate side-chains 142 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 94 optimal weight: 0.2980 chunk 91 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN A 427 ASN C 191 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12868 Z= 0.165 Angle : 0.505 10.144 17396 Z= 0.264 Chirality : 0.041 0.141 1908 Planarity : 0.003 0.039 2208 Dihedral : 4.004 15.733 1740 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.45 % Allowed : 17.36 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.27 (0.21), residues: 1576 helix: 2.30 (0.22), residues: 528 sheet: 1.01 (0.44), residues: 148 loop : -0.04 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 395 HIS 0.012 0.001 HIS C 191 PHE 0.011 0.001 PHE D 374 TYR 0.015 0.001 TYR A 328 ARG 0.006 0.000 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 125 time to evaluate : 1.558 Fit side-chains REVERT: A 177 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8392 (mp) REVERT: A 190 GLN cc_start: 0.8271 (mp10) cc_final: 0.8038 (mm-40) REVERT: A 228 LYS cc_start: 0.7513 (mtmp) cc_final: 0.7081 (mmmt) REVERT: A 355 ASP cc_start: 0.8199 (t70) cc_final: 0.7981 (t0) REVERT: A 469 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7715 (ptt90) REVERT: B 106 ARG cc_start: 0.7547 (ttp80) cc_final: 0.6918 (ttp80) REVERT: B 362 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: C 190 GLN cc_start: 0.7534 (mt0) cc_final: 0.7298 (mt0) REVERT: C 191 HIS cc_start: 0.7657 (OUTLIER) cc_final: 0.7090 (t-90) REVERT: C 200 GLU cc_start: 0.6895 (tt0) cc_final: 0.6572 (tt0) REVERT: C 373 ARG cc_start: 0.7450 (mtp85) cc_final: 0.7232 (mmm160) REVERT: C 540 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7253 (mt-10) REVERT: D 232 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6801 (tm-30) outliers start: 33 outliers final: 19 residues processed: 156 average time/residue: 1.5990 time to fit residues: 267.4809 Evaluate side-chains 135 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 102 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN C 190 GLN C 191 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12868 Z= 0.143 Angle : 0.485 7.915 17396 Z= 0.255 Chirality : 0.040 0.137 1908 Planarity : 0.003 0.038 2208 Dihedral : 3.900 14.879 1740 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.93 % Allowed : 18.40 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.21), residues: 1576 helix: 2.35 (0.22), residues: 528 sheet: 1.05 (0.44), residues: 148 loop : 0.03 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 395 HIS 0.025 0.001 HIS C 191 PHE 0.010 0.001 PHE A 374 TYR 0.014 0.001 TYR A 328 ARG 0.006 0.000 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 1.537 Fit side-chains REVERT: A 177 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8377 (mp) REVERT: A 190 GLN cc_start: 0.8269 (mp10) cc_final: 0.8040 (mm-40) REVERT: A 228 LYS cc_start: 0.7470 (mtmp) cc_final: 0.6808 (mmmt) REVERT: A 232 GLU cc_start: 0.7382 (pp20) cc_final: 0.7064 (mp0) REVERT: B 106 ARG cc_start: 0.7511 (ttp80) cc_final: 0.6881 (ttp80) REVERT: C 190 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7293 (mt0) REVERT: C 200 GLU cc_start: 0.6878 (tt0) cc_final: 0.6550 (tt0) REVERT: C 348 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7123 (tp-100) REVERT: C 373 ARG cc_start: 0.7434 (mtp85) cc_final: 0.7213 (mmm160) outliers start: 26 outliers final: 14 residues processed: 142 average time/residue: 1.4782 time to fit residues: 225.9267 Evaluate side-chains 128 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN C 190 GLN C 191 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12868 Z= 0.164 Angle : 0.507 11.905 17396 Z= 0.265 Chirality : 0.041 0.136 1908 Planarity : 0.003 0.035 2208 Dihedral : 3.888 15.466 1740 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.78 % Allowed : 18.62 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.27 (0.21), residues: 1576 helix: 2.28 (0.22), residues: 532 sheet: 1.02 (0.44), residues: 148 loop : -0.04 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 395 HIS 0.012 0.001 HIS C 191 PHE 0.011 0.001 PHE D 374 TYR 0.014 0.001 TYR A 328 ARG 0.005 0.000 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8392 (mp) REVERT: A 190 GLN cc_start: 0.8285 (mp10) cc_final: 0.8022 (mm-40) REVERT: A 228 LYS cc_start: 0.7473 (mtmp) cc_final: 0.7053 (mmmt) REVERT: B 106 ARG cc_start: 0.7514 (ttp80) cc_final: 0.6873 (ttp80) REVERT: B 502 GLU cc_start: 0.6783 (pm20) cc_final: 0.6467 (mp0) REVERT: C 191 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.7068 (t-90) REVERT: C 320 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: C 348 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7137 (tp-100) outliers start: 24 outliers final: 16 residues processed: 142 average time/residue: 1.5013 time to fit residues: 231.1794 Evaluate side-chains 132 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain C residue 320 GLN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 0.0470 chunk 98 optimal weight: 1.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN A 427 ASN C 191 HIS C 348 GLN C 509 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12868 Z= 0.174 Angle : 0.517 10.103 17396 Z= 0.269 Chirality : 0.041 0.136 1908 Planarity : 0.003 0.038 2208 Dihedral : 3.901 15.488 1740 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.71 % Allowed : 18.92 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.26 (0.21), residues: 1576 helix: 2.25 (0.22), residues: 532 sheet: 1.02 (0.44), residues: 148 loop : -0.03 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 395 HIS 0.014 0.001 HIS C 191 PHE 0.011 0.001 PHE D 374 TYR 0.014 0.001 TYR A 328 ARG 0.005 0.000 ARG B 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.456 Fit side-chains REVERT: A 177 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8360 (mp) REVERT: A 190 GLN cc_start: 0.8275 (mp10) cc_final: 0.8053 (mm-40) REVERT: A 228 LYS cc_start: 0.7462 (mtmp) cc_final: 0.6812 (mmmt) REVERT: A 232 GLU cc_start: 0.7331 (pp20) cc_final: 0.7037 (mp0) REVERT: B 502 GLU cc_start: 0.6800 (pm20) cc_final: 0.6488 (mp0) REVERT: C 191 HIS cc_start: 0.7617 (OUTLIER) cc_final: 0.7163 (t-90) REVERT: C 320 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: C 348 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7166 (tp-100) outliers start: 23 outliers final: 16 residues processed: 135 average time/residue: 1.4406 time to fit residues: 210.0545 Evaluate side-chains 130 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain C residue 320 GLN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 0.0050 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN C 348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.105149 restraints weight = 16624.467| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.76 r_work: 0.3128 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 12868 Z= 0.211 Angle : 0.869 59.200 17396 Z= 0.508 Chirality : 0.042 0.342 1908 Planarity : 0.006 0.196 2208 Dihedral : 3.911 15.381 1740 Min Nonbonded Distance : 1.536 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.71 % Allowed : 18.77 % Favored : 79.53 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.88 % 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: 1.24 (0.21), residues: 1576 helix: 2.23 (0.22), residues: 532 sheet: 1.01 (0.44), residues: 148 loop : -0.03 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 395 HIS 0.320 0.007 HIS C 191 PHE 0.011 0.001 PHE D 374 TYR 0.014 0.001 TYR A 328 ARG 0.004 0.000 ARG B 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4778.67 seconds wall clock time: 85 minutes 23.47 seconds (5123.47 seconds total)