Starting phenix.real_space_refine on Sat Dec 9 22:51:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1z_31631/12_2023/7v1z_31631.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1z_31631/12_2023/7v1z_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_31631/12_2023/7v1z_31631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1z_31631/12_2023/7v1z_31631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1z_31631/12_2023/7v1z_31631.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1z_31631/12_2023/7v1z_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-1.21rc1-5172/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: 7.21, per 1000 atoms: 0.57 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: 4.90 Conformation dependent library (CDL) restraints added in 3.3 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: 4.13 Time building geometry restraints manager: 5.26 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.120 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 36.560 Find NCS groups from input model: 0.750 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.200 ------------------------------------------------------------------------------- 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 : 1.453 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 250 average time/residue: 1.5833 time to fit residues: 422.8619 Evaluate side-chains 133 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9523 ------------------------------------------------------------------------------- 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: 0.9980 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: 5.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 481 HIS 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: 0.8010 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12868 Z= 0.168 Angle : 0.506 6.017 17396 Z= 0.270 Chirality : 0.042 0.139 1908 Planarity : 0.004 0.039 2208 Dihedral : 3.949 16.203 1740 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.63 % Allowed : 10.98 % Favored : 87.39 % 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: 1.41 (0.21), residues: 1576 helix: 2.18 (0.22), residues: 532 sheet: 1.33 (0.38), residues: 188 loop : 0.09 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 0.004 0.000 ARG B 545 *********************** 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 160 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 1.617 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 157 average time/residue: 1.5901 time to fit residues: 267.8064 Evaluate side-chains 134 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.8893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 126 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN C 191 HIS C 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 12868 Z= 0.492 Angle : 0.713 8.103 17396 Z= 0.377 Chirality : 0.049 0.156 1908 Planarity : 0.005 0.045 2208 Dihedral : 4.690 19.246 1740 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.89 % Allowed : 13.20 % Favored : 83.90 % 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: 0.74 (0.20), residues: 1576 helix: 1.71 (0.22), residues: 528 sheet: 1.33 (0.43), residues: 140 loop : -0.37 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 178 HIS 0.011 0.002 HIS C 191 PHE 0.022 0.002 PHE D 423 TYR 0.020 0.003 TYR B 473 ARG 0.005 0.001 ARG A 151 *********************** 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 170 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 131 time to evaluate : 1.529 Fit side-chains outliers start: 39 outliers final: 16 residues processed: 161 average time/residue: 1.5986 time to fit residues: 275.9454 Evaluate side-chains 129 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.642 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 4 average time/residue: 0.4294 time to fit residues: 4.2186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2987 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= 0.206 Angle : 0.535 7.760 17396 Z= 0.282 Chirality : 0.042 0.138 1908 Planarity : 0.004 0.041 2208 Dihedral : 4.287 16.979 1740 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.45 % Allowed : 15.06 % Favored : 82.49 % 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: 1.01 (0.21), residues: 1576 helix: 2.00 (0.22), residues: 528 sheet: 1.17 (0.44), residues: 148 loop : -0.21 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 178 HIS 0.009 0.001 HIS B 191 PHE 0.014 0.001 PHE D 374 TYR 0.016 0.001 TYR A 328 ARG 0.003 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 158 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 125 time to evaluate : 1.657 Fit side-chains outliers start: 33 outliers final: 18 residues processed: 155 average time/residue: 1.5809 time to fit residues: 262.9459 Evaluate side-chains 128 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.517 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 0.1606 time to fit residues: 2.2983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.0570 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 0.0570 chunk 128 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 509 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3047 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= 0.150 Angle : 0.490 8.208 17396 Z= 0.259 Chirality : 0.041 0.133 1908 Planarity : 0.003 0.040 2208 Dihedral : 3.985 15.304 1740 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.37 % Allowed : 17.06 % Favored : 80.56 % 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: 2.27 (0.22), residues: 528 sheet: 1.15 (0.44), residues: 148 loop : -0.06 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 178 HIS 0.013 0.001 HIS C 191 PHE 0.009 0.001 PHE D 374 TYR 0.015 0.001 TYR A 328 ARG 0.004 0.000 ARG D 469 *********************** 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 160 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 1.723 Fit side-chains outliers start: 32 outliers final: 18 residues processed: 155 average time/residue: 1.6642 time to fit residues: 277.1122 Evaluate side-chains 131 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.593 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 0.1686 time to fit residues: 2.3949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 125 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12868 Z= 0.158 Angle : 0.497 9.167 17396 Z= 0.261 Chirality : 0.041 0.131 1908 Planarity : 0.003 0.039 2208 Dihedral : 3.924 14.959 1740 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.00 % Allowed : 17.80 % 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: 1.34 (0.21), residues: 1576 helix: 2.32 (0.22), residues: 528 sheet: 1.09 (0.44), residues: 148 loop : 0.02 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 395 HIS 0.006 0.001 HIS B 191 PHE 0.010 0.001 PHE D 374 TYR 0.014 0.001 TYR A 328 ARG 0.006 0.000 ARG B 106 *********************** 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 154 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 1.503 Fit side-chains outliers start: 27 outliers final: 18 residues processed: 151 average time/residue: 1.6064 time to fit residues: 260.7947 Evaluate side-chains 133 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 2.1008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 0.4980 chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 0.0980 chunk 150 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12868 Z= 0.147 Angle : 0.488 10.034 17396 Z= 0.256 Chirality : 0.040 0.130 1908 Planarity : 0.003 0.040 2208 Dihedral : 3.823 14.794 1740 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.37 % Allowed : 17.80 % Favored : 79.82 % 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: 1.41 (0.21), residues: 1576 helix: 2.36 (0.22), residues: 528 sheet: 1.07 (0.44), residues: 148 loop : 0.10 (0.21), residues: 900 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 0.010 0.001 PHE A 374 TYR 0.013 0.001 TYR A 328 ARG 0.011 0.000 ARG A 306 *********************** 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 152 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 1.689 Fit side-chains outliers start: 32 outliers final: 19 residues processed: 147 average time/residue: 1.6168 time to fit residues: 255.7499 Evaluate side-chains 126 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 1.514 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.1662 time to fit residues: 2.3132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 95 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12868 Z= 0.147 Angle : 0.490 8.867 17396 Z= 0.255 Chirality : 0.041 0.129 1908 Planarity : 0.003 0.046 2208 Dihedral : 3.790 14.807 1740 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.85 % Allowed : 18.62 % Favored : 79.53 % 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: 1.46 (0.21), residues: 1576 helix: 2.38 (0.22), residues: 528 sheet: 1.06 (0.44), residues: 148 loop : 0.14 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 395 HIS 0.008 0.001 HIS B 191 PHE 0.010 0.001 PHE D 374 TYR 0.013 0.001 TYR A 328 ARG 0.013 0.000 ARG A 306 *********************** 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 147 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 1.598 Fit side-chains outliers start: 25 outliers final: 19 residues processed: 145 average time/residue: 1.5090 time to fit residues: 235.8275 Evaluate side-chains 131 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 1.390 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 0 time to fit residues: 2.0005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 8.9990 chunk 140 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8074 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12868 Z= 0.156 Angle : 0.497 9.652 17396 Z= 0.259 Chirality : 0.041 0.131 1908 Planarity : 0.003 0.057 2208 Dihedral : 3.803 15.110 1740 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.00 % Allowed : 18.62 % 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: 1.38 (0.21), residues: 1576 helix: 2.35 (0.22), residues: 528 sheet: 1.02 (0.44), residues: 148 loop : 0.07 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 395 HIS 0.011 0.001 HIS C 191 PHE 0.011 0.001 PHE D 374 TYR 0.013 0.001 TYR A 328 ARG 0.014 0.000 ARG A 306 *********************** 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 147 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 1.550 Fit side-chains outliers start: 27 outliers final: 21 residues processed: 146 average time/residue: 1.5870 time to fit residues: 249.9805 Evaluate side-chains 138 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.493 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 0.1601 time to fit residues: 2.1124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 12 optimal weight: 0.0270 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 98 optimal weight: 0.0870 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 GLN A 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12868 Z= 0.135 Angle : 0.489 10.356 17396 Z= 0.253 Chirality : 0.040 0.130 1908 Planarity : 0.003 0.058 2208 Dihedral : 3.728 14.446 1740 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.63 % Allowed : 18.84 % Favored : 79.53 % 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: 1.43 (0.21), residues: 1576 helix: 2.34 (0.22), residues: 532 sheet: 1.09 (0.44), residues: 148 loop : 0.11 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 395 HIS 0.008 0.001 HIS B 191 PHE 0.009 0.001 PHE A 374 TYR 0.012 0.001 TYR A 328 ARG 0.014 0.000 ARG A 306 ********************** 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 145 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.661 Fit side-chains outliers start: 22 outliers final: 20 residues processed: 144 average time/residue: 1.5050 time to fit residues: 233.7211 Evaluate side-chains 134 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 1.546 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 2.0054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 127 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 GLN A 425 ASN A 427 ASN C 191 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106480 restraints weight = 16672.215| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.76 r_work: 0.3150 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12868 Z= 0.149 Angle : 0.501 10.468 17396 Z= 0.259 Chirality : 0.040 0.129 1908 Planarity : 0.003 0.059 2208 Dihedral : 3.733 14.727 1740 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.85 % Allowed : 18.62 % Favored : 79.53 % 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: 1.43 (0.21), residues: 1576 helix: 2.34 (0.22), residues: 532 sheet: 1.09 (0.44), residues: 148 loop : 0.12 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 395 HIS 0.011 0.001 HIS C 191 PHE 0.010 0.001 PHE D 374 TYR 0.013 0.001 TYR A 328 ARG 0.014 0.000 ARG A 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4751.91 seconds wall clock time: 85 minutes 21.60 seconds (5121.60 seconds total)