Starting phenix.real_space_refine on Mon Dec 11 22:36:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekl_28206/12_2023/8ekl_28206.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekl_28206/12_2023/8ekl_28206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekl_28206/12_2023/8ekl_28206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekl_28206/12_2023/8ekl_28206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekl_28206/12_2023/8ekl_28206.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekl_28206/12_2023/8ekl_28206.pdb" } resolution = 3.06 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= 0.001 sd= 0.052 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: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 35 5.16 5 C 12061 2.51 5 N 3157 2.21 5 O 4067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 263": "OE1" <-> "OE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B ASP 417": "OD1" <-> "OD2" Residue "B ASP 471": "OD1" <-> "OD2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 582": "OD1" <-> "OD2" Residue "C ASP 417": "OD1" <-> "OD2" Residue "C ASP 471": "OD1" <-> "OD2" Residue "C ASP 511": "OD1" <-> "OD2" Residue "D ASP 471": "OD1" <-> "OD2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 417": "OD1" <-> "OD2" Residue "E ASP 471": "OD1" <-> "OD2" Residue "E PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 471": "OD1" <-> "OD2" Residue "F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 522": "OE1" <-> "OE2" Residue "G ASP 471": "OD1" <-> "OD2" Residue "G PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 511": "OD1" <-> "OD2" Residue "G GLU 524": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 19334 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "B" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "C" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "D" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "E" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "F" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "G" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.96, per 1000 atoms: 0.52 Number of scatterers: 19334 At special positions: 0 Unit cell: (139.573, 139.573, 124.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 35 16.00 O 4067 8.00 N 3157 7.00 C 12061 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: 7.12 Conformation dependent library (CDL) restraints added in 3.7 seconds 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4634 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 50 sheets defined 22.0% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.506A pdb=" N ALA A 250 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.771A pdb=" N LYS A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 512 removed outlier: 4.506A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 581 through 595 removed outlier: 3.560A pdb=" N ASP A 590 " --> pdb=" O ASN A 586 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.506A pdb=" N ALA B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 425 through 429 removed outlier: 4.019A pdb=" N ILE B 429 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.906A pdb=" N LYS B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 512 removed outlier: 4.489A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 581 through 595 removed outlier: 3.893A pdb=" N ASP B 590 " --> pdb=" O ASN B 586 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B 591 " --> pdb=" O LYS B 587 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'C' and resid 249 through 254 removed outlier: 3.567A pdb=" N GLY C 253 " --> pdb=" O PHE C 249 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 254' Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 463 through 471 removed outlier: 3.919A pdb=" N LYS C 469 " --> pdb=" O ASP C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 512 removed outlier: 4.549A pdb=" N SER C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 581 through 594 removed outlier: 3.730A pdb=" N ASP C 590 " --> pdb=" O ASN C 586 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 246 through 253 removed outlier: 3.508A pdb=" N ALA D 250 " --> pdb=" O ASP D 247 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU D 251 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.542A pdb=" N ARG D 290 " --> pdb=" O THR D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.957A pdb=" N ILE D 429 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 503 through 512 removed outlier: 4.492A pdb=" N SER D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLN D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 512 " --> pdb=" O SER D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 556 Processing helix chain 'D' and resid 581 through 590 removed outlier: 3.787A pdb=" N ASP D 590 " --> pdb=" O ASN D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 253 removed outlier: 4.066A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 463 through 471 removed outlier: 3.875A pdb=" N LYS E 469 " --> pdb=" O ASP E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 512 removed outlier: 4.554A pdb=" N SER E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLN E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 581 through 594 removed outlier: 3.807A pdb=" N ASP E 590 " --> pdb=" O ASN E 586 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER E 591 " --> pdb=" O LYS E 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 592 " --> pdb=" O ILE E 588 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR E 594 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'F' and resid 227 through 234 removed outlier: 3.796A pdb=" N GLU F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN F 233 " --> pdb=" O SER F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 253 removed outlier: 4.023A pdb=" N GLU F 251 " --> pdb=" O SER F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 463 through 471 removed outlier: 3.625A pdb=" N LYS F 469 " --> pdb=" O ASP F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 512 removed outlier: 4.594A pdb=" N SER F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN F 509 " --> pdb=" O ASP F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 581 through 590 removed outlier: 3.834A pdb=" N ASP F 590 " --> pdb=" O ASN F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 Processing helix chain 'G' and resid 227 through 234 removed outlier: 3.705A pdb=" N GLU G 231 " --> pdb=" O PRO G 227 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG G 232 " --> pdb=" O ASP G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 253 removed outlier: 3.515A pdb=" N ALA G 250 " --> pdb=" O ASP G 247 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU G 251 " --> pdb=" O SER G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 290 Processing helix chain 'G' and resid 463 through 471 removed outlier: 3.780A pdb=" N LYS G 469 " --> pdb=" O ASP G 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 512 removed outlier: 4.593A pdb=" N SER G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLN G 509 " --> pdb=" O ASP G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 556 Processing helix chain 'G' and resid 581 through 590 removed outlier: 3.843A pdb=" N ASP G 590 " --> pdb=" O ASN G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 311 removed outlier: 6.664A pdb=" N ASN A 392 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 439 removed outlier: 3.979A pdb=" N ALA A 387 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 372 through 382 removed outlier: 3.621A pdb=" N SER D 380 " --> pdb=" O HIS D 314 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 374 through 382 current: chain 'C' and resid 313 through 322 removed outlier: 3.527A pdb=" N LYS C 321 " --> pdb=" O TRP B 375 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 374 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 316 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 321 " --> pdb=" O TRP G 375 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP G 375 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER G 374 " --> pdb=" O GLY G 320 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 320 " --> pdb=" O SER G 374 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER G 380 " --> pdb=" O HIS G 314 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER F 374 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY F 320 " --> pdb=" O SER F 374 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS F 321 " --> pdb=" O TRP E 375 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP E 375 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER E 374 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY E 320 " --> pdb=" O SER E 374 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS E 321 " --> pdb=" O TRP D 375 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP D 375 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 374 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 320 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 320 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 374 " --> pdb=" O GLY D 320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.792A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 531 Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA9, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 311 removed outlier: 5.556A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 438 through 439 removed outlier: 3.938A pdb=" N ALA B 387 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.677A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS B 405 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 485 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB5, first strand: chain 'B' and resid 526 through 531 Processing sheet with id=AB6, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AB7, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 311 removed outlier: 6.666A pdb=" N ASN C 392 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 438 through 439 removed outlier: 3.546A pdb=" N TYR C 439 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 387 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.758A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS C 405 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY C 485 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR C 407 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL C 483 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AC3, first strand: chain 'C' and resid 524 through 531 removed outlier: 3.809A pdb=" N GLU C 524 " --> pdb=" O THR C 521 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AC5, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AC6, first strand: chain 'D' and resid 301 through 311 removed outlier: 6.696A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 301 through 311 removed outlier: 6.696A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA D 387 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.719A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LYS D 405 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN D 486 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 482 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN D 411 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N THR D 480 " --> pdb=" O ASN D 411 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL D 413 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU D 478 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD1, first strand: chain 'D' and resid 524 through 531 removed outlier: 3.825A pdb=" N GLU D 524 " --> pdb=" O THR D 521 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N ILE D 611 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AD3, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AD4, first strand: chain 'E' and resid 301 through 311 removed outlier: 6.712A pdb=" N ASN E 392 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU E 307 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN E 390 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE E 309 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR E 388 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 438 through 439 removed outlier: 4.012A pdb=" N ALA E 387 " --> pdb=" O ILE E 462 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.778A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS E 405 " --> pdb=" O GLY E 485 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY E 485 " --> pdb=" O LYS E 405 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR E 407 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL E 483 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR E 409 " --> pdb=" O THR E 481 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AD8, first strand: chain 'E' and resid 524 through 531 removed outlier: 3.822A pdb=" N GLU E 524 " --> pdb=" O THR E 521 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N ILE E 611 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AE1, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AE2, first strand: chain 'F' and resid 300 through 311 removed outlier: 5.811A pdb=" N VAL F 302 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR F 396 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N MET F 304 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG F 394 " --> pdb=" O MET F 304 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS F 306 " --> pdb=" O ASN F 392 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 438 through 439 removed outlier: 3.523A pdb=" N TYR F 439 " --> pdb=" O TYR F 395 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA F 387 " --> pdb=" O ILE F 462 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.690A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS F 405 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY F 485 " --> pdb=" O LYS F 405 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR F 407 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N VAL F 483 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 489 through 490 Processing sheet with id=AE6, first strand: chain 'F' and resid 526 through 531 removed outlier: 9.296A pdb=" N ILE F 611 " --> pdb=" O SER F 514 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER F 516 " --> pdb=" O ILE F 611 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE F 613 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 518 " --> pdb=" O ILE F 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AE8, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AE9, first strand: chain 'G' and resid 301 through 311 removed outlier: 6.876A pdb=" N ASN G 392 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 438 through 439 removed outlier: 3.972A pdb=" N ALA G 387 " --> pdb=" O ILE G 462 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.823A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS G 405 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN G 486 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN G 482 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN G 411 " --> pdb=" O THR G 480 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N THR G 480 " --> pdb=" O ASN G 411 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL G 413 " --> pdb=" O LEU G 478 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU G 478 " --> pdb=" O VAL G 413 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AF4, first strand: chain 'G' and resid 526 through 531 Processing sheet with id=AF5, first strand: chain 'G' and resid 558 through 559 592 hydrogen bonds defined for protein. 1464 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: 5.97 Time building geometry restraints manager: 7.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6419 1.34 - 1.46: 3530 1.46 - 1.57: 9616 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 19628 Sorted by residual: bond pdb=" CB ASP E 471 " pdb=" CG ASP E 471 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.35e+00 bond pdb=" CB ASP A 471 " pdb=" CG ASP A 471 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.32e+00 bond pdb=" CB ASP B 471 " pdb=" CG ASP B 471 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.30e+00 bond pdb=" CB ASP G 471 " pdb=" CG ASP G 471 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.24e+00 bond pdb=" CB ASP F 471 " pdb=" CG ASP F 471 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.13e+00 ... (remaining 19623 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.72: 427 106.72 - 113.54: 10970 113.54 - 120.35: 6830 120.35 - 127.17: 8250 127.17 - 133.98: 123 Bond angle restraints: 26600 Sorted by residual: angle pdb=" CA GLU A 522 " pdb=" CB GLU A 522 " pdb=" CG GLU A 522 " ideal model delta sigma weight residual 114.10 120.34 -6.24 2.00e+00 2.50e-01 9.72e+00 angle pdb=" CA GLU G 522 " pdb=" CB GLU G 522 " pdb=" CG GLU G 522 " ideal model delta sigma weight residual 114.10 120.22 -6.12 2.00e+00 2.50e-01 9.36e+00 angle pdb=" C GLU G 522 " pdb=" CA GLU G 522 " pdb=" CB GLU G 522 " ideal model delta sigma weight residual 109.53 114.32 -4.79 1.65e+00 3.67e-01 8.42e+00 angle pdb=" C ARG G 290 " pdb=" N ASP G 291 " pdb=" CA ASP G 291 " ideal model delta sigma weight residual 120.97 113.58 7.39 2.84e+00 1.24e-01 6.76e+00 angle pdb=" C GLU A 522 " pdb=" CA GLU A 522 " pdb=" CB GLU A 522 " ideal model delta sigma weight residual 109.53 113.77 -4.24 1.65e+00 3.67e-01 6.61e+00 ... (remaining 26595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10050 17.97 - 35.95: 1396 35.95 - 53.92: 442 53.92 - 71.89: 68 71.89 - 89.87: 35 Dihedral angle restraints: 11991 sinusoidal: 4760 harmonic: 7231 Sorted by residual: dihedral pdb=" CA ASN G 223 " pdb=" C ASN G 223 " pdb=" N ASP G 224 " pdb=" CA ASP G 224 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASN C 223 " pdb=" C ASN C 223 " pdb=" N ASP C 224 " pdb=" CA ASP C 224 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASN A 223 " pdb=" C ASN A 223 " pdb=" N ASP A 224 " pdb=" CA ASP A 224 " ideal model delta harmonic sigma weight residual 180.00 158.16 21.84 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 11988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1752 0.028 - 0.057: 784 0.057 - 0.085: 255 0.085 - 0.113: 183 0.113 - 0.141: 50 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CA ILE A 460 " pdb=" N ILE A 460 " pdb=" C ILE A 460 " pdb=" CB ILE A 460 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE G 460 " pdb=" N ILE G 460 " pdb=" C ILE G 460 " pdb=" CB ILE G 460 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE D 460 " pdb=" N ILE D 460 " pdb=" C ILE D 460 " pdb=" CB ILE D 460 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 3021 not shown) Planarity restraints: 3472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 269 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO B 270 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 269 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO C 270 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 270 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 270 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 522 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.56e+00 pdb=" C GLU A 522 " 0.022 2.00e-02 2.50e+03 pdb=" O GLU A 522 " -0.008 2.00e-02 2.50e+03 pdb=" N ASN A 523 " -0.007 2.00e-02 2.50e+03 ... (remaining 3469 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 455 2.67 - 3.23: 16720 3.23 - 3.79: 27800 3.79 - 4.34: 40059 4.34 - 4.90: 68324 Nonbonded interactions: 153358 Sorted by model distance: nonbonded pdb=" OE1 GLU G 522 " pdb=" ND2 ASN G 523 " model vdw 2.117 2.520 nonbonded pdb=" OD1 ASP C 222 " pdb="CA CA C 901 " model vdw 2.183 2.510 nonbonded pdb=" OE1 GLU A 522 " pdb=" ND2 ASN A 523 " model vdw 2.193 2.520 nonbonded pdb=" OD1 ASP E 222 " pdb="CA CA E 901 " model vdw 2.194 2.510 nonbonded pdb=" OD1 ASP A 222 " pdb="CA CA A 901 " model vdw 2.197 2.510 ... (remaining 153353 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' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.020 Extract box with map and model: 4.760 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 49.910 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.120 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 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 0.030 19628 Z= 0.175 Angle : 0.471 7.386 26600 Z= 0.256 Chirality : 0.043 0.141 3024 Planarity : 0.003 0.037 3472 Dihedral : 18.449 89.867 7357 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.18 % Allowed : 35.07 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.87 (0.16), residues: 2457 helix: -1.18 (0.25), residues: 385 sheet: 0.09 (0.21), residues: 630 loop : -0.66 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 503 HIS 0.003 0.001 HIS D 314 PHE 0.013 0.001 PHE D 281 TYR 0.009 0.001 TYR B 439 ARG 0.002 0.000 ARG C 529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 219 time to evaluate : 2.277 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 219 average time/residue: 0.2697 time to fit residues: 96.0060 Evaluate side-chains 220 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 217 time to evaluate : 2.257 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1686 time to fit residues: 3.9457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 0.5980 chunk 185 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 125 optimal weight: 0.3980 chunk 99 optimal weight: 9.9990 chunk 192 optimal weight: 0.4980 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN B 425 GLN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.0538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19628 Z= 0.261 Angle : 0.500 8.002 26600 Z= 0.268 Chirality : 0.044 0.143 3024 Planarity : 0.004 0.044 3472 Dihedral : 4.328 22.834 2646 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.87 % Allowed : 33.04 % Favored : 63.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.98 (0.16), residues: 2457 helix: -1.23 (0.23), residues: 434 sheet: 0.27 (0.21), residues: 616 loop : -0.85 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 503 HIS 0.002 0.000 HIS F 314 PHE 0.020 0.002 PHE C 281 TYR 0.012 0.001 TYR B 439 ARG 0.002 0.000 ARG G 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 215 time to evaluate : 2.303 Fit side-chains outliers start: 84 outliers final: 48 residues processed: 283 average time/residue: 0.2600 time to fit residues: 120.8987 Evaluate side-chains 259 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 211 time to evaluate : 2.449 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.1874 time to fit residues: 19.7045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 61 optimal weight: 0.0270 chunk 222 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 198 optimal weight: 0.9990 chunk 221 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 178 optimal weight: 7.9990 overall best weight: 2.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN B 425 GLN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 ASN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19628 Z= 0.278 Angle : 0.503 8.288 26600 Z= 0.269 Chirality : 0.045 0.142 3024 Planarity : 0.004 0.044 3472 Dihedral : 4.419 23.603 2646 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.30 % Allowed : 33.92 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.00 (0.16), residues: 2457 helix: -1.19 (0.23), residues: 427 sheet: 0.26 (0.21), residues: 616 loop : -0.89 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 503 HIS 0.001 0.000 HIS D 314 PHE 0.022 0.002 PHE G 281 TYR 0.017 0.001 TYR C 396 ARG 0.002 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 213 time to evaluate : 2.266 Fit side-chains outliers start: 50 outliers final: 28 residues processed: 257 average time/residue: 0.2651 time to fit residues: 111.3002 Evaluate side-chains 236 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 2.207 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1776 time to fit residues: 12.3647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 chunk 115 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 19628 Z= 0.233 Angle : 0.489 8.242 26600 Z= 0.260 Chirality : 0.044 0.143 3024 Planarity : 0.004 0.042 3472 Dihedral : 4.350 23.314 2646 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.57 % Allowed : 34.79 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.98 (0.16), residues: 2457 helix: -1.18 (0.23), residues: 434 sheet: 0.30 (0.21), residues: 616 loop : -0.89 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 503 HIS 0.001 0.000 HIS A 314 PHE 0.019 0.002 PHE F 281 TYR 0.016 0.001 TYR C 396 ARG 0.002 0.000 ARG G 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 215 time to evaluate : 2.160 Fit side-chains outliers start: 34 outliers final: 20 residues processed: 242 average time/residue: 0.2719 time to fit residues: 106.5829 Evaluate side-chains 230 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 210 time to evaluate : 2.230 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2167 time to fit residues: 10.4768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 0.4980 chunk 134 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 212 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 ASN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 19628 Z= 0.374 Angle : 0.555 8.900 26600 Z= 0.294 Chirality : 0.047 0.142 3024 Planarity : 0.004 0.043 3472 Dihedral : 4.647 25.663 2646 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.17 % Allowed : 34.61 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.13 (0.16), residues: 2457 helix: -1.25 (0.23), residues: 427 sheet: 0.17 (0.21), residues: 616 loop : -0.99 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 503 HIS 0.001 0.000 HIS A 314 PHE 0.030 0.003 PHE C 281 TYR 0.015 0.001 TYR C 396 ARG 0.002 0.000 ARG G 458 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 206 time to evaluate : 2.302 Fit side-chains outliers start: 47 outliers final: 27 residues processed: 245 average time/residue: 0.2710 time to fit residues: 108.6311 Evaluate side-chains 230 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 2.424 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1825 time to fit residues: 12.4998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 139 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 237 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 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 411 ASN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19628 Z= 0.268 Angle : 0.508 8.813 26600 Z= 0.270 Chirality : 0.045 0.144 3024 Planarity : 0.004 0.043 3472 Dihedral : 4.505 25.343 2646 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.61 % Allowed : 34.88 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2457 helix: -1.21 (0.23), residues: 434 sheet: 0.21 (0.21), residues: 616 loop : -0.97 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 503 HIS 0.001 0.000 HIS F 314 PHE 0.022 0.002 PHE C 281 TYR 0.014 0.001 TYR C 396 ARG 0.001 0.000 ARG G 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 210 time to evaluate : 2.043 Fit side-chains outliers start: 35 outliers final: 19 residues processed: 232 average time/residue: 0.2573 time to fit residues: 96.9756 Evaluate side-chains 226 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 207 time to evaluate : 2.029 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1710 time to fit residues: 8.8129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 173 optimal weight: 0.0170 chunk 134 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 236 optimal weight: 8.9990 chunk 147 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 ASN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19628 Z= 0.138 Angle : 0.444 7.927 26600 Z= 0.237 Chirality : 0.042 0.143 3024 Planarity : 0.004 0.039 3472 Dihedral : 4.083 21.808 2646 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.55 % Allowed : 35.62 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.82 (0.16), residues: 2457 helix: -0.98 (0.23), residues: 434 sheet: 0.28 (0.20), residues: 616 loop : -0.74 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 375 HIS 0.001 0.000 HIS F 314 PHE 0.008 0.001 PHE G 281 TYR 0.015 0.001 TYR C 396 ARG 0.002 0.000 ARG C 529 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 223 time to evaluate : 2.136 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 233 average time/residue: 0.2755 time to fit residues: 104.1165 Evaluate side-chains 214 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 210 time to evaluate : 2.527 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1957 time to fit residues: 4.9021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 ASN ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 ASN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 19628 Z= 0.399 Angle : 0.571 8.738 26600 Z= 0.302 Chirality : 0.047 0.147 3024 Planarity : 0.004 0.046 3472 Dihedral : 4.646 26.014 2646 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.01 % Allowed : 35.94 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.16), residues: 2457 helix: -1.17 (0.23), residues: 427 sheet: 0.24 (0.21), residues: 616 loop : -0.94 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 503 HIS 0.002 0.001 HIS F 314 PHE 0.033 0.003 PHE G 281 TYR 0.013 0.002 TYR B 439 ARG 0.002 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 200 time to evaluate : 2.440 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 217 average time/residue: 0.2762 time to fit residues: 98.0015 Evaluate side-chains 213 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 199 time to evaluate : 2.252 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1712 time to fit residues: 7.6944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 0.9980 chunk 226 optimal weight: 0.5980 chunk 206 optimal weight: 1.9990 chunk 220 optimal weight: 8.9990 chunk 132 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 ASN ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 ASN G 425 GLN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19628 Z= 0.143 Angle : 0.457 8.355 26600 Z= 0.244 Chirality : 0.043 0.141 3024 Planarity : 0.004 0.043 3472 Dihedral : 4.157 23.039 2646 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.41 % Allowed : 35.90 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2457 helix: -0.97 (0.23), residues: 434 sheet: 0.60 (0.21), residues: 602 loop : -0.86 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 375 HIS 0.001 0.000 HIS B 314 PHE 0.008 0.001 PHE G 281 TYR 0.014 0.001 TYR C 396 ARG 0.001 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 213 time to evaluate : 2.437 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 218 average time/residue: 0.2668 time to fit residues: 95.2455 Evaluate side-chains 217 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 212 time to evaluate : 2.188 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1758 time to fit residues: 4.6177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 142 optimal weight: 0.3980 chunk 110 optimal weight: 0.8980 chunk 161 optimal weight: 0.0980 chunk 244 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 194 optimal weight: 0.0010 chunk 20 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN C 425 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 ASN ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 GLN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19628 Z= 0.123 Angle : 0.432 7.896 26600 Z= 0.230 Chirality : 0.042 0.145 3024 Planarity : 0.004 0.043 3472 Dihedral : 3.866 19.009 2646 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.09 % Allowed : 36.27 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.55 (0.17), residues: 2457 helix: -0.70 (0.24), residues: 434 sheet: 0.64 (0.21), residues: 602 loop : -0.67 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 503 HIS 0.000 0.000 HIS E 314 PHE 0.010 0.001 PHE E 281 TYR 0.014 0.001 TYR C 396 ARG 0.002 0.000 ARG C 529 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 233 time to evaluate : 2.503 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 234 average time/residue: 0.2771 time to fit residues: 105.5988 Evaluate side-chains 214 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 2.318 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1679 time to fit residues: 3.3238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 179 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 ASN D 376 ASN ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 ASN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.121936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.098010 restraints weight = 27528.626| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.15 r_work: 0.3017 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19628 Z= 0.301 Angle : 0.508 8.270 26600 Z= 0.270 Chirality : 0.045 0.144 3024 Planarity : 0.004 0.046 3472 Dihedral : 4.276 23.396 2646 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.32 % Allowed : 36.18 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.16), residues: 2457 helix: -0.88 (0.24), residues: 434 sheet: 0.51 (0.21), residues: 616 loop : -0.80 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 503 HIS 0.001 0.001 HIS F 314 PHE 0.023 0.002 PHE A 281 TYR 0.014 0.001 TYR E 396 ARG 0.002 0.000 ARG C 458 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3695.03 seconds wall clock time: 68 minutes 35.92 seconds (4115.92 seconds total)