Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 17:44:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlg_22243/08_2023/6xlg_22243_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlg_22243/08_2023/6xlg_22243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlg_22243/08_2023/6xlg_22243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlg_22243/08_2023/6xlg_22243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlg_22243/08_2023/6xlg_22243_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlg_22243/08_2023/6xlg_22243_updated.pdb" } resolution = 2.71 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 6 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 7836 2.51 5 N 2010 2.21 5 O 2378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 11": "OE1" <-> "OE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B ARG 595": "NH1" <-> "NH2" Residue "B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 12258 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4906 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 20, 'TRANS': 586} Chain breaks: 3 Chain: "B" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4906 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 20, 'TRANS': 586} Chain breaks: 3 Chain: "C" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1190 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "D" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1190 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.53, per 1000 atoms: 0.53 Number of scatterers: 12258 At special positions: 0 Unit cell: (106.038, 96.174, 131.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 24 16.00 P 6 15.00 Mg 2 11.99 O 2378 8.00 N 2010 7.00 C 7836 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: 4.74 Conformation dependent library (CDL) restraints added in 2.0 seconds 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2872 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 10 sheets defined 36.0% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 4.460A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 50 removed outlier: 3.792A pdb=" N ILE A 35 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE A 45 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG A 46 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 385 through 405 Processing helix chain 'A' and resid 407 through 427 removed outlier: 4.127A pdb=" N LYS A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LYS A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 removed outlier: 4.011A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 476 through 479 No H-bonds generated for 'chain 'A' and resid 476 through 479' Processing helix chain 'A' and resid 482 through 489 removed outlier: 4.290A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 488 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 removed outlier: 3.853A pdb=" N GLU A 503 " --> pdb=" O PRO A 500 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 507 " --> pdb=" O TYR A 504 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 542 removed outlier: 3.923A pdb=" N LYS A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 removed outlier: 3.606A pdb=" N ILE A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 589 Processing helix chain 'A' and resid 616 through 627 Processing helix chain 'A' and resid 633 through 650 Processing helix chain 'A' and resid 657 through 671 Processing helix chain 'B' and resid 12 through 21 removed outlier: 4.464A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 50 removed outlier: 3.527A pdb=" N GLU B 33 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 35 " --> pdb=" O ARG B 32 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE B 45 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG B 46 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 182 through 185 Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 385 through 405 Processing helix chain 'B' and resid 407 through 427 removed outlier: 4.125A pdb=" N LYS B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 416 " --> pdb=" O LYS B 412 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LYS B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASN B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 removed outlier: 4.023A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 476 through 479 No H-bonds generated for 'chain 'B' and resid 476 through 479' Processing helix chain 'B' and resid 482 through 489 removed outlier: 4.299A pdb=" N ALA B 486 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 488 " --> pdb=" O ASP B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 509 removed outlier: 3.858A pdb=" N GLU B 503 " --> pdb=" O PRO B 500 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 507 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 509 " --> pdb=" O PHE B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 542 removed outlier: 3.834A pdb=" N LYS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 554 removed outlier: 3.622A pdb=" N ILE B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 554 " --> pdb=" O LEU B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 591 Processing helix chain 'B' and resid 616 through 627 Processing helix chain 'B' and resid 633 through 650 Processing helix chain 'B' and resid 657 through 671 Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 236 through 243 removed outlier: 3.665A pdb=" N ALA C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 330 removed outlier: 3.834A pdb=" N GLU C 325 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASP C 326 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG C 327 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 329 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA C 330 " --> pdb=" O ARG C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 335 No H-bonds generated for 'chain 'C' and resid 332 through 335' Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.743A pdb=" N PHE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 243 removed outlier: 3.624A pdb=" N ALA D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 335 removed outlier: 3.839A pdb=" N GLU D 325 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP D 326 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG D 327 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG D 329 " --> pdb=" O ASP D 326 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA D 330 " --> pdb=" O ARG D 327 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN D 331 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR D 335 " --> pdb=" O PHE D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 Processing sheet with id= A, first strand: chain 'A' and resid 157 through 160 removed outlier: 7.167A pdb=" N PHE A 176 " --> pdb=" O ASP A 132 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL A 134 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG A 174 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL A 136 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 172 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER A 138 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY A 170 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE A 66 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN A 206 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 208 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 301 through 307 Processing sheet with id= C, first strand: chain 'A' and resid 516 through 519 Processing sheet with id= D, first strand: chain 'A' and resid 561 through 564 removed outlier: 8.626A pdb=" N VAL A 562 " --> pdb=" O LYS A 607 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A 609 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER A 564 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE A 611 " --> pdb=" O SER A 564 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 157 through 160 removed outlier: 7.164A pdb=" N PHE B 176 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL B 134 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG B 174 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL B 136 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL B 172 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER B 138 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY B 170 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE B 66 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLN B 206 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU B 208 " --> pdb=" O PRO B 68 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 301 through 307 Processing sheet with id= G, first strand: chain 'B' and resid 516 through 519 Processing sheet with id= H, first strand: chain 'B' and resid 561 through 564 removed outlier: 8.629A pdb=" N VAL B 562 " --> pdb=" O LYS B 607 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE B 609 " --> pdb=" O VAL B 562 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER B 564 " --> pdb=" O PHE B 609 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE B 611 " --> pdb=" O SER B 564 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 246 through 248 removed outlier: 3.766A pdb=" N GLU C 259 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL C 282 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS C 275 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS C 280 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR C 214 " --> pdb=" O GLY C 319 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 246 through 248 removed outlier: 3.763A pdb=" N GLU D 259 " --> pdb=" O LEU D 272 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 272 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL D 282 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS D 275 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS D 280 " --> pdb=" O CYS D 275 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N THR D 214 " --> pdb=" O GLY D 319 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 4044 1.37 - 1.52: 3712 1.52 - 1.66: 4686 1.66 - 1.81: 40 1.81 - 1.95: 4 Bond restraints: 12486 Sorted by residual: bond pdb=" CA LYS D 279 " pdb=" CB LYS D 279 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.69e-02 3.50e+03 3.02e-01 bond pdb=" C GLY B 170 " pdb=" O GLY B 170 " ideal model delta sigma weight residual 1.230 1.236 -0.006 1.28e-02 6.10e+03 2.50e-01 bond pdb=" CA VAL B 122 " pdb=" C VAL B 122 " ideal model delta sigma weight residual 1.520 1.525 -0.005 1.00e-02 1.00e+04 2.36e-01 bond pdb=" C1' AGS A 801 " pdb=" C2' AGS A 801 " ideal model delta sigma weight residual 1.530 1.536 -0.006 1.30e-02 5.92e+03 2.04e-01 bond pdb=" N GLU A 351 " pdb=" CA GLU A 351 " ideal model delta sigma weight residual 1.463 1.458 0.005 1.08e-02 8.57e+03 1.94e-01 ... (remaining 12481 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.11: 290 107.11 - 113.83: 6986 113.83 - 120.55: 5099 120.55 - 127.26: 4380 127.26 - 133.98: 97 Bond angle restraints: 16852 Sorted by residual: angle pdb=" C LEU B 509 " pdb=" N LYS B 510 " pdb=" CA LYS B 510 " ideal model delta sigma weight residual 121.54 124.83 -3.29 1.91e+00 2.74e-01 2.97e+00 angle pdb=" C LEU A 509 " pdb=" N LYS A 510 " pdb=" CA LYS A 510 " ideal model delta sigma weight residual 121.54 124.78 -3.24 1.91e+00 2.74e-01 2.88e+00 angle pdb=" C GLU B 351 " pdb=" N ASP B 352 " pdb=" CA ASP B 352 " ideal model delta sigma weight residual 123.25 120.59 2.66 1.69e+00 3.50e-01 2.48e+00 angle pdb=" NE ARG D 327 " pdb=" CZ ARG D 327 " pdb=" NH1 ARG D 327 " ideal model delta sigma weight residual 121.50 119.99 1.51 1.00e+00 1.00e+00 2.29e+00 angle pdb=" NE ARG A 275 " pdb=" CZ ARG A 275 " pdb=" NH1 ARG A 275 " ideal model delta sigma weight residual 121.50 120.02 1.48 1.00e+00 1.00e+00 2.19e+00 ... (remaining 16847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 7536 34.71 - 69.43: 29 69.43 - 104.14: 27 104.14 - 138.85: 0 138.85 - 173.57: 2 Dihedral angle restraints: 7594 sinusoidal: 3184 harmonic: 4410 Sorted by residual: dihedral pdb=" O1A AGS B 801 " pdb=" O3A AGS B 801 " pdb=" PA AGS B 801 " pdb=" PB AGS B 801 " ideal model delta sinusoidal sigma weight residual -67.73 105.84 -173.57 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS A 801 " pdb=" O3A AGS A 801 " pdb=" PA AGS A 801 " pdb=" PB AGS A 801 " ideal model delta sinusoidal sigma weight residual -67.73 102.91 -170.64 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N GLU B 544 " pdb=" CA GLU B 544 " pdb=" CB GLU B 544 " pdb=" CG GLU B 544 " ideal model delta sinusoidal sigma weight residual 180.00 -130.55 -49.45 3 1.50e+01 4.44e-03 8.78e+00 ... (remaining 7591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1114 0.025 - 0.051: 494 0.051 - 0.076: 157 0.076 - 0.102: 62 0.102 - 0.127: 59 Chirality restraints: 1886 Sorted by residual: chirality pdb=" CA ILE A 319 " pdb=" N ILE A 319 " pdb=" C ILE A 319 " pdb=" CB ILE A 319 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA ILE B 319 " pdb=" N ILE B 319 " pdb=" C ILE B 319 " pdb=" CB ILE B 319 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 1883 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " -0.016 5.00e-02 4.00e+02 2.45e-02 9.60e-01 pdb=" N PRO A 355 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 354 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.07e-01 pdb=" N PRO B 355 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO B 355 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 355 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 320 " 0.015 5.00e-02 4.00e+02 2.25e-02 8.11e-01 pdb=" N PRO C 321 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO C 321 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 321 " 0.013 5.00e-02 4.00e+02 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.71: 328 2.71 - 3.32: 13786 3.32 - 3.93: 24167 3.93 - 4.53: 33109 4.53 - 5.14: 51457 Nonbonded interactions: 122847 Sorted by model distance: nonbonded pdb=" O2G AGS B 801 " pdb="MG MG B 802 " model vdw 2.105 2.170 nonbonded pdb=" O2G AGS A 801 " pdb="MG MG A 802 " model vdw 2.106 2.170 nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.137 2.170 nonbonded pdb=" OD1 ASN A 37 " pdb="MG MG A 802 " model vdw 2.141 2.170 nonbonded pdb=" O TRP D 242 " pdb=" OG SER D 339 " model vdw 2.253 2.440 ... (remaining 122842 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' } ncs_group { reference = 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: 1.530 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: 7.980 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 34.950 Find NCS groups from input model: 0.660 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:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.001 0.012 12486 Z= 0.076 Angle : 0.356 4.802 16852 Z= 0.206 Chirality : 0.037 0.127 1886 Planarity : 0.002 0.024 2148 Dihedral : 10.115 173.566 4722 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.18), residues: 1484 helix: -2.39 (0.16), residues: 568 sheet: -1.01 (0.27), residues: 338 loop : -1.96 (0.22), residues: 578 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 1.4223 time to fit residues: 638.7565 Evaluate side-chains 195 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.476 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 44 optimal weight: 0.0770 chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 92 ASN A 135 GLN A 145 GLN A 282 GLN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 430 GLN A 508 GLN A 557 GLN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN B 14 GLN B 92 ASN B 135 GLN B 145 GLN B 282 GLN B 409 GLN B 430 GLN B 508 GLN B 557 GLN ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN C 212 ASN C 223 ASN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN D 223 ASN D 284 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 12486 Z= 0.231 Angle : 0.552 8.180 16852 Z= 0.289 Chirality : 0.043 0.157 1886 Planarity : 0.004 0.045 2148 Dihedral : 7.870 179.285 1622 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.20), residues: 1484 helix: -1.17 (0.19), residues: 578 sheet: -0.66 (0.27), residues: 328 loop : -1.33 (0.24), residues: 578 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 203 time to evaluate : 1.501 Fit side-chains revert: symmetry clash outliers start: 52 outliers final: 19 residues processed: 236 average time/residue: 1.3718 time to fit residues: 349.5882 Evaluate side-chains 170 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 1.444 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 6 average time/residue: 0.1130 time to fit residues: 3.2469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 111 optimal weight: 0.0970 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 134 optimal weight: 0.0570 chunk 145 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN B 430 GLN ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 ASN D 331 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 12486 Z= 0.265 Angle : 0.536 5.520 16852 Z= 0.284 Chirality : 0.043 0.159 1886 Planarity : 0.004 0.044 2148 Dihedral : 7.858 155.964 1622 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 4.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1484 helix: -0.60 (0.20), residues: 580 sheet: -0.41 (0.28), residues: 328 loop : -1.02 (0.25), residues: 576 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 160 time to evaluate : 1.672 Fit side-chains outliers start: 60 outliers final: 19 residues processed: 203 average time/residue: 1.3488 time to fit residues: 295.2518 Evaluate side-chains 161 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 1.370 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.1132 time to fit residues: 2.7074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 135 optimal weight: 0.4980 chunk 143 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 128 optimal weight: 0.0270 chunk 38 optimal weight: 0.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN A 592 GLN B 430 GLN B 592 GLN C 223 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 ASN D 314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 12486 Z= 0.136 Angle : 0.456 5.224 16852 Z= 0.240 Chirality : 0.040 0.139 1886 Planarity : 0.003 0.032 2148 Dihedral : 7.815 158.206 1622 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.21), residues: 1484 helix: -0.19 (0.21), residues: 576 sheet: -0.34 (0.28), residues: 328 loop : -0.66 (0.25), residues: 580 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 150 time to evaluate : 1.416 Fit side-chains outliers start: 40 outliers final: 20 residues processed: 178 average time/residue: 1.2463 time to fit residues: 242.2915 Evaluate side-chains 159 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 1.522 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 5 average time/residue: 0.1382 time to fit residues: 3.3301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 chunk 98 optimal weight: 0.0470 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 ASN D 247 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12486 Z= 0.198 Angle : 0.486 9.069 16852 Z= 0.253 Chirality : 0.041 0.141 1886 Planarity : 0.003 0.032 2148 Dihedral : 7.770 152.787 1622 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1484 helix: -0.05 (0.21), residues: 576 sheet: -0.28 (0.28), residues: 328 loop : -0.54 (0.26), residues: 580 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 152 time to evaluate : 1.508 Fit side-chains outliers start: 47 outliers final: 22 residues processed: 182 average time/residue: 1.2929 time to fit residues: 256.0303 Evaluate side-chains 166 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 1.495 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 0.1711 time to fit residues: 3.1233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.9990 chunk 128 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN C 284 HIS C 295 ASN D 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 12486 Z= 0.159 Angle : 0.464 8.447 16852 Z= 0.241 Chirality : 0.041 0.142 1886 Planarity : 0.003 0.044 2148 Dihedral : 7.750 151.981 1622 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.22), residues: 1484 helix: 0.07 (0.22), residues: 576 sheet: -0.22 (0.28), residues: 326 loop : -0.44 (0.26), residues: 582 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 152 time to evaluate : 1.497 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 27 residues processed: 181 average time/residue: 1.2868 time to fit residues: 253.3805 Evaluate side-chains 172 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 1.423 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 20 residues processed: 7 average time/residue: 0.8184 time to fit residues: 8.2970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN D 223 ASN D 295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 12486 Z= 0.355 Angle : 0.576 7.079 16852 Z= 0.300 Chirality : 0.046 0.222 1886 Planarity : 0.004 0.035 2148 Dihedral : 7.885 141.000 1622 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 3.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1484 helix: -0.13 (0.21), residues: 576 sheet: -0.21 (0.29), residues: 324 loop : -0.45 (0.25), residues: 584 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 151 time to evaluate : 1.492 Fit side-chains outliers start: 46 outliers final: 22 residues processed: 185 average time/residue: 1.3082 time to fit residues: 263.1120 Evaluate side-chains 167 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.544 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 15 residues processed: 7 average time/residue: 0.8847 time to fit residues: 8.9569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN B 14 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN D 223 ASN D 284 HIS D 314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 12486 Z= 0.165 Angle : 0.485 7.459 16852 Z= 0.253 Chirality : 0.041 0.143 1886 Planarity : 0.003 0.033 2148 Dihedral : 7.793 143.075 1622 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1484 helix: 0.02 (0.22), residues: 576 sheet: -0.26 (0.28), residues: 328 loop : -0.34 (0.26), residues: 580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.684 Fit side-chains outliers start: 32 outliers final: 24 residues processed: 173 average time/residue: 1.2634 time to fit residues: 238.3981 Evaluate side-chains 168 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.556 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 8 average time/residue: 0.7998 time to fit residues: 9.3248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 104 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN C 223 ASN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN D 212 ASN D 223 ASN D 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 12486 Z= 0.165 Angle : 0.486 7.136 16852 Z= 0.252 Chirality : 0.041 0.139 1886 Planarity : 0.004 0.048 2148 Dihedral : 7.757 144.347 1622 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1484 helix: 0.13 (0.22), residues: 580 sheet: -0.27 (0.28), residues: 328 loop : -0.28 (0.26), residues: 576 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 149 time to evaluate : 1.567 Fit side-chains outliers start: 31 outliers final: 20 residues processed: 172 average time/residue: 1.2489 time to fit residues: 234.9405 Evaluate side-chains 165 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 1.491 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.5498 time to fit residues: 4.7229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 97 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 125 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN C 314 GLN D 212 ASN D 223 ASN D 314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 12486 Z= 0.148 Angle : 0.474 7.095 16852 Z= 0.247 Chirality : 0.041 0.140 1886 Planarity : 0.003 0.033 2148 Dihedral : 7.729 145.326 1622 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1484 helix: 0.21 (0.22), residues: 580 sheet: -0.27 (0.28), residues: 330 loop : -0.21 (0.26), residues: 574 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 1.546 Fit side-chains outliers start: 22 outliers final: 17 residues processed: 172 average time/residue: 1.2761 time to fit residues: 239.4680 Evaluate side-chains 163 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.1108 time to fit residues: 2.4539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN D 212 ASN D 314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107244 restraints weight = 17048.738| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.75 r_work: 0.3164 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12486 Z= 0.206 Angle : 0.506 6.788 16852 Z= 0.263 Chirality : 0.042 0.149 1886 Planarity : 0.004 0.043 2148 Dihedral : 7.761 143.794 1622 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1484 helix: 0.18 (0.22), residues: 580 sheet: -0.25 (0.28), residues: 328 loop : -0.25 (0.26), residues: 576 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4985.19 seconds wall clock time: 89 minutes 18.26 seconds (5358.26 seconds total)