Starting phenix.real_space_refine on Fri Jan 19 16:05:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz7_25563/01_2024/7sz7_25563.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz7_25563/01_2024/7sz7_25563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz7_25563/01_2024/7sz7_25563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz7_25563/01_2024/7sz7_25563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz7_25563/01_2024/7sz7_25563.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz7_25563/01_2024/7sz7_25563.pdb" } resolution = 3.4 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1694 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 6306 2.51 5 N 1824 2.21 5 O 1956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 48": "NH1" <-> "NH2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "B GLU 2": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B GLU 521": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "D ARG 42": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10218 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4723 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 30, 'TRANS': 583} Chain: "C" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 386 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "B" Number of atoms: 4723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4723 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 30, 'TRANS': 583} Chain: "D" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 386 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Time building chain proxies: 5.80, per 1000 atoms: 0.57 Number of scatterers: 10218 At special positions: 0 Unit cell: (80.955, 144.64, 130.607, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 1956 8.00 N 1824 7.00 C 6306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 34 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 224 " distance=2.03 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 267 " distance=2.03 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 502 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 593 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 612 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 21 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 32 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 175 " distance=2.02 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 227 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 267 " distance=2.03 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 283 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 491 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 499 " distance=2.04 Simple disulfide: pdb=" SG CYS B 502 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 547 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 555 " distance=2.05 Simple disulfide: pdb=" SG CYS B 558 " - pdb=" SG CYS B 567 " distance=2.05 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 593 " distance=2.04 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 612 " distance=2.04 Simple disulfide: pdb=" SG CYS D 8 " - pdb=" SG CYS D 21 " distance=2.04 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 32 " distance=2.03 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 43 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.84 Conformation dependent library (CDL) restraints added in 1.9 seconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2444 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 26 sheets defined 13.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 removed outlier: 4.424A pdb=" N LEU A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.685A pdb=" N LEU A 55 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR A 57 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.600A pdb=" N ASN A 91 " --> pdb=" O TYR A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.799A pdb=" N GLY A 173 " --> pdb=" O CYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 removed outlier: 4.016A pdb=" N ASP A 206 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS A 207 " --> pdb=" O PRO A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 207' Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 348 through 354 removed outlier: 4.269A pdb=" N PHE A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.577A pdb=" N LEU A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.613A pdb=" N PHE A 396 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 410 removed outlier: 3.824A pdb=" N GLY A 410 " --> pdb=" O LYS A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 407 through 410' Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 471 through 476 Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.655A pdb=" N CYS A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 608 through 612 removed outlier: 4.050A pdb=" N GLY A 611 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N CYS A 612 " --> pdb=" O LEU A 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 608 through 612' Processing helix chain 'B' and resid 19 through 32 removed outlier: 3.815A pdb=" N MET B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.659A pdb=" N SER B 137 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 138 " --> pdb=" O VAL B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 134 through 138' Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.654A pdb=" N GLY B 173 " --> pdb=" O CYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.781A pdb=" N LYS B 333 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 354 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 369 through 373 removed outlier: 3.936A pdb=" N THR B 373 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.608A pdb=" N GLY B 410 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.507A pdb=" N PHE B 457 " --> pdb=" O TRP B 453 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 458' Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 495 through 499 removed outlier: 3.544A pdb=" N CYS B 499 " --> pdb=" O PRO B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 555 removed outlier: 3.819A pdb=" N CYS B 555 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 removed outlier: 3.947A pdb=" N ASN B 580 " --> pdb=" O GLY B 577 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 43 removed outlier: 5.338A pdb=" N ALA A 123 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 95 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 247 removed outlier: 3.721A pdb=" N GLN A 252 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 261 through 262 Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 277 Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 295 Processing sheet with id=AA7, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.290A pdb=" N CYS A 313 " --> pdb=" O SER A 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 345 through 347 removed outlier: 5.423A pdb=" N PHE A 412 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE A 438 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A 414 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N SER A 440 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 416 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 437 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 377 Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 506 Processing sheet with id=AB2, first strand: chain 'A' and resid 562 through 563 Processing sheet with id=AB3, first strand: chain 'A' and resid 573 through 576 removed outlier: 5.364A pdb=" N ALA A 573 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LYS A 585 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 23 through 24 removed outlier: 3.762A pdb=" N LEU C 24 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 29 " --> pdb=" O LEU C 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AB6, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.547A pdb=" N LEU B 41 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ALA B 68 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 43 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL B 65 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU B 98 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE B 67 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ALA B 123 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 95 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL B 124 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 244 through 246 Processing sheet with id=AB8, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AB9, first strand: chain 'B' and resid 276 through 277 Processing sheet with id=AC1, first strand: chain 'B' and resid 291 through 296 Processing sheet with id=AC2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.189A pdb=" N CYS B 313 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 346 through 347 removed outlier: 6.342A pdb=" N LEU B 414 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N SER B 440 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL B 416 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 467 " --> pdb=" O ILE B 439 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 524 through 527 removed outlier: 3.683A pdb=" N PHE B 525 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 532 " --> pdb=" O PHE B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 561 through 563 Processing sheet with id=AC6, first strand: chain 'B' and resid 585 through 587 Processing sheet with id=AC7, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.722A pdb=" N LEU D 24 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D 29 " --> pdb=" O LEU D 24 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.691A pdb=" N THR D 20 " --> pdb=" O VAL D 33 " (cutoff:3.500A) 135 hydrogen bonds defined for protein. 261 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: 3.02 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1769 1.32 - 1.44: 2647 1.44 - 1.57: 5856 1.57 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 10424 Sorted by residual: bond pdb=" N CYS B 571 " pdb=" CA CYS B 571 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.14e-02 7.69e+03 1.23e+01 bond pdb=" C ASN B 128 " pdb=" O ASN B 128 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.28e-02 6.10e+03 1.18e+01 bond pdb=" N ARG B 503 " pdb=" CA ARG B 503 " ideal model delta sigma weight residual 1.454 1.494 -0.039 1.16e-02 7.43e+03 1.15e+01 bond pdb=" N VAL D 2 " pdb=" CA VAL D 2 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.06e+01 bond pdb=" N LEU B 595 " pdb=" CA LEU B 595 " ideal model delta sigma weight residual 1.454 1.497 -0.044 1.34e-02 5.57e+03 1.06e+01 ... (remaining 10419 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.96: 369 106.96 - 113.71: 5689 113.71 - 120.46: 3789 120.46 - 127.21: 4146 127.21 - 133.96: 111 Bond angle restraints: 14104 Sorted by residual: angle pdb=" N SER A 169 " pdb=" CA SER A 169 " pdb=" C SER A 169 " ideal model delta sigma weight residual 113.30 105.00 8.30 1.34e+00 5.57e-01 3.83e+01 angle pdb=" CA SER C 3 " pdb=" C SER C 3 " pdb=" O SER C 3 " ideal model delta sigma weight residual 120.55 114.15 6.40 1.06e+00 8.90e-01 3.65e+01 angle pdb=" CA HIS B 560 " pdb=" C HIS B 560 " pdb=" N TYR B 561 " ideal model delta sigma weight residual 119.56 116.13 3.43 5.80e-01 2.97e+00 3.49e+01 angle pdb=" N HIS D 4 " pdb=" CA HIS D 4 " pdb=" C HIS D 4 " ideal model delta sigma weight residual 113.61 105.11 8.50 1.50e+00 4.44e-01 3.21e+01 angle pdb=" CA ASN B 128 " pdb=" C ASN B 128 " pdb=" O ASN B 128 " ideal model delta sigma weight residual 121.84 115.48 6.36 1.16e+00 7.43e-01 3.00e+01 ... (remaining 14099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5742 17.70 - 35.40: 575 35.40 - 53.10: 117 53.10 - 70.80: 36 70.80 - 88.49: 14 Dihedral angle restraints: 6484 sinusoidal: 2682 harmonic: 3802 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 163 " pdb=" CB CYS A 163 " ideal model delta sinusoidal sigma weight residual 93.00 179.87 -86.87 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 604 " pdb=" CB CYS A 604 " ideal model delta sinusoidal sigma weight residual -86.00 -166.71 80.71 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS B 287 " pdb=" SG CYS B 287 " pdb=" SG CYS B 302 " pdb=" CB CYS B 302 " ideal model delta sinusoidal sigma weight residual 93.00 158.56 -65.56 1 1.00e+01 1.00e-02 5.63e+01 ... (remaining 6481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1205 0.059 - 0.118: 285 0.118 - 0.177: 48 0.177 - 0.235: 4 0.235 - 0.294: 2 Chirality restraints: 1544 Sorted by residual: chirality pdb=" CA CYS B 596 " pdb=" N CYS B 596 " pdb=" C CYS B 596 " pdb=" CB CYS B 596 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB VAL B 505 " pdb=" CA VAL B 505 " pdb=" CG1 VAL B 505 " pdb=" CG2 VAL B 505 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA CYS B 534 " pdb=" N CYS B 534 " pdb=" C CYS B 534 " pdb=" CB CYS B 534 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1541 not shown) Planarity restraints: 1872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 128 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C ASN B 128 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN B 128 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN B 129 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 513 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ASP B 513 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP B 513 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS B 514 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 505 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C VAL B 505 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL B 505 " -0.013 2.00e-02 2.50e+03 pdb=" N SER B 506 " -0.012 2.00e-02 2.50e+03 ... (remaining 1869 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 23 2.35 - 2.98: 5458 2.98 - 3.62: 13721 3.62 - 4.26: 21850 4.26 - 4.90: 37458 Nonbonded interactions: 78510 Sorted by model distance: nonbonded pdb=" O VAL B 505 " pdb=" CG2 VAL B 512 " model vdw 1.707 3.460 nonbonded pdb=" OH TYR A 447 " pdb=" O GLN A 480 " model vdw 2.002 2.440 nonbonded pdb=" OE1 GLU B 397 " pdb=" NH1 ARG B 427 " model vdw 2.226 2.520 nonbonded pdb=" CE1 TYR A 602 " pdb=" SG CYS A 612 " model vdw 2.235 3.700 nonbonded pdb=" NE2 GLN A 252 " pdb=" O ALA B 286 " model vdw 2.236 2.520 ... (remaining 78505 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: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 14.700 Check model and map are aligned: 1.270 Set scattering table: 0.000 Process input model: 28.890 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 0.005 0.044 10424 Z= 0.350 Angle : 0.794 10.555 14104 Z= 0.507 Chirality : 0.052 0.294 1544 Planarity : 0.004 0.042 1872 Dihedral : 14.425 88.495 3872 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.98 % Favored : 88.64 % Rotamer: Outliers : 1.81 % Allowed : 6.04 % Favored : 92.14 % 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: -4.49 (0.19), residues: 1320 helix: -4.31 (0.32), residues: 73 sheet: -3.11 (0.39), residues: 145 loop : -3.19 (0.16), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 492 HIS 0.005 0.001 HIS A 409 PHE 0.010 0.001 PHE C 15 TYR 0.010 0.001 TYR B 45 ARG 0.003 0.000 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8544 (mmt) cc_final: 0.8304 (mmm) REVERT: B 560 HIS cc_start: 0.7672 (m90) cc_final: 0.7459 (m90) REVERT: B 561 TYR cc_start: 0.8690 (m-80) cc_final: 0.8218 (m-80) REVERT: D 10 ASP cc_start: 0.7561 (t0) cc_final: 0.7340 (t0) outliers start: 21 outliers final: 8 residues processed: 88 average time/residue: 0.2793 time to fit residues: 34.0563 Evaluate side-chains 53 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 514 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 12 ASN ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN A 462 GLN A 469 ASN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 GLN A 580 ASN A 599 ASN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS B 70 ASN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS B 252 GLN B 366 GLN ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 HIS ** D 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10424 Z= 0.426 Angle : 0.702 8.179 14104 Z= 0.369 Chirality : 0.047 0.173 1544 Planarity : 0.004 0.040 1872 Dihedral : 6.380 56.207 1431 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.12 % Favored : 87.73 % Rotamer: Outliers : 1.38 % Allowed : 13.13 % Favored : 85.49 % 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: -3.69 (0.21), residues: 1320 helix: -3.12 (0.49), residues: 80 sheet: -3.01 (0.37), residues: 162 loop : -2.54 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 584 HIS 0.007 0.001 HIS B 209 PHE 0.010 0.002 PHE A 380 TYR 0.012 0.001 TYR B 45 ARG 0.005 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 562 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7965 (tt) REVERT: D 10 ASP cc_start: 0.7582 (t0) cc_final: 0.7332 (t0) outliers start: 16 outliers final: 8 residues processed: 60 average time/residue: 0.2356 time to fit residues: 20.9125 Evaluate side-chains 49 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain D residue 28 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 120 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 ASN A 504 ASN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 139 GLN B 394 HIS ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10424 Z= 0.226 Angle : 0.577 9.209 14104 Z= 0.306 Chirality : 0.045 0.142 1544 Planarity : 0.004 0.038 1872 Dihedral : 5.492 48.133 1422 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.70 % Favored : 90.23 % Rotamer: Outliers : 1.73 % Allowed : 14.34 % Favored : 83.94 % 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: -3.05 (0.22), residues: 1320 helix: -2.61 (0.55), residues: 80 sheet: -2.59 (0.40), residues: 152 loop : -2.08 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 584 HIS 0.005 0.001 HIS B 591 PHE 0.009 0.001 PHE C 15 TYR 0.008 0.001 TYR D 38 ARG 0.003 0.000 ARG B 523 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 50 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 561 TYR cc_start: 0.8934 (m-80) cc_final: 0.8567 (m-80) REVERT: D 10 ASP cc_start: 0.7498 (t0) cc_final: 0.7217 (t0) outliers start: 20 outliers final: 7 residues processed: 67 average time/residue: 0.2390 time to fit residues: 23.4908 Evaluate side-chains 46 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain D residue 28 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 0.2980 chunk 127 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 ASN ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10424 Z= 0.185 Angle : 0.553 8.071 14104 Z= 0.292 Chirality : 0.044 0.167 1544 Planarity : 0.003 0.038 1872 Dihedral : 5.241 49.636 1422 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.86 % Favored : 91.06 % Rotamer: Outliers : 1.64 % Allowed : 16.58 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.22), residues: 1320 helix: -2.68 (0.53), residues: 86 sheet: -2.24 (0.39), residues: 169 loop : -1.80 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 584 HIS 0.004 0.001 HIS B 591 PHE 0.010 0.001 PHE C 15 TYR 0.008 0.001 TYR B 88 ARG 0.002 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 41 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 561 TYR cc_start: 0.8996 (m-80) cc_final: 0.8610 (m-80) outliers start: 19 outliers final: 10 residues processed: 59 average time/residue: 0.2202 time to fit residues: 19.2949 Evaluate side-chains 48 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain D residue 28 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 114 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10424 Z= 0.260 Angle : 0.576 6.612 14104 Z= 0.305 Chirality : 0.044 0.140 1544 Planarity : 0.004 0.041 1872 Dihedral : 5.192 48.948 1422 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.70 % Favored : 90.23 % Rotamer: Outliers : 2.42 % Allowed : 16.58 % Favored : 81.00 % 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: -2.58 (0.22), residues: 1320 helix: -2.57 (0.54), residues: 86 sheet: -2.28 (0.40), residues: 164 loop : -1.68 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 584 HIS 0.005 0.001 HIS D 4 PHE 0.010 0.001 PHE C 15 TYR 0.012 0.001 TYR B 292 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 40 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 561 TYR cc_start: 0.9072 (m-80) cc_final: 0.8687 (m-80) outliers start: 28 outliers final: 17 residues processed: 65 average time/residue: 0.2266 time to fit residues: 22.0146 Evaluate side-chains 55 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 38 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 584 TRP Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain D residue 28 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 123 optimal weight: 0.1980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10424 Z= 0.209 Angle : 0.564 7.094 14104 Z= 0.296 Chirality : 0.044 0.139 1544 Planarity : 0.003 0.037 1872 Dihedral : 5.075 49.422 1422 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.62 % Favored : 90.30 % Rotamer: Outliers : 1.99 % Allowed : 17.62 % Favored : 80.40 % 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: -2.43 (0.22), residues: 1320 helix: -2.50 (0.52), residues: 92 sheet: -2.15 (0.41), residues: 159 loop : -1.57 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 584 HIS 0.004 0.001 HIS B 591 PHE 0.017 0.001 PHE B 31 TYR 0.008 0.001 TYR A 251 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 38 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 561 TYR cc_start: 0.9087 (m-80) cc_final: 0.8682 (m-80) outliers start: 23 outliers final: 20 residues processed: 58 average time/residue: 0.2101 time to fit residues: 18.8881 Evaluate side-chains 57 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 37 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 584 TRP Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 28 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10424 Z= 0.276 Angle : 0.595 9.571 14104 Z= 0.310 Chirality : 0.044 0.140 1544 Planarity : 0.003 0.037 1872 Dihedral : 5.118 49.383 1422 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.61 % Favored : 89.32 % Rotamer: Outliers : 2.25 % Allowed : 17.36 % Favored : 80.40 % 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: -2.39 (0.23), residues: 1320 helix: -2.32 (0.53), residues: 92 sheet: -2.05 (0.40), residues: 164 loop : -1.56 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 584 HIS 0.004 0.001 HIS B 591 PHE 0.010 0.001 PHE C 15 TYR 0.011 0.001 TYR B 292 ARG 0.002 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 40 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.7726 (p0) REVERT: B 561 TYR cc_start: 0.9113 (m-80) cc_final: 0.8766 (m-80) outliers start: 26 outliers final: 22 residues processed: 62 average time/residue: 0.2268 time to fit residues: 21.0118 Evaluate side-chains 60 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 37 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 584 TRP Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 28 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 0.0070 chunk 121 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10424 Z= 0.164 Angle : 0.547 9.162 14104 Z= 0.285 Chirality : 0.044 0.140 1544 Planarity : 0.003 0.037 1872 Dihedral : 4.880 49.824 1422 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.94 % Favored : 90.98 % Rotamer: Outliers : 1.99 % Allowed : 17.88 % Favored : 80.14 % 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: -2.22 (0.23), residues: 1320 helix: -1.94 (0.59), residues: 86 sheet: -1.80 (0.41), residues: 164 loop : -1.50 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 584 HIS 0.004 0.001 HIS B 591 PHE 0.011 0.001 PHE C 15 TYR 0.008 0.001 TYR A 251 ARG 0.005 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 38 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 561 TYR cc_start: 0.9085 (m-80) cc_final: 0.8809 (m-80) outliers start: 23 outliers final: 19 residues processed: 58 average time/residue: 0.2253 time to fit residues: 19.6433 Evaluate side-chains 55 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 36 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 584 TRP Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 28 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 0.0030 chunk 112 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 125 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10424 Z= 0.174 Angle : 0.542 9.081 14104 Z= 0.283 Chirality : 0.044 0.139 1544 Planarity : 0.003 0.037 1872 Dihedral : 4.784 49.122 1422 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.94 % Favored : 90.98 % Rotamer: Outliers : 1.99 % Allowed : 17.88 % Favored : 80.14 % 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: -2.16 (0.23), residues: 1320 helix: -1.89 (0.59), residues: 86 sheet: -1.69 (0.41), residues: 168 loop : -1.46 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 584 HIS 0.004 0.001 HIS B 591 PHE 0.010 0.001 PHE C 15 TYR 0.011 0.001 TYR B 292 ARG 0.004 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 36 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.6975 (tpt) cc_final: 0.6498 (mmm) REVERT: B 561 TYR cc_start: 0.9086 (m-80) cc_final: 0.8764 (m-80) outliers start: 23 outliers final: 19 residues processed: 56 average time/residue: 0.2046 time to fit residues: 18.1599 Evaluate side-chains 55 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 36 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 584 TRP Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 28 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 0.0270 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10424 Z= 0.255 Angle : 0.584 8.839 14104 Z= 0.303 Chirality : 0.044 0.139 1544 Planarity : 0.003 0.037 1872 Dihedral : 4.910 49.293 1422 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.62 % Favored : 90.30 % Rotamer: Outliers : 1.73 % Allowed : 18.05 % Favored : 80.22 % 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: -2.13 (0.23), residues: 1320 helix: -1.89 (0.59), residues: 86 sheet: -1.63 (0.42), residues: 164 loop : -1.45 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 584 HIS 0.004 0.001 HIS B 591 PHE 0.010 0.001 PHE C 15 TYR 0.008 0.001 TYR A 45 ARG 0.005 0.000 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 36 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.7159 (tpt) cc_final: 0.6707 (mmm) REVERT: B 561 TYR cc_start: 0.9103 (m-80) cc_final: 0.8795 (m-80) outliers start: 20 outliers final: 19 residues processed: 53 average time/residue: 0.2065 time to fit residues: 17.0836 Evaluate side-chains 55 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 36 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 584 TRP Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 28 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.0170 chunk 92 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 158 ASN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.052579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.034790 restraints weight = 53708.089| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 5.91 r_work: 0.2599 rms_B_bonded: 5.70 restraints_weight: 2.0000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10424 Z= 0.156 Angle : 0.548 8.802 14104 Z= 0.286 Chirality : 0.044 0.141 1544 Planarity : 0.003 0.037 1872 Dihedral : 4.587 20.760 1418 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.71 % Favored : 91.21 % Rotamer: Outliers : 1.81 % Allowed : 18.22 % Favored : 79.97 % 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: -2.07 (0.23), residues: 1320 helix: -1.88 (0.59), residues: 86 sheet: -1.55 (0.41), residues: 172 loop : -1.40 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 584 HIS 0.009 0.001 HIS D 4 PHE 0.011 0.001 PHE C 15 TYR 0.008 0.001 TYR B 292 ARG 0.004 0.000 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2306.26 seconds wall clock time: 43 minutes 2.89 seconds (2582.89 seconds total)