Starting phenix.real_space_refine on Sun Feb 18 00:57:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sye_25523/02_2024/7sye_25523.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sye_25523/02_2024/7sye_25523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sye_25523/02_2024/7sye_25523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sye_25523/02_2024/7sye_25523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sye_25523/02_2024/7sye_25523.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sye_25523/02_2024/7sye_25523.pdb" } resolution = 3.3 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= 0.036 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 10192 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 134 5.16 5 C 6316 2.51 5 N 1810 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 60": "OE1" <-> "OE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B GLU 521": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10216 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: "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: "C" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "D" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Time building chain proxies: 5.72, per 1000 atoms: 0.56 Number of scatterers: 10216 At special positions: 0 Unit cell: (71.2404, 141.401, 126.29, 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 134 16.00 O 1956 8.00 N 1810 7.00 C 6316 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 224 " distance=2.02 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 502 " - pdb=" SG CYS A 511 " distance=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 612 " 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=2.03 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=2.02 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=2.04 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=2.04 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=2.07 Simple disulfide: pdb=" SG CYS B 502 " - pdb=" SG CYS B 511 " distance=2.02 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=2.06 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 593 " distance=2.06 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 604 " distance=2.01 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 612 " distance=2.04 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 31 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 42 " distance=2.02 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 20 " distance=2.04 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS D 31 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 42 " 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: 3.70 Conformation dependent library (CDL) restraints added in 2.2 seconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 29 sheets defined 12.3% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.960A pdb=" N THR A 57 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.778A 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 147 through 151 removed outlier: 4.007A pdb=" N SER A 150 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 151 " --> pdb=" O PHE A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 151' Processing helix chain 'A' and resid 170 through 174 removed outlier: 4.071A pdb=" N GLY A 173 " --> pdb=" O CYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 removed outlier: 3.710A pdb=" N ASP A 206 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 4.296A 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: 4.098A pdb=" N PHE A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.654A pdb=" N ASP A 369 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 407 through 410 removed outlier: 3.649A 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 475 Processing helix chain 'B' and resid 19 through 31 Processing helix chain 'B' and resid 139 through 144 removed outlier: 4.242A pdb=" N ILE B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 144 " --> pdb=" O TRP B 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 139 through 144' Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.618A pdb=" N ILE B 332 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 333 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 354 removed outlier: 3.599A pdb=" N ARG B 353 " --> pdb=" O PRO B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.528A pdb=" N ASP B 369 " --> pdb=" O GLN B 366 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B 373 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.870A pdb=" N GLY B 410 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.750A pdb=" N GLY B 479 " --> pdb=" O LYS B 476 " (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: 3.946A pdb=" N ASN B 580 " --> pdb=" O GLY B 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.685A pdb=" N ASP C 11 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 50 removed outlier: 3.631A pdb=" N TRP C 50 " --> pdb=" O LEU C 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 50' Processing helix chain 'D' and resid 7 through 11 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 44 removed outlier: 5.871A pdb=" N ALA A 123 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 95 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.742A pdb=" N GLN A 252 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 262 Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 277 Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 removed outlier: 3.676A pdb=" N LYS A 301 " --> pdb=" O MET A 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.372A pdb=" N CYS A 313 " --> pdb=" O SER A 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 345 through 347 removed outlier: 4.849A pdb=" N PHE A 412 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE A 438 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 414 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER A 440 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 416 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 437 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A 467 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 439 " --> pdb=" O ILE A 467 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 401 through 402 Processing sheet with id=AB2, first strand: chain 'A' and resid 505 through 507 removed outlier: 3.538A pdb=" N GLU A 510 " --> pdb=" O ARG A 507 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 573 through 575 removed outlier: 5.538A pdb=" N VAL A 583 " --> pdb=" O GLY A 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.321A pdb=" N VAL B 65 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 98 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE B 67 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR B 93 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ARG B 125 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 95 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER B 127 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 97 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AB7, first strand: chain 'B' and resid 244 through 247 removed outlier: 3.641A pdb=" N ASN B 247 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN B 252 " --> pdb=" O ASN B 247 " (cutoff:3.500A) 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 293 Processing sheet with id=AC2, first strand: chain 'B' and resid 312 through 314 removed outlier: 3.503A pdb=" N CYS B 313 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 342 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 341 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 345 through 347 removed outlier: 6.232A pdb=" N LEU B 345 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 437 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE B 467 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 439 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 505 through 506 removed outlier: 4.141A pdb=" N VAL B 505 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 524 through 527 removed outlier: 3.531A pdb=" N GLU B 527 " --> pdb=" O GLU B 530 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 561 through 563 Processing sheet with id=AC7, first strand: chain 'B' and resid 585 through 587 Processing sheet with id=AC8, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.641A pdb=" N ALA C 30 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 28 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AD1, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.544A pdb=" N LYS D 28 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 37 through 38 131 hydrogen bonds defined for protein. 249 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: 2.77 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3391 1.34 - 1.46: 2076 1.46 - 1.58: 4799 1.58 - 1.70: 0 1.70 - 1.83: 156 Bond restraints: 10422 Sorted by residual: bond pdb=" N VAL B 500 " pdb=" CA VAL B 500 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.19e-02 7.06e+03 1.68e+01 bond pdb=" N CYS B 170 " pdb=" CA CYS B 170 " ideal model delta sigma weight residual 1.456 1.495 -0.038 9.40e-03 1.13e+04 1.65e+01 bond pdb=" N CYS A 538 " pdb=" CA CYS A 538 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" N ARG B 503 " pdb=" CA ARG B 503 " ideal model delta sigma weight residual 1.457 1.503 -0.045 1.29e-02 6.01e+03 1.22e+01 bond pdb=" N CYS A 482 " pdb=" CA CYS A 482 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.14e-02 7.69e+03 1.22e+01 ... (remaining 10417 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.68: 237 105.68 - 112.77: 5366 112.77 - 119.86: 3577 119.86 - 126.94: 4791 126.94 - 134.03: 129 Bond angle restraints: 14100 Sorted by residual: angle pdb=" N ASN B 504 " pdb=" CA ASN B 504 " pdb=" C ASN B 504 " ideal model delta sigma weight residual 113.28 102.07 11.21 1.22e+00 6.72e-01 8.45e+01 angle pdb=" C CYS B 571 " pdb=" N PRO B 572 " pdb=" CA PRO B 572 " ideal model delta sigma weight residual 119.90 125.34 -5.44 1.02e+00 9.61e-01 2.85e+01 angle pdb=" N VAL B 500 " pdb=" CA VAL B 500 " pdb=" CB VAL B 500 " ideal model delta sigma weight residual 110.13 117.72 -7.59 1.68e+00 3.54e-01 2.04e+01 angle pdb=" C CYS B 170 " pdb=" N PRO B 171 " pdb=" CA PRO B 171 " ideal model delta sigma weight residual 119.84 125.39 -5.55 1.25e+00 6.40e-01 1.97e+01 angle pdb=" N VAL B 526 " pdb=" CA VAL B 526 " pdb=" C VAL B 526 " ideal model delta sigma weight residual 107.75 114.11 -6.36 1.46e+00 4.69e-01 1.90e+01 ... (remaining 14095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 5769 17.42 - 34.85: 547 34.85 - 52.27: 116 52.27 - 69.69: 28 69.69 - 87.11: 20 Dihedral angle restraints: 6480 sinusoidal: 2692 harmonic: 3788 Sorted by residual: dihedral pdb=" CB CYS B 195 " pdb=" SG CYS B 195 " pdb=" SG CYS B 207 " pdb=" CB CYS B 207 " ideal model delta sinusoidal sigma weight residual 93.00 -179.89 -87.11 1 1.00e+01 1.00e-02 9.12e+01 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 93.00 176.89 -83.89 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS A 515 " pdb=" SG CYS A 515 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual 93.00 166.48 -73.48 1 1.00e+01 1.00e-02 6.87e+01 ... (remaining 6477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1216 0.061 - 0.122: 284 0.122 - 0.183: 26 0.183 - 0.244: 5 0.244 - 0.305: 3 Chirality restraints: 1534 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 2.82 -0.30 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA CYS A 538 " pdb=" N CYS A 538 " pdb=" C CYS A 538 " pdb=" CB CYS A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA VAL A 481 " pdb=" N VAL A 481 " pdb=" C VAL A 481 " pdb=" CB VAL A 481 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1531 not shown) Planarity restraints: 1864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 503 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C ARG B 503 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG B 503 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN B 504 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 169 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C SER A 169 " -0.031 2.00e-02 2.50e+03 pdb=" O SER A 169 " 0.012 2.00e-02 2.50e+03 pdb=" N CYS A 170 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 501 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C SER B 501 " -0.031 2.00e-02 2.50e+03 pdb=" O SER B 501 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS B 502 " 0.010 2.00e-02 2.50e+03 ... (remaining 1861 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 130 2.63 - 3.20: 9474 3.20 - 3.76: 14330 3.76 - 4.33: 21089 4.33 - 4.90: 34765 Nonbonded interactions: 79788 Sorted by model distance: nonbonded pdb=" OG1 THR B 391 " pdb=" OG1 THR B 422 " model vdw 2.060 2.440 nonbonded pdb=" O GLU A 397 " pdb=" OG SER A 428 " model vdw 2.127 2.440 nonbonded pdb=" OG1 THR B 10 " pdb=" OE1 GLU B 42 " model vdw 2.155 2.440 nonbonded pdb=" OG1 THR A 10 " pdb=" OE1 GLU A 42 " model vdw 2.158 2.440 nonbonded pdb=" OG SER B 413 " pdb=" O ASP B 434 " model vdw 2.183 2.440 ... (remaining 79783 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=0.38 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.000 Extract box with map and model: 6.100 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.580 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 : 0.007 0.049 10422 Z= 0.425 Angle : 0.857 11.213 14100 Z= 0.533 Chirality : 0.052 0.305 1534 Planarity : 0.004 0.042 1864 Dihedral : 14.404 86.804 3884 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.30 % Allowed : 14.84 % Favored : 84.86 % Rotamer: Outliers : 1.65 % Allowed : 8.06 % Favored : 90.29 % Cbeta Deviations : 0.16 % 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: -4.43 (0.19), residues: 1314 helix: -4.23 (0.32), residues: 86 sheet: -2.51 (0.54), residues: 87 loop : -3.22 (0.15), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 140 HIS 0.005 0.001 HIS A 535 PHE 0.010 0.001 PHE A 156 TYR 0.011 0.002 TYR B 246 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 MET cc_start: 0.7645 (tmm) cc_final: 0.7321 (tmm) outliers start: 19 outliers final: 5 residues processed: 88 average time/residue: 0.2431 time to fit residues: 30.7588 Evaluate side-chains 51 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain B residue 515 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 33 optimal weight: 0.0270 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 0.0070 chunk 118 optimal weight: 0.0040 overall best weight: 0.5470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN A 384 GLN A 452 ASN A 473 ASN A 483 HIS A 599 ASN B 23 HIS B 79 ASN B 115 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 389 ASN B 408 GLN B 420 ASN B 462 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10422 Z= 0.158 Angle : 0.595 8.406 14100 Z= 0.312 Chirality : 0.045 0.172 1534 Planarity : 0.004 0.049 1864 Dihedral : 5.874 48.384 1430 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.04 % Favored : 88.66 % Rotamer: Outliers : 1.21 % Allowed : 12.91 % Favored : 85.88 % 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: -3.44 (0.21), residues: 1314 helix: -2.59 (0.56), residues: 69 sheet: -2.66 (0.47), residues: 121 loop : -2.47 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 492 HIS 0.004 0.001 HIS A 535 PHE 0.006 0.001 PHE B 380 TYR 0.008 0.001 TYR B 561 ARG 0.005 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: B 253 MET cc_start: 0.8481 (mmm) cc_final: 0.8262 (mmm) outliers start: 14 outliers final: 10 residues processed: 67 average time/residue: 0.2053 time to fit residues: 21.5484 Evaluate side-chains 60 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain C residue 19 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 118 optimal weight: 50.0000 chunk 127 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 HIS ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10422 Z= 0.197 Angle : 0.569 6.645 14100 Z= 0.296 Chirality : 0.044 0.140 1534 Planarity : 0.004 0.045 1864 Dihedral : 5.575 46.665 1429 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.88 % Favored : 88.89 % Rotamer: Outliers : 2.77 % Allowed : 13.95 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.04 (0.22), residues: 1314 helix: -2.45 (0.51), residues: 88 sheet: -2.42 (0.47), residues: 119 loop : -2.14 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 584 HIS 0.003 0.001 HIS A 394 PHE 0.006 0.001 PHE B 525 TYR 0.010 0.001 TYR A 251 ARG 0.006 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 53 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8766 (p0) REVERT: B 294 MET cc_start: 0.7447 (tmm) cc_final: 0.7231 (tmm) outliers start: 32 outliers final: 17 residues processed: 80 average time/residue: 0.1936 time to fit residues: 24.3077 Evaluate side-chains 67 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 49 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain C residue 19 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 0.0270 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 30.0000 chunk 125 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 overall best weight: 1.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS B 128 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10422 Z= 0.269 Angle : 0.595 9.070 14100 Z= 0.306 Chirality : 0.044 0.136 1534 Planarity : 0.004 0.042 1864 Dihedral : 5.488 43.521 1427 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.57 % Favored : 88.36 % Rotamer: Outliers : 2.77 % Allowed : 15.25 % Favored : 81.98 % 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: -2.75 (0.22), residues: 1314 helix: -2.16 (0.54), residues: 89 sheet: -1.99 (0.53), residues: 109 loop : -1.97 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 584 HIS 0.004 0.001 HIS A 394 PHE 0.005 0.001 PHE B 525 TYR 0.007 0.001 TYR B 251 ARG 0.006 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 51 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.7723 (tmm) cc_final: 0.7173 (tmm) outliers start: 32 outliers final: 20 residues processed: 79 average time/residue: 0.1940 time to fit residues: 23.6161 Evaluate side-chains 68 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 48 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain D residue 17 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 47 GLN A 117 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN A 480 GLN B 164 GLN B 389 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10422 Z= 0.409 Angle : 0.686 9.610 14100 Z= 0.351 Chirality : 0.046 0.146 1534 Planarity : 0.004 0.042 1864 Dihedral : 5.716 46.926 1425 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer: Outliers : 2.95 % Allowed : 16.03 % Favored : 81.02 % 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: -2.75 (0.22), residues: 1314 helix: -2.29 (0.49), residues: 100 sheet: -2.01 (0.51), residues: 119 loop : -1.94 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 584 HIS 0.006 0.001 HIS A 394 PHE 0.007 0.001 PHE A 335 TYR 0.011 0.001 TYR D 37 ARG 0.006 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 50 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ARG cc_start: 0.5410 (OUTLIER) cc_final: 0.4711 (pmt-80) REVERT: B 253 MET cc_start: 0.8603 (mmm) cc_final: 0.8386 (mmm) REVERT: B 294 MET cc_start: 0.7619 (tmm) cc_final: 0.7370 (tmm) outliers start: 34 outliers final: 24 residues processed: 79 average time/residue: 0.2098 time to fit residues: 24.8941 Evaluate side-chains 73 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 48 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain D residue 17 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.6980 chunk 113 optimal weight: 0.0050 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 58 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN B 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10422 Z= 0.132 Angle : 0.561 9.899 14100 Z= 0.285 Chirality : 0.044 0.138 1534 Planarity : 0.003 0.051 1864 Dihedral : 5.105 43.896 1425 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 2.25 % Allowed : 17.33 % Favored : 80.42 % 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: -2.29 (0.23), residues: 1314 helix: -1.51 (0.59), residues: 82 sheet: -1.89 (0.50), residues: 126 loop : -1.62 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 584 HIS 0.003 0.000 HIS A 394 PHE 0.007 0.001 PHE B 525 TYR 0.010 0.001 TYR B 447 ARG 0.007 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 54 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 40 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7458 (tm-30) outliers start: 26 outliers final: 16 residues processed: 77 average time/residue: 0.2040 time to fit residues: 24.1362 Evaluate side-chains 66 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain C residue 19 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 0.0980 chunk 91 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10422 Z= 0.311 Angle : 0.631 9.553 14100 Z= 0.320 Chirality : 0.045 0.161 1534 Planarity : 0.004 0.044 1864 Dihedral : 5.313 44.991 1425 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 2.69 % Allowed : 17.33 % Favored : 79.98 % 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: -2.25 (0.23), residues: 1314 helix: -1.80 (0.56), residues: 89 sheet: -1.92 (0.55), residues: 109 loop : -1.57 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 584 HIS 0.004 0.001 HIS A 394 PHE 0.007 0.001 PHE A 412 TYR 0.009 0.001 TYR D 37 ARG 0.007 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 53 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.7886 (pmm) cc_final: 0.7611 (ptp) outliers start: 31 outliers final: 22 residues processed: 81 average time/residue: 0.1912 time to fit residues: 24.0586 Evaluate side-chains 72 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 50 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain C residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.1980 chunk 74 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 0.0040 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10422 Z= 0.137 Angle : 0.568 10.415 14100 Z= 0.286 Chirality : 0.044 0.175 1534 Planarity : 0.003 0.048 1864 Dihedral : 4.976 43.543 1425 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.59 % Favored : 90.33 % Rotamer: Outliers : 2.17 % Allowed : 18.20 % Favored : 79.64 % 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: -2.09 (0.23), residues: 1314 helix: -1.46 (0.60), residues: 82 sheet: -1.80 (0.51), residues: 126 loop : -1.46 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 584 HIS 0.003 0.000 HIS A 535 PHE 0.007 0.001 PHE B 525 TYR 0.010 0.001 TYR B 447 ARG 0.008 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 53 time to evaluate : 1.436 Fit side-chains REVERT: D 21 MET cc_start: 0.7837 (pmm) cc_final: 0.7562 (ptp) outliers start: 25 outliers final: 19 residues processed: 76 average time/residue: 0.2025 time to fit residues: 25.1819 Evaluate side-chains 71 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 52 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain C residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 120 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 123 optimal weight: 0.0010 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10422 Z= 0.241 Angle : 0.604 11.101 14100 Z= 0.305 Chirality : 0.044 0.156 1534 Planarity : 0.003 0.043 1864 Dihedral : 4.958 44.308 1421 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.65 % Favored : 89.27 % Rotamer: Outliers : 2.34 % Allowed : 18.37 % Favored : 79.29 % 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: -2.02 (0.23), residues: 1314 helix: -1.45 (0.60), residues: 82 sheet: -1.68 (0.51), residues: 126 loop : -1.41 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 584 HIS 0.003 0.001 HIS A 394 PHE 0.007 0.001 PHE B 525 TYR 0.019 0.001 TYR C 44 ARG 0.009 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 51 time to evaluate : 1.288 Fit side-chains REVERT: A 30 MET cc_start: 0.8515 (tpp) cc_final: 0.8307 (tpt) outliers start: 27 outliers final: 24 residues processed: 73 average time/residue: 0.1856 time to fit residues: 21.4775 Evaluate side-chains 74 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 50 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain D residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.9980 chunk 58 optimal weight: 30.0000 chunk 85 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 119 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10422 Z= 0.167 Angle : 0.583 12.849 14100 Z= 0.292 Chirality : 0.044 0.153 1534 Planarity : 0.003 0.047 1864 Dihedral : 4.834 42.684 1421 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.82 % Favored : 90.11 % Rotamer: Outliers : 1.91 % Allowed : 18.80 % Favored : 79.29 % 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: -1.95 (0.23), residues: 1314 helix: -1.47 (0.60), residues: 82 sheet: -1.61 (0.51), residues: 126 loop : -1.36 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP A 584 HIS 0.003 0.000 HIS A 535 PHE 0.007 0.001 PHE B 525 TYR 0.010 0.001 TYR B 447 ARG 0.010 0.000 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 51 time to evaluate : 1.197 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 20 residues processed: 71 average time/residue: 0.1855 time to fit residues: 20.7132 Evaluate side-chains 70 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 50 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain D residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.078876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.052450 restraints weight = 44690.665| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 5.71 r_work: 0.2809 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10422 Z= 0.204 Angle : 0.593 13.436 14100 Z= 0.297 Chirality : 0.044 0.146 1534 Planarity : 0.003 0.044 1864 Dihedral : 4.844 42.911 1421 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.35 % Favored : 89.57 % Rotamer: Outliers : 2.43 % Allowed : 18.46 % Favored : 79.12 % 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: -1.91 (0.23), residues: 1314 helix: -1.43 (0.60), residues: 82 sheet: -1.61 (0.51), residues: 126 loop : -1.33 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 584 HIS 0.004 0.001 HIS A 535 PHE 0.008 0.001 PHE A 412 TYR 0.030 0.001 TYR C 44 ARG 0.010 0.000 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2221.06 seconds wall clock time: 40 minutes 53.14 seconds (2453.14 seconds total)