Starting phenix.real_space_refine on Sun Feb 18 00:51:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz0_25558/02_2024/7sz0_25558.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz0_25558/02_2024/7sz0_25558.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/7sz0_25558/02_2024/7sz0_25558.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz0_25558/02_2024/7sz0_25558.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz0_25558/02_2024/7sz0_25558.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz0_25558/02_2024/7sz0_25558.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= -0.001 sd= 0.035 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 10184 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 GLU 2": "OE1" <-> "OE2" Residue "A GLU 3": "OE1" <-> "OE2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B GLU 521": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "D GLU 5": "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: "B" 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: "B" Number of atoms: 4723 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 614, 4723 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 30, 'TRANS': 583} 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: 5.80, per 1000 atoms: 0.57 Number of scatterers: 10216 At special positions: 0 Unit cell: (82.0344, 144.64, 129.528, 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=2.03 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=2.05 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 612 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 42 " distance=2.02 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=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 502 " - pdb=" SG CYS B 511 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 558 " - pdb=" SG CYS B 567 " distance=2.04 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 593 " distance=2.05 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=2.07 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 20 " distance=2.03 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=2.02 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: 3.78 Conformation dependent library (CDL) restraints added in 1.9 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 12.0% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 removed outlier: 3.605A pdb=" N PHE A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.852A pdb=" N LEU A 55 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 56 " --> pdb=" O SER A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 56' Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.853A 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 134 through 138 removed outlier: 4.119A pdb=" N SER A 137 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 138 " --> pdb=" O VAL A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 134 through 138' Processing helix chain 'A' and resid 147 through 151 removed outlier: 4.417A pdb=" N SER A 150 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.772A 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 203 through 207 removed outlier: 4.118A pdb=" N CYS A 207 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.985A pdb=" N ASP A 369 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 370 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.603A pdb=" N GLU A 397 " --> pdb=" O HIS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 410 Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 473 through 479 Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.747A pdb=" N CYS A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.856A pdb=" N CYS A 555 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 29 removed outlier: 3.760A pdb=" N PHE B 24 " --> pdb=" O PHE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 removed outlier: 3.517A pdb=" N LEU B 55 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 57 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 58 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 91 removed outlier: 3.994A pdb=" N ASN B 91 " --> pdb=" O TYR B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.635A pdb=" N SER B 137 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 3.922A 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 318 through 322 removed outlier: 3.755A pdb=" N LYS B 322 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 364 through 374 removed outlier: 3.767A pdb=" N LEU B 368 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR B 373 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 407 through 410 Processing helix chain 'B' and resid 471 through 477 Processing helix chain 'B' and resid 495 through 499 removed outlier: 3.815A pdb=" N CYS B 499 " --> pdb=" O PRO B 496 " (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 42 removed outlier: 6.225A pdb=" N LEU A 41 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ALA A 68 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG A 125 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 96 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N SER A 127 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU A 98 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 124 " --> pdb=" O SER A 153 " (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 246 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 278 removed outlier: 4.093A pdb=" N SER A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 291 through 296 Processing sheet with id=AA8, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.317A 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: 6.238A pdb=" N LEU A 345 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP A 436 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 440 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 376 through 377 Processing sheet with id=AB2, first strand: chain 'A' and resid 524 through 525 removed outlier: 3.731A pdb=" N ILE A 532 " --> pdb=" O PHE A 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 562 through 563 Processing sheet with id=AB4, first strand: chain 'A' and resid 573 through 576 removed outlier: 4.774A pdb=" N VAL A 575 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 583 " --> pdb=" O VAL A 575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AB6, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AB7, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AB8, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.267A pdb=" N ALA B 123 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL B 124 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 246 through 247 removed outlier: 3.787A pdb=" N GLN B 252 " --> pdb=" O ASN B 247 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AC2, first strand: chain 'B' and resid 276 through 277 Processing sheet with id=AC3, first strand: chain 'B' and resid 291 through 296 Processing sheet with id=AC4, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.589A pdb=" N CYS B 313 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 345 through 347 removed outlier: 6.299A pdb=" N LEU B 345 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 381 " --> pdb=" O SER B 413 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N PHE B 412 " --> pdb=" O ASP B 436 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE B 438 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU B 414 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 505 through 506 removed outlier: 3.572A pdb=" N VAL B 505 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 524 through 527 removed outlier: 3.529A pdb=" N GLU B 527 " --> pdb=" O GLU B 530 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 561 through 563 Processing sheet with id=AC9, first strand: chain 'B' and resid 585 through 587 Processing sheet with id=AD1, first strand: chain 'D' and resid 21 through 23 Processing sheet with id=AD2, first strand: chain 'D' and resid 37 through 38 130 hydrogen bonds defined for protein. 246 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: 2.94 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3424 1.34 - 1.46: 1905 1.46 - 1.58: 4937 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 10422 Sorted by residual: bond pdb=" N CYS B 571 " pdb=" CA CYS B 571 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.14e-02 7.69e+03 1.40e+01 bond pdb=" N VAL A 481 " pdb=" CA VAL A 481 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.23e+01 bond pdb=" N SER A 11 " pdb=" CA SER A 11 " ideal model delta sigma weight residual 1.457 1.502 -0.044 1.29e-02 6.01e+03 1.17e+01 bond pdb=" N VAL B 500 " pdb=" CA VAL B 500 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.10e-02 8.26e+03 1.05e+01 bond pdb=" N CYS A 482 " pdb=" CA CYS A 482 " ideal model delta sigma weight residual 1.453 1.494 -0.041 1.31e-02 5.83e+03 1.00e+01 ... (remaining 10417 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.31: 326 106.31 - 113.23: 5483 113.23 - 120.16: 3771 120.16 - 127.08: 4402 127.08 - 134.01: 118 Bond angle restraints: 14100 Sorted by residual: angle pdb=" CA HIS B 560 " pdb=" C HIS B 560 " pdb=" N TYR B 561 " ideal model delta sigma weight residual 119.56 116.22 3.34 5.80e-01 2.97e+00 3.31e+01 angle pdb=" N SER B 169 " pdb=" CA SER B 169 " pdb=" C SER B 169 " ideal model delta sigma weight residual 112.93 107.94 4.99 1.12e+00 7.97e-01 1.99e+01 angle pdb=" N VAL B 526 " pdb=" CA VAL B 526 " pdb=" C VAL B 526 " ideal model delta sigma weight residual 107.75 114.08 -6.33 1.46e+00 4.69e-01 1.88e+01 angle pdb=" CA HIS C 16 " pdb=" C HIS C 16 " pdb=" O HIS C 16 " ideal model delta sigma weight residual 122.64 117.27 5.37 1.25e+00 6.40e-01 1.84e+01 angle pdb=" C GLY B 564 " pdb=" N PRO B 565 " pdb=" CA PRO B 565 " ideal model delta sigma weight residual 119.28 123.99 -4.71 1.10e+00 8.26e-01 1.83e+01 ... (remaining 14095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 5742 17.30 - 34.60: 575 34.60 - 51.90: 123 51.90 - 69.20: 23 69.20 - 86.51: 17 Dihedral angle restraints: 6480 sinusoidal: 2692 harmonic: 3788 Sorted by residual: 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 93.00 175.50 -82.50 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CB CYS D 14 " pdb=" SG CYS D 14 " pdb=" SG CYS D 31 " pdb=" CB CYS D 31 " ideal model delta sinusoidal sigma weight residual 93.00 163.59 -70.59 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CB CYS C 14 " pdb=" SG CYS C 14 " pdb=" SG CYS C 31 " pdb=" CB CYS C 31 " ideal model delta sinusoidal sigma weight residual 93.00 152.40 -59.40 1 1.00e+01 1.00e-02 4.71e+01 ... (remaining 6477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1136 0.055 - 0.109: 330 0.109 - 0.164: 55 0.164 - 0.218: 8 0.218 - 0.273: 5 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 2.78 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA SER A 11 " pdb=" N SER A 11 " pdb=" C SER A 11 " pdb=" CB SER A 11 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LEU A 517 " pdb=" N LEU A 517 " pdb=" C LEU A 517 " pdb=" CB LEU A 517 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1531 not shown) Planarity restraints: 1864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 12 " 0.015 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C ASN B 12 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN B 12 " 0.021 2.00e-02 2.50e+03 pdb=" N LYS B 13 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 168 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C PRO B 168 " -0.040 2.00e-02 2.50e+03 pdb=" O PRO B 168 " 0.015 2.00e-02 2.50e+03 pdb=" N SER B 169 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 486 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C CYS B 486 " -0.038 2.00e-02 2.50e+03 pdb=" O CYS B 486 " 0.014 2.00e-02 2.50e+03 pdb=" N SER B 487 " 0.013 2.00e-02 2.50e+03 ... (remaining 1861 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 531 2.72 - 3.27: 10059 3.27 - 3.81: 14845 3.81 - 4.36: 19769 4.36 - 4.90: 34034 Nonbonded interactions: 79238 Sorted by model distance: nonbonded pdb=" OG SER A 203 " pdb=" OD2 ASP A 206 " model vdw 2.175 2.440 nonbonded pdb=" OD1 ASP B 51 " pdb=" OG SER B 53 " model vdw 2.214 2.440 nonbonded pdb=" OG1 THR B 278 " pdb=" OG SER B 282 " model vdw 2.227 2.440 nonbonded pdb=" OD1 ASP A 51 " pdb=" OG SER A 53 " model vdw 2.241 2.440 nonbonded pdb=" OE1 GLU A 118 " pdb=" NH2 ARG A 198 " model vdw 2.242 2.520 ... (remaining 79233 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 7.280 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.870 Find NCS groups from input model: 0.550 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 0.047 10422 Z= 0.332 Angle : 0.785 6.933 14100 Z= 0.494 Chirality : 0.053 0.273 1534 Planarity : 0.004 0.042 1864 Dihedral : 14.456 86.506 3884 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.13 % Favored : 88.57 % Rotamer: Outliers : 1.73 % Allowed : 5.89 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.19), residues: 1314 helix: -4.18 (0.31), residues: 67 sheet: -3.56 (0.32), residues: 189 loop : -2.96 (0.16), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 492 HIS 0.004 0.001 HIS C 16 PHE 0.014 0.001 PHE A 380 TYR 0.012 0.001 TYR A 64 ARG 0.004 0.000 ARG A 503 *********************** 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 76 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 56 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 561 TYR cc_start: 0.8392 (m-80) cc_final: 0.8057 (m-80) outliers start: 20 outliers final: 3 residues processed: 75 average time/residue: 0.2241 time to fit residues: 24.8650 Evaluate side-chains 41 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 562 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 70 ASN A 100 ASN A 128 ASN A 194 GLN A 209 HIS A 394 HIS ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 GLN A 528 ASN A 599 ASN C 16 HIS B 134 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN B 252 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 HIS D 16 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10422 Z= 0.353 Angle : 0.663 17.496 14100 Z= 0.337 Chirality : 0.047 0.170 1534 Planarity : 0.004 0.036 1864 Dihedral : 5.339 19.825 1424 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 1.13 % Allowed : 11.79 % Favored : 87.09 % 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: -3.40 (0.21), residues: 1314 helix: -2.97 (0.49), residues: 75 sheet: -3.07 (0.35), residues: 181 loop : -2.24 (0.17), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 492 HIS 0.003 0.001 HIS B 483 PHE 0.008 0.001 PHE A 380 TYR 0.018 0.001 TYR B 561 ARG 0.005 0.000 ARG B 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 52 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 47 average time/residue: 0.1615 time to fit residues: 13.1525 Evaluate side-chains 44 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain D residue 17 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8189 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10422 Z= 0.164 Angle : 0.547 8.743 14100 Z= 0.283 Chirality : 0.045 0.159 1534 Planarity : 0.003 0.036 1864 Dihedral : 4.785 19.924 1422 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 1.91 % Allowed : 12.56 % Favored : 85.53 % 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: -2.83 (0.21), residues: 1314 helix: -2.72 (0.50), residues: 80 sheet: -2.63 (0.38), residues: 174 loop : -1.82 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 492 HIS 0.002 0.000 HIS A 346 PHE 0.007 0.001 PHE A 380 TYR 0.012 0.001 TYR B 447 ARG 0.003 0.000 ARG B 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 62 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 40 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 58 average time/residue: 0.1556 time to fit residues: 15.5808 Evaluate side-chains 51 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D 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: 2.9990 chunk 88 optimal weight: 4.9990 chunk 61 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 79 optimal weight: 0.1980 chunk 118 optimal weight: 4.9990 chunk 125 optimal weight: 40.0000 chunk 62 optimal weight: 0.8980 chunk 112 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN ** 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: 0.8190 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10422 Z= 0.161 Angle : 0.538 8.613 14100 Z= 0.275 Chirality : 0.045 0.153 1534 Planarity : 0.003 0.037 1864 Dihedral : 4.557 20.363 1422 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.99 % Allowed : 13.43 % Favored : 84.58 % 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: -2.41 (0.22), residues: 1314 helix: -2.49 (0.54), residues: 80 sheet: -2.33 (0.40), residues: 156 loop : -1.53 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 492 HIS 0.002 0.000 HIS A 346 PHE 0.008 0.001 PHE A 380 TYR 0.010 0.001 TYR B 447 ARG 0.003 0.000 ARG B 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 62 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 39 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 59 average time/residue: 0.1586 time to fit residues: 16.0177 Evaluate side-chains 54 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 38 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 553 ASP Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 19 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8210 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10422 Z= 0.202 Angle : 0.542 7.895 14100 Z= 0.277 Chirality : 0.045 0.150 1534 Planarity : 0.003 0.037 1864 Dihedral : 4.523 19.244 1422 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.00 % Favored : 91.92 % Rotamer: Outliers : 2.34 % Allowed : 13.86 % Favored : 83.80 % 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: -2.18 (0.22), residues: 1314 helix: -2.31 (0.55), residues: 80 sheet: -2.34 (0.39), residues: 172 loop : -1.31 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 49 HIS 0.002 0.000 HIS A 209 PHE 0.008 0.001 PHE A 380 TYR 0.011 0.001 TYR B 447 ARG 0.002 0.000 ARG B 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 69 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 42 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 505 VAL cc_start: 0.6807 (OUTLIER) cc_final: 0.6511 (p) outliers start: 27 outliers final: 21 residues processed: 65 average time/residue: 0.1737 time to fit residues: 18.5794 Evaluate side-chains 62 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 40 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 553 ASP Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 24 optimal weight: 0.0050 chunk 73 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 125 optimal weight: 40.0000 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 overall best weight: 1.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN B 23 HIS ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 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: 0.8252 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10422 Z= 0.289 Angle : 0.588 9.446 14100 Z= 0.299 Chirality : 0.046 0.152 1534 Planarity : 0.003 0.039 1864 Dihedral : 4.727 19.719 1422 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.30 % Favored : 90.62 % Rotamer: Outliers : 2.34 % Allowed : 14.82 % Favored : 82.84 % 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: -2.06 (0.23), residues: 1314 helix: -2.07 (0.56), residues: 81 sheet: -2.35 (0.40), residues: 172 loop : -1.21 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 140 HIS 0.003 0.001 HIS B 535 PHE 0.007 0.001 PHE A 126 TYR 0.010 0.001 TYR B 447 ARG 0.002 0.000 ARG B 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 68 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 41 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 MET cc_start: 0.8565 (pmm) cc_final: 0.7939 (pmm) REVERT: B 154 MET cc_start: 0.8434 (mmt) cc_final: 0.8137 (mmp) REVERT: B 253 MET cc_start: 0.8688 (mmm) cc_final: 0.8428 (mmp) outliers start: 27 outliers final: 22 residues processed: 63 average time/residue: 0.1792 time to fit residues: 18.3976 Evaluate side-chains 62 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 40 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 ASP Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain D 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: 9.9990 chunk 14 optimal weight: 0.0980 chunk 71 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 125 optimal weight: 40.0000 chunk 78 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10422 Z= 0.163 Angle : 0.537 7.854 14100 Z= 0.274 Chirality : 0.045 0.164 1534 Planarity : 0.003 0.039 1864 Dihedral : 4.452 18.960 1422 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.62 % Favored : 92.30 % Rotamer: Outliers : 2.17 % Allowed : 14.73 % Favored : 83.10 % 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: -1.92 (0.23), residues: 1314 helix: -2.01 (0.55), residues: 81 sheet: -2.27 (0.40), residues: 170 loop : -1.11 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 140 HIS 0.002 0.000 HIS B 346 PHE 0.006 0.001 PHE A 380 TYR 0.010 0.001 TYR B 447 ARG 0.002 0.000 ARG B 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 66 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 41 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 MET cc_start: 0.8569 (pmm) cc_final: 0.7938 (pmm) outliers start: 25 outliers final: 20 residues processed: 63 average time/residue: 0.1881 time to fit residues: 18.9632 Evaluate side-chains 59 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 39 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 ASP Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain D 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: 5.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10422 Z= 0.219 Angle : 0.563 8.323 14100 Z= 0.286 Chirality : 0.045 0.212 1534 Planarity : 0.003 0.038 1864 Dihedral : 4.506 19.254 1422 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.46 % Favored : 91.46 % Rotamer: Outliers : 1.82 % Allowed : 14.99 % Favored : 83.19 % 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: -1.77 (0.23), residues: 1314 helix: -1.74 (0.57), residues: 81 sheet: -2.11 (0.40), residues: 173 loop : -1.02 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 49 HIS 0.002 0.001 HIS A 209 PHE 0.007 0.001 PHE A 380 TYR 0.010 0.001 TYR B 447 ARG 0.002 0.000 ARG B 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 60 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 39 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 MET cc_start: 0.8519 (pmm) cc_final: 0.7875 (pmm) REVERT: B 253 MET cc_start: 0.8538 (mmm) cc_final: 0.8226 (mmp) outliers start: 21 outliers final: 21 residues processed: 58 average time/residue: 0.1820 time to fit residues: 17.4641 Evaluate side-chains 59 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 38 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 ASP Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain D 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: 3.9990 chunk 116 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10422 Z= 0.176 Angle : 0.556 10.088 14100 Z= 0.280 Chirality : 0.045 0.198 1534 Planarity : 0.003 0.038 1864 Dihedral : 4.399 19.061 1422 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.85 % Favored : 92.07 % Rotamer: Outliers : 2.08 % Allowed : 14.99 % Favored : 82.93 % 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: -1.70 (0.23), residues: 1314 helix: -1.57 (0.58), residues: 81 sheet: -2.21 (0.40), residues: 170 loop : -0.96 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 49 HIS 0.002 0.000 HIS A 394 PHE 0.007 0.001 PHE A 380 TYR 0.010 0.001 TYR B 447 ARG 0.002 0.000 ARG B 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 62 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 38 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 MET cc_start: 0.8546 (pmm) cc_final: 0.8056 (pmm) REVERT: B 253 MET cc_start: 0.8644 (mmm) cc_final: 0.8321 (mmp) outliers start: 24 outliers final: 21 residues processed: 59 average time/residue: 0.1697 time to fit residues: 16.6446 Evaluate side-chains 59 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 38 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 ASP Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain D residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 129 optimal weight: 0.0970 chunk 119 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10422 Z= 0.150 Angle : 0.556 12.159 14100 Z= 0.279 Chirality : 0.045 0.197 1534 Planarity : 0.003 0.038 1864 Dihedral : 4.257 18.413 1422 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.77 % Favored : 92.15 % Rotamer: Outliers : 1.82 % Allowed : 15.42 % Favored : 82.76 % 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: -1.65 (0.23), residues: 1314 helix: -1.45 (0.60), residues: 81 sheet: -2.25 (0.40), residues: 165 loop : -0.93 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 492 HIS 0.002 0.000 HIS B 121 PHE 0.007 0.001 PHE A 380 TYR 0.009 0.001 TYR B 447 ARG 0.002 0.000 ARG A 29 ********************** 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 59 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 38 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.8133 (tpt) cc_final: 0.7904 (tpt) REVERT: A 294 MET cc_start: 0.8543 (pmm) cc_final: 0.7969 (pmm) REVERT: B 83 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8880 (mt) REVERT: B 253 MET cc_start: 0.8675 (mmm) cc_final: 0.8343 (mmp) REVERT: B 543 MET cc_start: 0.7392 (ppp) cc_final: 0.7121 (tmm) outliers start: 21 outliers final: 18 residues processed: 57 average time/residue: 0.1854 time to fit residues: 17.3630 Evaluate side-chains 56 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 37 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 553 ASP Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain D residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 90 optimal weight: 0.1980 chunk 5 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.049269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.034848 restraints weight = 50073.320| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 4.44 r_work: 0.2567 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2563 r_free = 0.2563 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10422 Z= 0.181 Angle : 0.563 12.463 14100 Z= 0.281 Chirality : 0.045 0.194 1534 Planarity : 0.003 0.037 1864 Dihedral : 4.274 18.610 1422 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.93 % Favored : 92.00 % Rotamer: Outliers : 1.73 % Allowed : 15.16 % Favored : 83.10 % 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: -1.54 (0.23), residues: 1314 helix: -1.35 (0.60), residues: 81 sheet: -2.00 (0.41), residues: 175 loop : -0.86 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 49 HIS 0.002 0.000 HIS B 121 PHE 0.007 0.001 PHE A 380 TYR 0.010 0.001 TYR B 447 ARG 0.002 0.000 ARG B 300 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2014.53 seconds wall clock time: 37 minutes 20.47 seconds (2240.47 seconds total)