Starting phenix.real_space_refine on Sun Feb 18 00:39:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz1_25559/02_2024/7sz1_25559.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz1_25559/02_2024/7sz1_25559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz1_25559/02_2024/7sz1_25559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz1_25559/02_2024/7sz1_25559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz1_25559/02_2024/7sz1_25559.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz1_25559/02_2024/7sz1_25559.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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 ARG 48": "NH1" <-> "NH2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "B GLU 2": "OE1" <-> "OE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B GLU 472": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B GLU 521": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "D ARG 41": "NH1" <-> "NH2" Time to flip residues: 0.05s 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: "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: "" 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: 5.85, per 1000 atoms: 0.57 Number of scatterers: 10216 At special positions: 0 Unit cell: (76.6374, 142.481, 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=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 224 " distance=2.03 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 267 " distance=2.03 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 499 " distance=2.04 Simple disulfide: pdb=" SG CYS A 502 " - pdb=" SG CYS A 511 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 42 " 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=2.02 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=2.04 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 593 " distance=2.03 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=2.03 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: 4.06 Conformation dependent library (CDL) restraints added in 2.1 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: 21 helices and 27 sheets defined 10.3% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.614A pdb=" N LYS A 56 " --> pdb=" O SER A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.723A pdb=" N ASN A 91 " --> pdb=" O TYR A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.829A pdb=" N CYS A 224 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 removed outlier: 3.812A pdb=" N LYS A 336 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 removed outlier: 4.135A pdb=" N PHE A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.537A pdb=" N ASP A 369 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 452 through 457 removed outlier: 4.032A pdb=" N LEU A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 477 Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.635A pdb=" N CYS A 555 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 29 removed outlier: 3.612A pdb=" N PHE B 24 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 25 " --> pdb=" O GLU B 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.640A pdb=" N ASN B 91 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 92 " --> pdb=" O TYR B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 92' Processing helix chain 'B' and resid 139 through 143 removed outlier: 4.095A pdb=" N ASP B 142 " --> pdb=" O GLN B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 349 through 354 removed outlier: 3.616A pdb=" N ARG B 353 " --> pdb=" O PRO B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 374 removed outlier: 3.757A pdb=" N THR B 373 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 551 through 555 removed outlier: 3.818A pdb=" N CYS B 555 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 removed outlier: 3.947A pdb=" N ASN B 580 " --> pdb=" O GLY B 577 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.794A pdb=" N VAL C 19 " --> pdb=" O ASN C 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 68 removed outlier: 7.644A pdb=" N ARG A 125 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA A 96 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N SER A 127 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A 98 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 245 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 292 through 293 removed outlier: 3.516A pdb=" N TYR A 292 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 303 " --> pdb=" O TYR A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AA8, first strand: chain 'A' and resid 345 through 347 removed outlier: 6.488A pdb=" N LEU A 345 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 414 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N SER A 440 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 416 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASN A 442 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER A 418 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL A 437 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 524 through 527 removed outlier: 3.578A pdb=" N GLU A 527 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 562 through 563 Processing sheet with id=AB2, first strand: chain 'A' and resid 573 through 576 Processing sheet with id=AB3, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AB4, first strand: chain 'B' and resid 41 through 42 removed outlier: 6.662A pdb=" N LEU B 41 " --> pdb=" O LEU B 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AB6, first strand: chain 'B' and resid 95 through 98 Processing sheet with id=AB7, first strand: chain 'B' and resid 244 through 247 removed outlier: 3.931A 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 262 Processing sheet with id=AB9, first strand: chain 'B' and resid 276 through 277 removed outlier: 3.558A pdb=" N VAL B 276 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 294 through 296 removed outlier: 3.691A pdb=" N GLU B 296 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.042A pdb=" N CYS B 313 " --> pdb=" O SER B 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 345 through 347 removed outlier: 6.382A pdb=" N LEU B 345 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP B 436 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 414 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 505 through 506 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 'D' and resid 19 through 23 removed outlier: 3.814A pdb=" N VAL D 19 " --> pdb=" O ASN D 32 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.574A pdb=" N ILE D 38 " --> pdb=" O TYR D 44 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 222 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: 2.83 Time building geometry restraints manager: 4.42 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: 3433 1.34 - 1.46: 1948 1.46 - 1.58: 4885 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 1.43e+01 bond pdb=" N VAL A 500 " pdb=" CA VAL A 500 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.35e+01 bond pdb=" N VAL B 500 " pdb=" CA VAL B 500 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" N LEU B 595 " pdb=" CA LEU B 595 " ideal model delta sigma weight residual 1.454 1.494 -0.041 1.34e-02 5.57e+03 9.22e+00 bond pdb=" N LEU B 399 " pdb=" CA LEU B 399 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.03e+00 ... (remaining 10417 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.60: 346 106.60 - 113.53: 5593 113.53 - 120.47: 3869 120.47 - 127.40: 4184 127.40 - 134.34: 108 Bond angle restraints: 14100 Sorted by residual: angle pdb=" N GLY B 288 " pdb=" CA GLY B 288 " pdb=" C GLY B 288 " ideal model delta sigma weight residual 110.21 118.47 -8.26 9.10e-01 1.21e+00 8.24e+01 angle pdb=" CA HIS B 560 " pdb=" C HIS B 560 " pdb=" N TYR B 561 " ideal model delta sigma weight residual 119.56 116.18 3.38 5.80e-01 2.97e+00 3.40e+01 angle pdb=" CA CYS A 499 " pdb=" C CYS A 499 " pdb=" O CYS A 499 " ideal model delta sigma weight residual 121.67 117.18 4.49 9.30e-01 1.16e+00 2.33e+01 angle pdb=" N SER C 9 " pdb=" CA SER C 9 " pdb=" C SER C 9 " ideal model delta sigma weight residual 114.62 109.16 5.46 1.14e+00 7.69e-01 2.29e+01 angle pdb=" N TRP B 492 " pdb=" CA TRP B 492 " pdb=" C TRP B 492 " ideal model delta sigma weight residual 113.01 107.74 5.27 1.20e+00 6.94e-01 1.93e+01 ... (remaining 14095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5751 17.64 - 35.29: 554 35.29 - 52.93: 130 52.93 - 70.57: 25 70.57 - 88.21: 20 Dihedral angle restraints: 6480 sinusoidal: 2692 harmonic: 3788 Sorted by residual: 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 -86.00 -169.36 83.36 1 1.00e+01 1.00e-02 8.49e+01 dihedral pdb=" CB CYS A 287 " pdb=" SG CYS A 287 " pdb=" SG CYS A 302 " pdb=" CB CYS A 302 " ideal model delta sinusoidal sigma weight residual 93.00 175.66 -82.66 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS B 287 " pdb=" SG CYS B 287 " pdb=" SG CYS B 302 " pdb=" CB CYS B 302 " ideal model delta sinusoidal sigma weight residual 93.00 172.97 -79.97 1 1.00e+01 1.00e-02 7.93e+01 ... (remaining 6477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1164 0.055 - 0.110: 306 0.110 - 0.165: 56 0.165 - 0.220: 4 0.220 - 0.275: 4 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 2.79 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA CYS B 491 " pdb=" N CYS B 491 " pdb=" C CYS B 491 " pdb=" CB CYS B 491 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB VAL B 500 " pdb=" CA VAL B 500 " pdb=" CG1 VAL B 500 " pdb=" CG2 VAL B 500 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1531 not shown) Planarity restraints: 1864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 611 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.02e+00 pdb=" C GLY B 611 " -0.039 2.00e-02 2.50e+03 pdb=" O GLY B 611 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS B 612 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 498 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C ASP A 498 " -0.031 2.00e-02 2.50e+03 pdb=" O ASP A 498 " 0.012 2.00e-02 2.50e+03 pdb=" N CYS A 499 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 557 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C GLN B 557 " -0.031 2.00e-02 2.50e+03 pdb=" O GLN B 557 " 0.012 2.00e-02 2.50e+03 pdb=" N CYS B 558 " 0.010 2.00e-02 2.50e+03 ... (remaining 1861 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 188 2.65 - 3.22: 9851 3.22 - 3.78: 14164 3.78 - 4.34: 20405 4.34 - 4.90: 33352 Nonbonded interactions: 77960 Sorted by model distance: nonbonded pdb=" O ARG A 403 " pdb=" OG SER A 433 " model vdw 2.092 2.440 nonbonded pdb=" O LEU A 539 " pdb=" OG1 THR A 546 " model vdw 2.122 2.440 nonbonded pdb=" O HIS B 23 " pdb=" OG SER B 26 " model vdw 2.167 2.440 nonbonded pdb=" OG1 THR B 10 " pdb=" OE1 GLU B 42 " model vdw 2.182 2.440 nonbonded pdb=" O ILE B 67 " pdb=" ND2 ASN B 100 " model vdw 2.196 2.520 ... (remaining 77955 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: 1.990 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: 0.010 Extract box with map and model: 7.250 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.780 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 0.046 10422 Z= 0.303 Angle : 0.788 8.262 14100 Z= 0.500 Chirality : 0.051 0.275 1534 Planarity : 0.004 0.042 1864 Dihedral : 14.469 88.214 3884 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.54 % Favored : 85.31 % Rotamer: Outliers : 1.65 % Allowed : 6.76 % Favored : 91.59 % 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: -4.74 (0.18), residues: 1314 helix: -4.40 (0.31), residues: 66 sheet: -3.32 (0.43), residues: 117 loop : -3.41 (0.15), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 492 HIS 0.005 0.001 HIS A 409 PHE 0.017 0.001 PHE A 156 TYR 0.009 0.001 TYR A 292 ARG 0.003 0.000 ARG A 125 *********************** 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 107 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 103 average time/residue: 0.2576 time to fit residues: 36.8791 Evaluate side-chains 55 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain B residue 505 VAL 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: 6.9990 chunk 98 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 0.0170 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 79 ASN A 134 ASN A 151 ASN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN A 334 HIS A 398 ASN A 469 ASN A 541 GLN A 580 ASN A 594 HIS A 597 HIS B 23 HIS ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 49 ASN B 115 ASN B 117 GLN B 134 ASN B 247 ASN B 384 GLN B 394 HIS B 411 GLN B 452 ASN B 504 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10422 Z= 0.181 Angle : 0.616 8.947 14100 Z= 0.325 Chirality : 0.046 0.233 1534 Planarity : 0.004 0.036 1864 Dihedral : 6.023 52.547 1432 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.72 % Favored : 88.13 % Rotamer: Outliers : 1.21 % Allowed : 13.08 % Favored : 85.70 % 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: -3.99 (0.20), residues: 1314 helix: -3.51 (0.42), residues: 70 sheet: -3.14 (0.41), residues: 124 loop : -2.82 (0.16), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 584 HIS 0.006 0.001 HIS B 560 PHE 0.009 0.001 PHE B 380 TYR 0.016 0.001 TYR D 44 ARG 0.003 0.000 ARG B 550 *********************** 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 : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 543 MET cc_start: 0.6682 (pmm) cc_final: 0.5778 (ttt) REVERT: B 576 MET cc_start: 0.7679 (tpp) cc_final: 0.7331 (tpp) outliers start: 14 outliers final: 11 residues processed: 68 average time/residue: 0.2243 time to fit residues: 23.0044 Evaluate side-chains 58 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 117 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 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: 0.7723 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10422 Z= 0.257 Angle : 0.612 9.435 14100 Z= 0.323 Chirality : 0.045 0.195 1534 Planarity : 0.004 0.075 1864 Dihedral : 5.761 54.177 1427 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.47 % Favored : 86.45 % Rotamer: Outliers : 2.60 % Allowed : 15.16 % Favored : 82.24 % 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: -3.57 (0.21), residues: 1314 helix: -3.24 (0.52), residues: 58 sheet: -2.98 (0.39), residues: 136 loop : -2.49 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 176 HIS 0.006 0.001 HIS B 560 PHE 0.009 0.001 PHE A 396 TYR 0.018 0.001 TYR D 44 ARG 0.018 0.000 ARG B 310 *********************** 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 81 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 51 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 TYR cc_start: 0.7629 (m-80) cc_final: 0.7373 (m-80) REVERT: B 543 MET cc_start: 0.6716 (pmm) cc_final: 0.5816 (ttt) REVERT: B 576 MET cc_start: 0.7661 (tpp) cc_final: 0.7273 (tpp) outliers start: 30 outliers final: 18 residues processed: 80 average time/residue: 0.1961 time to fit residues: 24.2720 Evaluate side-chains 64 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 46 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 523 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 6.9990 chunk 88 optimal weight: 0.3980 chunk 61 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 79 optimal weight: 0.0980 chunk 118 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 62 optimal weight: 0.2980 chunk 112 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10422 Z= 0.178 Angle : 0.576 11.305 14100 Z= 0.302 Chirality : 0.045 0.156 1534 Planarity : 0.003 0.037 1864 Dihedral : 5.417 56.674 1423 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.64 % Favored : 88.28 % Rotamer: Outliers : 2.60 % Allowed : 16.55 % Favored : 80.85 % 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: -3.29 (0.22), residues: 1314 helix: -2.97 (0.53), residues: 63 sheet: -2.82 (0.38), residues: 146 loop : -2.26 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 492 HIS 0.007 0.001 HIS B 560 PHE 0.010 0.001 PHE A 126 TYR 0.012 0.001 TYR D 44 ARG 0.007 0.000 ARG B 310 *********************** 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 81 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 51 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8334 (tp-100) REVERT: B 543 MET cc_start: 0.6943 (pmm) cc_final: 0.6184 (ptt) outliers start: 30 outliers final: 15 residues processed: 79 average time/residue: 0.1750 time to fit residues: 22.3082 Evaluate side-chains 61 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 516 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 31 optimal weight: 0.4980 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 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: 0.7823 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 10422 Z= 0.366 Angle : 0.679 10.089 14100 Z= 0.354 Chirality : 0.047 0.228 1534 Planarity : 0.004 0.037 1864 Dihedral : 5.838 58.840 1423 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.84 % Favored : 85.08 % Rotamer: Outliers : 2.86 % Allowed : 18.89 % Favored : 78.25 % 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: -3.19 (0.22), residues: 1314 helix: -2.85 (0.58), residues: 57 sheet: -2.68 (0.42), residues: 131 loop : -2.23 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 176 HIS 0.008 0.001 HIS B 560 PHE 0.011 0.001 PHE A 156 TYR 0.012 0.001 TYR D 37 ARG 0.007 0.000 ARG B 310 *********************** 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 73 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 40 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8362 (tp-100) REVERT: B 244 MET cc_start: 0.8090 (mmm) cc_final: 0.7583 (mmm) outliers start: 33 outliers final: 22 residues processed: 72 average time/residue: 0.1712 time to fit residues: 20.1908 Evaluate side-chains 60 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 37 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain D residue 20 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 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: 0.7758 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10422 Z= 0.196 Angle : 0.595 12.200 14100 Z= 0.310 Chirality : 0.046 0.164 1534 Planarity : 0.003 0.039 1864 Dihedral : 5.550 56.294 1423 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.49 % Favored : 88.43 % Rotamer: Outliers : 2.51 % Allowed : 19.41 % Favored : 78.08 % 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: -3.04 (0.22), residues: 1314 helix: -2.80 (0.56), residues: 65 sheet: -2.66 (0.41), residues: 141 loop : -2.08 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 386 HIS 0.007 0.001 HIS B 560 PHE 0.008 0.001 PHE A 126 TYR 0.015 0.001 TYR D 37 ARG 0.004 0.000 ARG B 310 *********************** 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 71 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 42 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 543 MET cc_start: 0.7027 (pmm) cc_final: 0.6298 (ptt) REVERT: B 576 MET cc_start: 0.8210 (tpp) cc_final: 0.6854 (tpp) outliers start: 29 outliers final: 19 residues processed: 70 average time/residue: 0.1659 time to fit residues: 19.5784 Evaluate side-chains 58 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 39 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain D residue 20 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 1.9990 chunk 14 optimal weight: 0.0020 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 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: 0.7765 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10422 Z= 0.207 Angle : 0.594 10.240 14100 Z= 0.309 Chirality : 0.045 0.149 1534 Planarity : 0.003 0.040 1864 Dihedral : 5.413 52.537 1423 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.94 % Favored : 86.99 % Rotamer: Outliers : 2.60 % Allowed : 20.28 % Favored : 77.12 % 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: -2.87 (0.22), residues: 1314 helix: -2.71 (0.56), residues: 65 sheet: -2.49 (0.44), residues: 129 loop : -1.97 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 176 HIS 0.009 0.001 HIS B 560 PHE 0.006 0.001 PHE B 380 TYR 0.015 0.001 TYR D 37 ARG 0.003 0.000 ARG B 310 *********************** 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 72 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 42 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8087 (tp-100) REVERT: B 543 MET cc_start: 0.6885 (pmm) cc_final: 0.6020 (ptt) outliers start: 30 outliers final: 22 residues processed: 70 average time/residue: 0.1969 time to fit residues: 21.7118 Evaluate side-chains 63 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 40 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain D residue 20 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN B 32 ASN B 33 ASN B 384 GLN ** B 516 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: 0.7722 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10422 Z= 0.159 Angle : 0.578 10.370 14100 Z= 0.298 Chirality : 0.045 0.144 1534 Planarity : 0.003 0.040 1864 Dihedral : 5.219 49.417 1423 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.34 % Favored : 88.58 % Rotamer: Outliers : 2.43 % Allowed : 20.19 % Favored : 77.38 % 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: -2.73 (0.23), residues: 1314 helix: -2.69 (0.53), residues: 71 sheet: -2.43 (0.44), residues: 129 loop : -1.84 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 386 HIS 0.007 0.001 HIS B 560 PHE 0.006 0.001 PHE A 380 TYR 0.009 0.001 TYR D 37 ARG 0.016 0.000 ARG B 310 *********************** 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 77 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 49 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8508 (pmm) cc_final: 0.8182 (pmm) REVERT: B 543 MET cc_start: 0.6843 (pmm) cc_final: 0.5993 (ptt) outliers start: 28 outliers final: 24 residues processed: 75 average time/residue: 0.1677 time to fit residues: 20.7801 Evaluate side-chains 67 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 43 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain D residue 20 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 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: 0.7751 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10422 Z= 0.216 Angle : 0.614 11.576 14100 Z= 0.317 Chirality : 0.045 0.142 1534 Planarity : 0.003 0.041 1864 Dihedral : 5.262 47.392 1423 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.10 % Favored : 87.82 % Rotamer: Outliers : 2.77 % Allowed : 20.10 % Favored : 77.12 % 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: -2.69 (0.23), residues: 1314 helix: -2.67 (0.54), residues: 71 sheet: -2.44 (0.43), residues: 129 loop : -1.81 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 176 HIS 0.008 0.001 HIS B 560 PHE 0.005 0.001 PHE B 380 TYR 0.013 0.001 TYR D 37 ARG 0.012 0.000 ARG B 310 *********************** 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 75 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 43 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8525 (pmm) cc_final: 0.8191 (pmm) REVERT: B 543 MET cc_start: 0.6923 (pmm) cc_final: 0.6029 (ptt) outliers start: 32 outliers final: 28 residues processed: 73 average time/residue: 0.1569 time to fit residues: 19.4710 Evaluate side-chains 71 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 43 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain D residue 20 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.1980 chunk 58 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 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: 0.7726 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10422 Z= 0.181 Angle : 0.605 11.623 14100 Z= 0.310 Chirality : 0.045 0.142 1534 Planarity : 0.003 0.040 1864 Dihedral : 5.150 44.793 1423 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.42 % Favored : 88.51 % Rotamer: Outliers : 2.51 % Allowed : 20.62 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.23), residues: 1314 helix: -2.57 (0.55), residues: 71 sheet: -2.41 (0.45), residues: 117 loop : -1.76 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 386 HIS 0.008 0.001 HIS B 560 PHE 0.005 0.001 PHE B 525 TYR 0.010 0.001 TYR D 37 ARG 0.009 0.000 ARG B 310 ********************** 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: 29 poor density : 44 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8525 (pmm) cc_final: 0.8197 (pmm) REVERT: B 543 MET cc_start: 0.6906 (pmm) cc_final: 0.6040 (ptt) outliers start: 29 outliers final: 27 residues processed: 71 average time/residue: 0.1545 time to fit residues: 18.5409 Evaluate side-chains 70 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 43 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain D residue 20 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 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 = 0.3560 r_free = 0.3560 target = 0.055857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.041998 restraints weight = 64704.580| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 5.72 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10422 Z= 0.173 Angle : 0.594 10.402 14100 Z= 0.304 Chirality : 0.045 0.165 1534 Planarity : 0.003 0.040 1864 Dihedral : 5.029 41.977 1423 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.96 % Favored : 88.96 % Rotamer: Outliers : 2.51 % Allowed : 20.62 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.23), residues: 1314 helix: -2.44 (0.56), residues: 71 sheet: -2.33 (0.45), residues: 117 loop : -1.69 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 492 HIS 0.009 0.001 HIS B 560 PHE 0.005 0.001 PHE B 525 TYR 0.010 0.001 TYR D 37 ARG 0.008 0.000 ARG B 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2065.05 seconds wall clock time: 38 minutes 21.78 seconds (2301.78 seconds total)