Starting phenix.real_space_refine on Mon Jun 16 08:13:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sz1_25559/06_2025/7sz1_25559.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sz1_25559/06_2025/7sz1_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/cci-nas-00/data/ceres_data/7sz1_25559/06_2025/7sz1_25559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sz1_25559/06_2025/7sz1_25559.map" model { file = "/net/cci-nas-00/data/ceres_data/7sz1_25559/06_2025/7sz1_25559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sz1_25559/06_2025/7sz1_25559.cif" } 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. Time to flip 23 residue(s): 0.47s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.45, per 1000 atoms: 0.63 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 - 3.00 Amino acid : True - 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: 2.33 Conformation dependent library (CDL) restraints added in 1.4 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: 1.28 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: 3.05 Time building geometry restraints manager: 2.83 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: 0.00 - 1.65: 13394 1.65 - 3.30: 603 3.30 - 4.96: 84 4.96 - 6.61: 16 6.61 - 8.26: 3 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 3.040 nonbonded pdb=" O LEU A 539 " pdb=" OG1 THR A 546 " model vdw 2.122 3.040 nonbonded pdb=" O HIS B 23 " pdb=" OG SER B 26 " model vdw 2.167 3.040 nonbonded pdb=" OG1 THR B 10 " pdb=" OE1 GLU B 42 " model vdw 2.182 3.040 nonbonded pdb=" O ILE B 67 " pdb=" ND2 ASN B 100 " model vdw 2.196 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 1.330 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.250 Find NCS groups from input model: 0.320 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.690 ------------------------------------------------------------------------------- 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 10478 Z= 0.274 Angle : 0.805 8.262 14212 Z= 0.505 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 Details of bonding type rmsd hydrogen bonds : bond 0.29203 ( 116) hydrogen bonds : angle 10.54256 ( 222) SS BOND : bond 0.00702 ( 56) SS BOND : angle 2.01865 ( 112) covalent geometry : bond 0.00460 (10422) covalent geometry : angle 0.78784 (14100) *********************** 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 to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.133 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: 0.2706 time to fit residues: 39.0048 Evaluate side-chains 55 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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: 5.9990 chunk 98 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 33 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 overall best weight: 0.4920 ------------------------------------------------------------------------------- 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 462 GLN A 469 ASN A 541 GLN A 580 ASN A 594 HIS A 597 HIS B 23 HIS B 32 ASN B 33 ASN B 40 ASN B 49 ASN B 115 ASN B 117 GLN B 134 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** B 566 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.057961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.043316 restraints weight = 58349.233| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 5.66 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10478 Z= 0.119 Angle : 0.646 9.211 14212 Z= 0.339 Chirality : 0.046 0.234 1534 Planarity : 0.004 0.055 1864 Dihedral : 6.062 53.285 1432 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.27 % Favored : 89.57 % Rotamer: Outliers : 1.04 % Allowed : 12.13 % Favored : 86.83 % 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: -3.94 (0.20), residues: 1314 helix: -3.50 (0.42), residues: 70 sheet: -3.15 (0.41), residues: 119 loop : -2.78 (0.16), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 584 HIS 0.006 0.001 HIS B 560 PHE 0.010 0.001 PHE B 380 TYR 0.016 0.001 TYR D 44 ARG 0.003 0.000 ARG B 198 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 116) hydrogen bonds : angle 6.83772 ( 222) SS BOND : bond 0.00278 ( 56) SS BOND : angle 1.20757 ( 112) covalent geometry : bond 0.00259 (10422) covalent geometry : angle 0.63924 (14100) *********************** 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 to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 CYS cc_start: 0.5643 (OUTLIER) cc_final: 0.5425 (m) REVERT: C 44 TYR cc_start: 0.8913 (m-10) cc_final: 0.8581 (m-80) REVERT: B 87 MET cc_start: 0.8423 (mpp) cc_final: 0.8173 (mpp) REVERT: B 543 MET cc_start: 0.8334 (pmm) cc_final: 0.7867 (ttt) REVERT: D 21 MET cc_start: 0.8639 (ptp) cc_final: 0.8032 (pmm) outliers start: 12 outliers final: 9 residues processed: 69 average time/residue: 0.2605 time to fit residues: 27.2858 Evaluate side-chains 58 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 A residue 534 CYS 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 500 VAL Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 523 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN B 139 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.055232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.040831 restraints weight = 63731.499| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 6.11 r_work: 0.2928 rms_B_bonded: 5.71 restraints_weight: 2.0000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10478 Z= 0.210 Angle : 0.679 9.628 14212 Z= 0.354 Chirality : 0.046 0.213 1534 Planarity : 0.005 0.121 1864 Dihedral : 5.762 55.356 1423 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.48 % Favored : 87.44 % Rotamer: Outliers : 2.08 % Allowed : 13.95 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.21), residues: 1314 helix: -3.24 (0.49), residues: 64 sheet: -2.90 (0.40), residues: 134 loop : -2.45 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 176 HIS 0.006 0.001 HIS B 560 PHE 0.013 0.001 PHE A 126 TYR 0.016 0.001 TYR D 44 ARG 0.022 0.001 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 116) hydrogen bonds : angle 6.38613 ( 222) SS BOND : bond 0.00357 ( 56) SS BOND : angle 1.23502 ( 112) covalent geometry : bond 0.00464 (10422) covalent geometry : angle 0.67297 (14100) *********************** 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 74 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.9185 (mtp) cc_final: 0.8983 (mtp) REVERT: C 44 TYR cc_start: 0.9214 (m-10) cc_final: 0.8955 (m-80) REVERT: B 294 MET cc_start: 0.8976 (tmm) cc_final: 0.8498 (ppp) REVERT: B 543 MET cc_start: 0.8328 (pmm) cc_final: 0.7926 (ttt) outliers start: 24 outliers final: 18 residues processed: 74 average time/residue: 0.1728 time to fit residues: 20.4895 Evaluate side-chains 63 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 A residue 534 CYS Chi-restraints excluded: chain B residue 7 CYS 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 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 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 113 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 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 = 0.3549 r_free = 0.3549 target = 0.055620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.041399 restraints weight = 63688.515| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 5.92 r_work: 0.2954 rms_B_bonded: 5.73 restraints_weight: 2.0000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10478 Z= 0.135 Angle : 0.608 11.098 14212 Z= 0.319 Chirality : 0.046 0.164 1534 Planarity : 0.004 0.048 1864 Dihedral : 5.593 59.179 1423 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.81 % Favored : 89.12 % Rotamer: Outliers : 2.51 % Allowed : 14.90 % Favored : 82.58 % 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: -3.18 (0.21), residues: 1314 helix: -2.98 (0.52), residues: 63 sheet: -2.71 (0.41), residues: 134 loop : -2.20 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 176 HIS 0.007 0.001 HIS B 560 PHE 0.007 0.001 PHE A 126 TYR 0.011 0.001 TYR D 37 ARG 0.011 0.000 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 116) hydrogen bonds : angle 6.02546 ( 222) SS BOND : bond 0.00286 ( 56) SS BOND : angle 1.10583 ( 112) covalent geometry : bond 0.00307 (10422) covalent geometry : angle 0.60279 (14100) *********************** 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 77 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 48 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 TYR cc_start: 0.9212 (m-10) cc_final: 0.8977 (m-80) REVERT: B 294 MET cc_start: 0.8948 (tmm) cc_final: 0.8371 (ppp) REVERT: B 543 MET cc_start: 0.8411 (pmm) cc_final: 0.8058 (ptt) outliers start: 29 outliers final: 16 residues processed: 77 average time/residue: 0.1761 time to fit residues: 21.7160 Evaluate side-chains 61 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 412 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain B residue 7 CYS 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 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 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 11 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 121 optimal weight: 0.0980 chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 0.1980 chunk 105 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 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 = 0.3561 r_free = 0.3561 target = 0.055922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.041707 restraints weight = 63284.182| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 6.13 r_work: 0.2966 rms_B_bonded: 5.72 restraints_weight: 2.0000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10478 Z= 0.104 Angle : 0.588 10.922 14212 Z= 0.305 Chirality : 0.045 0.218 1534 Planarity : 0.004 0.039 1864 Dihedral : 5.374 58.458 1423 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.04 % Favored : 88.89 % Rotamer: Outliers : 2.25 % Allowed : 16.98 % Favored : 80.76 % 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: -2.96 (0.22), residues: 1314 helix: -2.87 (0.53), residues: 65 sheet: -2.55 (0.43), residues: 124 loop : -2.04 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 176 HIS 0.007 0.001 HIS B 560 PHE 0.008 0.001 PHE A 380 TYR 0.007 0.001 TYR A 561 ARG 0.005 0.000 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 116) hydrogen bonds : angle 6.02498 ( 222) SS BOND : bond 0.00231 ( 56) SS BOND : angle 1.09564 ( 112) covalent geometry : bond 0.00242 (10422) covalent geometry : angle 0.58248 (14100) *********************** 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 78 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 TYR cc_start: 0.9257 (m-10) cc_final: 0.8865 (m-80) REVERT: B 152 MET cc_start: 0.8518 (ppp) cc_final: 0.7954 (ppp) REVERT: B 154 MET cc_start: 0.9034 (ptm) cc_final: 0.8804 (ptm) REVERT: B 244 MET cc_start: 0.9345 (mmm) cc_final: 0.8664 (mmm) REVERT: B 294 MET cc_start: 0.9035 (tmm) cc_final: 0.8628 (ppp) REVERT: B 543 MET cc_start: 0.8370 (pmm) cc_final: 0.8046 (ptt) outliers start: 26 outliers final: 19 residues processed: 75 average time/residue: 0.1806 time to fit residues: 21.2288 Evaluate side-chains 65 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 534 CYS 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 227 CYS Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 313 CYS 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 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 55 optimal weight: 0.0980 chunk 87 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 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 = 0.3555 r_free = 0.3555 target = 0.055645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.041314 restraints weight = 63885.714| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 5.92 r_work: 0.2958 rms_B_bonded: 5.75 restraints_weight: 2.0000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10478 Z= 0.117 Angle : 0.592 12.782 14212 Z= 0.306 Chirality : 0.045 0.163 1534 Planarity : 0.004 0.038 1864 Dihedral : 5.319 55.452 1423 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.43 % Favored : 89.50 % Rotamer: Outliers : 2.43 % Allowed : 17.24 % Favored : 80.33 % 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: -2.82 (0.22), residues: 1314 helix: -2.77 (0.54), residues: 65 sheet: -2.43 (0.44), residues: 124 loop : -1.94 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 176 HIS 0.008 0.001 HIS B 560 PHE 0.008 0.001 PHE A 380 TYR 0.006 0.001 TYR A 275 ARG 0.003 0.000 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.02812 ( 116) hydrogen bonds : angle 5.76648 ( 222) SS BOND : bond 0.00235 ( 56) SS BOND : angle 1.06577 ( 112) covalent geometry : bond 0.00268 (10422) covalent geometry : angle 0.58648 (14100) *********************** 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 77 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 49 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 MET cc_start: 0.9048 (ptp) cc_final: 0.8584 (pmm) REVERT: C 44 TYR cc_start: 0.9252 (m-10) cc_final: 0.8863 (m-80) REVERT: B 60 GLU cc_start: 0.9282 (tt0) cc_final: 0.8904 (tm-30) REVERT: B 152 MET cc_start: 0.8449 (ppp) cc_final: 0.7802 (ppp) REVERT: B 154 MET cc_start: 0.9107 (ptm) cc_final: 0.8869 (ptm) REVERT: B 244 MET cc_start: 0.9205 (mmm) cc_final: 0.8666 (mmm) REVERT: B 294 MET cc_start: 0.9010 (tmm) cc_final: 0.8707 (tmm) REVERT: B 543 MET cc_start: 0.8363 (pmm) cc_final: 0.8067 (ptt) REVERT: B 576 MET cc_start: 0.8910 (tpp) cc_final: 0.8502 (tpp) outliers start: 28 outliers final: 22 residues processed: 73 average time/residue: 0.1616 time to fit residues: 19.4927 Evaluate side-chains 67 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 PHE 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 382 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 534 CYS 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 227 CYS Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 313 CYS 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 45 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 4 optimal weight: 0.0050 chunk 19 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 32 optimal weight: 0.0770 chunk 101 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.056247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.042068 restraints weight = 64048.519| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 5.94 r_work: 0.2984 rms_B_bonded: 5.80 restraints_weight: 2.0000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10478 Z= 0.091 Angle : 0.573 12.888 14212 Z= 0.294 Chirality : 0.045 0.147 1534 Planarity : 0.003 0.036 1864 Dihedral : 5.098 51.058 1423 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.43 % Favored : 89.50 % Rotamer: Outliers : 2.43 % Allowed : 17.50 % Favored : 80.07 % 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: -2.63 (0.22), residues: 1314 helix: -2.38 (0.55), residues: 71 sheet: -2.17 (0.49), residues: 107 loop : -1.84 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 492 HIS 0.009 0.001 HIS B 560 PHE 0.009 0.001 PHE A 380 TYR 0.006 0.001 TYR C 13 ARG 0.002 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.02562 ( 116) hydrogen bonds : angle 5.56262 ( 222) SS BOND : bond 0.00195 ( 56) SS BOND : angle 0.99549 ( 112) covalent geometry : bond 0.00209 (10422) covalent geometry : angle 0.56817 (14100) *********************** 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 79 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.9320 (mmm) cc_final: 0.9055 (mmm) REVERT: A 294 MET cc_start: 0.8950 (ptp) cc_final: 0.8350 (pmm) REVERT: C 44 TYR cc_start: 0.9218 (m-10) cc_final: 0.8745 (m-80) REVERT: B 60 GLU cc_start: 0.9278 (tt0) cc_final: 0.8916 (tm-30) REVERT: B 152 MET cc_start: 0.8425 (ppp) cc_final: 0.8069 (ppp) REVERT: B 244 MET cc_start: 0.9319 (mmm) cc_final: 0.8824 (mmm) REVERT: B 543 MET cc_start: 0.8219 (pmm) cc_final: 0.7964 (ptt) REVERT: D 40 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8424 (tm-30) REVERT: D 44 TYR cc_start: 0.8129 (m-80) cc_final: 0.7893 (m-80) outliers start: 28 outliers final: 19 residues processed: 77 average time/residue: 0.1694 time to fit residues: 21.3263 Evaluate side-chains 65 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 421 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 538 CYS 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 227 CYS Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 438 ILE 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 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 35 optimal weight: 6.9990 chunk 120 optimal weight: 0.4980 chunk 84 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.054339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.040030 restraints weight = 65379.513| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 5.85 r_work: 0.2916 rms_B_bonded: 5.73 restraints_weight: 2.0000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 : 0.005 0.052 10478 Z= 0.217 Angle : 0.673 13.685 14212 Z= 0.345 Chirality : 0.046 0.154 1534 Planarity : 0.004 0.040 1864 Dihedral : 5.465 48.336 1423 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.40 % Favored : 87.52 % Rotamer: Outliers : 2.17 % Allowed : 18.11 % Favored : 79.72 % 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: -2.64 (0.22), residues: 1314 helix: -2.59 (0.56), residues: 65 sheet: -2.17 (0.46), residues: 117 loop : -1.83 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 176 HIS 0.007 0.001 HIS B 560 PHE 0.014 0.001 PHE B 148 TYR 0.017 0.001 TYR D 37 ARG 0.003 0.000 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 116) hydrogen bonds : angle 5.83580 ( 222) SS BOND : bond 0.00447 ( 56) SS BOND : angle 1.39809 ( 112) covalent geometry : bond 0.00486 (10422) covalent geometry : angle 0.66362 (14100) *********************** 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 70 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8488 (pmm) cc_final: 0.8162 (pmm) REVERT: A 294 MET cc_start: 0.9029 (ptp) cc_final: 0.8302 (pmm) REVERT: B 152 MET cc_start: 0.8770 (ppp) cc_final: 0.8243 (ppp) REVERT: B 244 MET cc_start: 0.9352 (mmm) cc_final: 0.8716 (mmm) REVERT: B 543 MET cc_start: 0.8322 (pmm) cc_final: 0.8034 (ptt) REVERT: B 576 MET cc_start: 0.8898 (tpp) cc_final: 0.8483 (tpp) outliers start: 25 outliers final: 19 residues processed: 69 average time/residue: 0.1858 time to fit residues: 20.2294 Evaluate side-chains 61 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 A residue 538 CYS 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 95 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 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 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 10 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 84 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.055814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.041369 restraints weight = 63768.383| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 5.91 r_work: 0.2969 rms_B_bonded: 5.73 restraints_weight: 2.0000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 10478 Z= 0.106 Angle : 0.640 15.206 14212 Z= 0.326 Chirality : 0.046 0.144 1534 Planarity : 0.004 0.039 1864 Dihedral : 5.243 44.986 1423 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.97 % Favored : 89.95 % Rotamer: Outliers : 2.17 % Allowed : 17.85 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.22), residues: 1314 helix: -2.45 (0.57), residues: 65 sheet: -2.18 (0.46), residues: 117 loop : -1.76 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 386 HIS 0.008 0.001 HIS B 560 PHE 0.007 0.001 PHE A 380 TYR 0.006 0.001 TYR B 251 ARG 0.012 0.000 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.02725 ( 116) hydrogen bonds : angle 5.69239 ( 222) SS BOND : bond 0.00230 ( 56) SS BOND : angle 1.31262 ( 112) covalent geometry : bond 0.00250 (10422) covalent geometry : angle 0.63207 (14100) *********************** 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 70 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8495 (pmm) cc_final: 0.8256 (pmm) REVERT: A 294 MET cc_start: 0.8962 (ptp) cc_final: 0.8327 (pmm) REVERT: B 60 GLU cc_start: 0.9278 (tt0) cc_final: 0.8863 (tm-30) REVERT: B 154 MET cc_start: 0.9157 (ptm) cc_final: 0.8929 (ptm) REVERT: B 244 MET cc_start: 0.9303 (mmm) cc_final: 0.8748 (mmm) REVERT: B 292 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: B 543 MET cc_start: 0.8219 (pmm) cc_final: 0.7959 (ptt) REVERT: B 576 MET cc_start: 0.8904 (tpp) cc_final: 0.8493 (tpp) REVERT: D 44 TYR cc_start: 0.8121 (m-80) cc_final: 0.7910 (m-80) outliers start: 25 outliers final: 20 residues processed: 69 average time/residue: 0.1733 time to fit residues: 19.6809 Evaluate side-chains 66 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 412 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 567 CYS 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 95 LEU Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 292 TYR 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 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 40 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 23 optimal weight: 0.4980 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 0.0170 chunk 75 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 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 = 0.3583 r_free = 0.3583 target = 0.056273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.041941 restraints weight = 63339.006| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 5.92 r_work: 0.2994 rms_B_bonded: 5.79 restraints_weight: 2.0000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 10478 Z= 0.099 Angle : 0.632 16.204 14212 Z= 0.317 Chirality : 0.045 0.152 1534 Planarity : 0.004 0.043 1864 Dihedral : 5.030 39.926 1423 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.12 % Favored : 89.80 % Rotamer: Outliers : 1.65 % Allowed : 18.46 % Favored : 79.90 % 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: -2.49 (0.22), residues: 1314 helix: -2.19 (0.54), residues: 77 sheet: -2.23 (0.47), residues: 107 loop : -1.72 (0.18), residues: 1130 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 0.010 0.001 PHE A 380 TYR 0.006 0.001 TYR C 13 ARG 0.011 0.000 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.02550 ( 116) hydrogen bonds : angle 5.43940 ( 222) SS BOND : bond 0.00188 ( 56) SS BOND : angle 1.08554 ( 112) covalent geometry : bond 0.00228 (10422) covalent geometry : angle 0.62662 (14100) ********************** 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 67 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8321 (pmm) cc_final: 0.8018 (pmm) REVERT: A 294 MET cc_start: 0.8978 (ptp) cc_final: 0.8493 (pmm) REVERT: C 44 TYR cc_start: 0.8972 (m-80) cc_final: 0.8458 (m-80) REVERT: B 60 GLU cc_start: 0.9274 (tt0) cc_final: 0.8838 (tm-30) REVERT: B 152 MET cc_start: 0.8083 (ppp) cc_final: 0.7550 (ppp) REVERT: B 154 MET cc_start: 0.9011 (ptm) cc_final: 0.8788 (ptm) REVERT: B 244 MET cc_start: 0.9298 (mmm) cc_final: 0.8722 (mmm) REVERT: B 292 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: B 543 MET cc_start: 0.8187 (pmm) cc_final: 0.7945 (ptt) REVERT: B 576 MET cc_start: 0.8919 (tpp) cc_final: 0.8484 (tpp) REVERT: D 40 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8484 (tm-30) outliers start: 19 outliers final: 17 residues processed: 66 average time/residue: 0.2044 time to fit residues: 21.6461 Evaluate side-chains 63 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 412 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 313 CYS 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 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 78 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 0.0030 chunk 99 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 114 optimal weight: 0.3980 chunk 119 optimal weight: 10.0000 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3584 r_free = 0.3584 target = 0.056290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.041987 restraints weight = 62667.154| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 5.93 r_work: 0.3000 rms_B_bonded: 5.83 restraints_weight: 2.0000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 10478 Z= 0.101 Angle : 0.630 15.810 14212 Z= 0.319 Chirality : 0.045 0.151 1534 Planarity : 0.004 0.042 1864 Dihedral : 4.954 37.630 1423 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.21 % Favored : 90.72 % Rotamer: Outliers : 1.99 % Allowed : 18.20 % Favored : 79.81 % 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: -2.19 (0.54), residues: 77 sheet: -2.15 (0.47), residues: 107 loop : -1.65 (0.18), residues: 1130 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 0.010 0.001 PHE A 380 TYR 0.008 0.001 TYR C 44 ARG 0.009 0.000 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.02605 ( 116) hydrogen bonds : angle 5.38462 ( 222) SS BOND : bond 0.00182 ( 56) SS BOND : angle 1.03665 ( 112) covalent geometry : bond 0.00233 (10422) covalent geometry : angle 0.62606 (14100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5785.90 seconds wall clock time: 100 minutes 59.91 seconds (6059.91 seconds total)