Starting phenix.real_space_refine on Wed Feb 14 20:34:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz5_25561/02_2024/7sz5_25561.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz5_25561/02_2024/7sz5_25561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz5_25561/02_2024/7sz5_25561.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz5_25561/02_2024/7sz5_25561.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz5_25561/02_2024/7sz5_25561.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz5_25561/02_2024/7sz5_25561.pdb" } resolution = 3.6 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= 0.025 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 847 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 114 5.16 5 C 5793 2.51 5 N 1668 2.21 5 O 1792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 3": "OE1" <-> "OE2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9367 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4723 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 30, 'TRANS': 583} Chain: "C" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 386 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "B" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3872 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 21, 'TRANS': 478} Chain: "D" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 386 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Time building chain proxies: 5.17, per 1000 atoms: 0.55 Number of scatterers: 9367 At special positions: 0 Unit cell: (64.764, 145.719, 130.607, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 1792 8.00 N 1668 7.00 C 5793 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 34 " distance=2.02 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 163 " distance=2.04 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=2.00 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=2.02 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 267 " distance=2.02 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 283 " distance=2.02 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 302 " distance=2.04 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 499 " distance=2.02 Simple disulfide: pdb=" SG CYS A 502 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 555 " distance=2.05 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 612 " distance=2.04 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 21 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 32 " distance=2.01 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 34 " distance=2.02 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 163 " distance=2.02 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=2.00 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=2.02 Simple disulfide: pdb=" SG CYS B 227 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 267 " distance=2.02 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 283 " distance=2.02 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 491 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 499 " distance=2.02 Simple disulfide: pdb=" SG CYS D 8 " - pdb=" SG CYS D 21 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 32 " distance=2.02 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 43 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.9 seconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 23 sheets defined 11.0% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 removed outlier: 3.654A pdb=" N PHE A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 139 through 144 removed outlier: 4.083A pdb=" N ILE A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.636A pdb=" N LYS A 372 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 410 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 452 through 457 removed outlier: 3.567A pdb=" N LEU A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 476 Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.843A pdb=" N ASN A 554 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.650A pdb=" N GLU A 610 " --> pdb=" O PRO A 607 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 611 " --> pdb=" O GLY A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 611' Processing helix chain 'B' and resid 19 through 31 removed outlier: 3.704A pdb=" N PHE B 24 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.641A pdb=" N GLU B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 475 through 479 removed outlier: 4.180A pdb=" N GLY B 479 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 68 removed outlier: 7.334A pdb=" N ARG A 125 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA A 96 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA4, first strand: chain 'A' and resid 261 through 262 Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 277 Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.229A pdb=" N CYS A 313 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 345 through 347 removed outlier: 6.502A pdb=" N LEU A 345 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE A 438 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA A 415 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N SER A 440 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL A 417 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 505 through 507 removed outlier: 4.162A pdb=" N GLU A 510 " --> pdb=" O ARG A 507 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 525 through 527 Processing sheet with id=AB1, first strand: chain 'A' and resid 573 through 576 removed outlier: 4.067A pdb=" N VAL A 575 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 586 through 587 removed outlier: 3.792A pdb=" N TYR A 586 " --> pdb=" O HIS A 594 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AB5, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AB6, first strand: chain 'B' and resid 16 through 17 Processing sheet with id=AB7, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.559A pdb=" N LEU B 41 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ALA B 68 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 43 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 65 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU B 98 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 67 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TYR B 93 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ARG B 125 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 95 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL B 124 " --> pdb=" O SER B 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 244 through 246 Processing sheet with id=AB9, first strand: chain 'B' and resid 261 through 262 Processing sheet with id=AC1, first strand: chain 'B' and resid 276 through 277 Processing sheet with id=AC2, first strand: chain 'B' and resid 291 through 295 Processing sheet with id=AC3, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AC4, first strand: chain 'B' and resid 346 through 347 removed outlier: 6.244A pdb=" N LEU B 381 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 414 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 5 through 7 103 hydrogen bonds defined for protein. 183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2984 1.33 - 1.46: 1962 1.46 - 1.58: 4474 1.58 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 9552 Sorted by residual: bond pdb=" CA SER A 196 " pdb=" CB SER A 196 " ideal model delta sigma weight residual 1.534 1.468 0.066 1.45e-02 4.76e+03 2.05e+01 bond pdb=" CA SER B 196 " pdb=" CB SER B 196 " ideal model delta sigma weight residual 1.533 1.471 0.062 1.60e-02 3.91e+03 1.49e+01 bond pdb=" CA SER C 3 " pdb=" CB SER C 3 " ideal model delta sigma weight residual 1.530 1.476 0.055 1.52e-02 4.33e+03 1.29e+01 bond pdb=" N CYS A 538 " pdb=" CA CYS A 538 " ideal model delta sigma weight residual 1.453 1.494 -0.042 1.31e-02 5.83e+03 1.01e+01 bond pdb=" N ASN A 134 " pdb=" CA ASN A 134 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.66e+00 ... (remaining 9547 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.20: 183 105.20 - 112.43: 4797 112.43 - 119.65: 3288 119.65 - 126.87: 4533 126.87 - 134.09: 116 Bond angle restraints: 12917 Sorted by residual: angle pdb=" CA PHE B 156 " pdb=" CB PHE B 156 " pdb=" CG PHE B 156 " ideal model delta sigma weight residual 113.80 119.25 -5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" C LYS B 430 " pdb=" N GLU B 431 " pdb=" CA GLU B 431 " ideal model delta sigma weight residual 122.87 116.59 6.28 1.44e+00 4.82e-01 1.90e+01 angle pdb=" N VAL A 500 " pdb=" CA VAL A 500 " pdb=" C VAL A 500 " ideal model delta sigma weight residual 113.53 109.28 4.25 9.80e-01 1.04e+00 1.88e+01 angle pdb=" N PRO B 171 " pdb=" CA PRO B 171 " pdb=" C PRO B 171 " ideal model delta sigma weight residual 112.47 121.14 -8.67 2.06e+00 2.36e-01 1.77e+01 angle pdb=" N ILE B 432 " pdb=" CA ILE B 432 " pdb=" C ILE B 432 " ideal model delta sigma weight residual 109.58 104.48 5.10 1.29e+00 6.01e-01 1.57e+01 ... (remaining 12912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5228 17.97 - 35.95: 562 35.95 - 53.92: 107 53.92 - 71.90: 26 71.90 - 89.87: 11 Dihedral angle restraints: 5934 sinusoidal: 2453 harmonic: 3481 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 604 " pdb=" CB CYS A 604 " ideal model delta sinusoidal sigma weight residual 93.00 7.81 85.19 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS A 195 " pdb=" SG CYS A 195 " pdb=" SG CYS A 207 " pdb=" CB CYS A 207 " ideal model delta sinusoidal sigma weight residual 93.00 175.50 -82.50 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 555 " pdb=" CB CYS A 555 " ideal model delta sinusoidal sigma weight residual -86.00 -16.01 -69.99 1 1.00e+01 1.00e-02 6.31e+01 ... (remaining 5931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1023 0.057 - 0.114: 327 0.114 - 0.170: 53 0.170 - 0.227: 12 0.227 - 0.284: 3 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CA ILE A 67 " pdb=" N ILE A 67 " pdb=" C ILE A 67 " pdb=" CB ILE A 67 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ILE A 43 " pdb=" N ILE A 43 " pdb=" C ILE A 43 " pdb=" CB ILE A 43 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ILE B 432 " pdb=" N ILE B 432 " pdb=" C ILE B 432 " pdb=" CB ILE B 432 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1415 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 158 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.80e+00 pdb=" C ASN B 158 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN B 158 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS B 159 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 192 " 0.011 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C ALA B 192 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA B 192 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN B 193 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 168 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C PRO B 168 " 0.037 2.00e-02 2.50e+03 pdb=" O PRO B 168 " -0.014 2.00e-02 2.50e+03 pdb=" N SER B 169 " -0.012 2.00e-02 2.50e+03 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 140 2.54 - 3.13: 7929 3.13 - 3.72: 13565 3.72 - 4.31: 19045 4.31 - 4.90: 31401 Nonbonded interactions: 72080 Sorted by model distance: nonbonded pdb=" CB MET B 154 " pdb=" CE1 PHE B 156 " model vdw 1.947 3.740 nonbonded pdb=" O ARG A 403 " pdb=" OG SER A 433 " model vdw 2.029 2.440 nonbonded pdb=" OH TYR B 101 " pdb=" OE1 GLN D 26 " model vdw 2.138 2.440 nonbonded pdb=" OG1 THR A 391 " pdb=" OG1 THR A 422 " model vdw 2.154 2.440 nonbonded pdb=" O VAL B 437 " pdb=" OG1 THR B 464 " model vdw 2.163 2.440 ... (remaining 72075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 13.410 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.180 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 9552 Z= 0.485 Angle : 0.902 8.671 12917 Z= 0.558 Chirality : 0.057 0.284 1418 Planarity : 0.005 0.043 1709 Dihedral : 14.971 89.870 3550 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 16.83 % Favored : 83.00 % Rotamer: Outliers : 2.83 % Allowed : 10.84 % Favored : 86.33 % 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: -5.33 (0.18), residues: 1206 helix: -5.02 (0.18), residues: 91 sheet: -3.65 (0.39), residues: 127 loop : -3.75 (0.16), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 176 HIS 0.006 0.001 HIS B 409 PHE 0.020 0.002 PHE B 156 TYR 0.017 0.002 TYR A 447 ARG 0.004 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 60 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 GLU cc_start: 0.5570 (OUTLIER) cc_final: 0.4767 (mm-30) outliers start: 30 outliers final: 5 residues processed: 87 average time/residue: 0.1966 time to fit residues: 25.2265 Evaluate side-chains 41 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 419 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 0.1980 chunk 50 optimal weight: 0.0670 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 40 ASN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN A 597 HIS B 23 HIS ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN D 4 HIS D 14 GLN D 18 HIS D 45 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9552 Z= 0.259 Angle : 0.648 7.983 12917 Z= 0.337 Chirality : 0.046 0.210 1418 Planarity : 0.004 0.041 1709 Dihedral : 6.391 52.643 1306 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 2.83 % Allowed : 14.61 % Favored : 82.56 % 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: -4.57 (0.20), residues: 1206 helix: -4.62 (0.24), residues: 91 sheet: -3.23 (0.40), residues: 130 loop : -3.15 (0.17), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 386 HIS 0.005 0.001 HIS D 18 PHE 0.012 0.001 PHE B 156 TYR 0.008 0.001 TYR A 447 ARG 0.002 0.000 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 39 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8146 (pp) REVERT: A 253 MET cc_start: 0.8955 (mmt) cc_final: 0.8645 (mmm) REVERT: B 498 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7107 (p0) outliers start: 30 outliers final: 13 residues processed: 67 average time/residue: 0.1689 time to fit residues: 18.4987 Evaluate side-chains 49 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 34 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 498 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 88 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 597 HIS B 40 ASN B 334 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9552 Z= 0.165 Angle : 0.568 9.008 12917 Z= 0.295 Chirality : 0.045 0.174 1418 Planarity : 0.004 0.044 1709 Dihedral : 5.480 50.840 1298 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer: Outliers : 2.92 % Allowed : 17.81 % Favored : 79.26 % 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: -3.83 (0.22), residues: 1206 helix: -3.75 (0.40), residues: 66 sheet: -2.75 (0.45), residues: 123 loop : -2.70 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 386 HIS 0.012 0.001 HIS A 597 PHE 0.011 0.001 PHE B 31 TYR 0.007 0.001 TYR A 447 ARG 0.002 0.000 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 41 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.8190 (tpp) cc_final: 0.7757 (tpt) REVERT: A 98 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8118 (pp) REVERT: A 152 MET cc_start: 0.8124 (ptm) cc_final: 0.7855 (ptp) REVERT: A 253 MET cc_start: 0.8904 (mmt) cc_final: 0.8649 (mmm) REVERT: B 498 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7053 (p0) outliers start: 31 outliers final: 14 residues processed: 69 average time/residue: 0.1590 time to fit residues: 17.9190 Evaluate side-chains 51 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 35 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 498 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9552 Z= 0.267 Angle : 0.608 8.692 12917 Z= 0.314 Chirality : 0.044 0.158 1418 Planarity : 0.004 0.052 1709 Dihedral : 5.543 55.791 1297 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 3.39 % Allowed : 19.51 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.22), residues: 1206 helix: -3.27 (0.46), residues: 72 sheet: -2.68 (0.44), residues: 130 loop : -2.51 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 386 HIS 0.009 0.001 HIS A 597 PHE 0.008 0.001 PHE B 156 TYR 0.008 0.001 TYR A 586 ARG 0.002 0.000 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 34 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8297 (pp) REVERT: B 498 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7061 (p0) outliers start: 36 outliers final: 22 residues processed: 66 average time/residue: 0.1515 time to fit residues: 17.0025 Evaluate side-chains 58 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 34 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain D residue 12 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 99 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9552 Z= 0.268 Angle : 0.615 8.953 12917 Z= 0.313 Chirality : 0.044 0.164 1418 Planarity : 0.004 0.051 1709 Dihedral : 5.560 59.348 1297 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.52 % Favored : 86.48 % Rotamer: Outliers : 3.77 % Allowed : 21.11 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.22), residues: 1206 helix: -2.96 (0.50), residues: 72 sheet: -2.62 (0.44), residues: 130 loop : -2.37 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 386 HIS 0.006 0.001 HIS A 597 PHE 0.007 0.001 PHE D 23 TYR 0.008 0.001 TYR A 586 ARG 0.002 0.000 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 35 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8295 (pp) REVERT: A 253 MET cc_start: 0.8625 (mmm) cc_final: 0.8382 (mmm) REVERT: B 498 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.6961 (p0) outliers start: 40 outliers final: 27 residues processed: 71 average time/residue: 0.1605 time to fit residues: 18.8376 Evaluate side-chains 62 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 33 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain D residue 12 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 112 optimal weight: 0.0070 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 100 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 HIS A 597 HIS B 411 GLN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9552 Z= 0.181 Angle : 0.582 10.681 12917 Z= 0.293 Chirality : 0.044 0.185 1418 Planarity : 0.004 0.055 1709 Dihedral : 5.336 55.263 1297 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 3.58 % Allowed : 21.87 % Favored : 74.55 % 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: -3.21 (0.23), residues: 1206 helix: -2.92 (0.50), residues: 78 sheet: -2.52 (0.43), residues: 145 loop : -2.19 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 176 HIS 0.002 0.001 HIS A 121 PHE 0.009 0.001 PHE D 23 TYR 0.006 0.001 TYR A 586 ARG 0.002 0.000 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 36 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8303 (pp) REVERT: B 498 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.6937 (p0) outliers start: 38 outliers final: 26 residues processed: 71 average time/residue: 0.1500 time to fit residues: 17.5985 Evaluate side-chains 61 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 33 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain D residue 12 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9552 Z= 0.322 Angle : 0.647 9.824 12917 Z= 0.329 Chirality : 0.045 0.171 1418 Planarity : 0.004 0.050 1709 Dihedral : 5.303 23.538 1296 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.60 % Favored : 86.40 % Rotamer: Outliers : 3.77 % Allowed : 22.62 % Favored : 73.61 % 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: -3.12 (0.23), residues: 1206 helix: -2.61 (0.54), residues: 72 sheet: -2.51 (0.43), residues: 140 loop : -2.16 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 176 HIS 0.007 0.001 HIS A 597 PHE 0.011 0.001 PHE B 412 TYR 0.008 0.001 TYR A 586 ARG 0.003 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 32 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8373 (pp) REVERT: A 253 MET cc_start: 0.8676 (mmm) cc_final: 0.8236 (tpp) REVERT: B 152 MET cc_start: 0.8460 (tmm) cc_final: 0.7424 (tmm) REVERT: B 498 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7007 (p0) outliers start: 40 outliers final: 25 residues processed: 69 average time/residue: 0.1420 time to fit residues: 16.5789 Evaluate side-chains 59 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 32 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 21 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 91 optimal weight: 0.0670 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 101 optimal weight: 0.3980 chunk 108 optimal weight: 0.6980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS B 40 ASN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9552 Z= 0.165 Angle : 0.571 10.111 12917 Z= 0.290 Chirality : 0.044 0.186 1418 Planarity : 0.004 0.049 1709 Dihedral : 5.008 23.035 1296 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 3.30 % Allowed : 23.19 % Favored : 73.52 % 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: -2.86 (0.23), residues: 1206 helix: -2.60 (0.52), residues: 78 sheet: -2.26 (0.46), residues: 135 loop : -1.96 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 176 HIS 0.004 0.001 HIS A 597 PHE 0.009 0.001 PHE C 23 TYR 0.008 0.001 TYR A 292 ARG 0.002 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 36 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8578 (mmm) cc_final: 0.8065 (tpt) REVERT: B 82 ILE cc_start: 0.8380 (mm) cc_final: 0.8152 (mm) REVERT: B 152 MET cc_start: 0.8283 (tmm) cc_final: 0.7388 (tmm) REVERT: B 154 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7196 (mmp) REVERT: B 498 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.6891 (p0) outliers start: 35 outliers final: 21 residues processed: 67 average time/residue: 0.1642 time to fit residues: 17.8507 Evaluate side-chains 57 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 34 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain D residue 12 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS D 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9552 Z= 0.155 Angle : 0.566 9.834 12917 Z= 0.286 Chirality : 0.044 0.204 1418 Planarity : 0.004 0.040 1709 Dihedral : 4.862 23.464 1296 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 2.83 % Allowed : 23.37 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.23), residues: 1206 helix: -2.34 (0.54), residues: 78 sheet: -2.13 (0.46), residues: 135 loop : -1.86 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 176 HIS 0.004 0.001 HIS A 597 PHE 0.008 0.001 PHE D 23 TYR 0.006 0.001 TYR A 292 ARG 0.002 0.000 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 34 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8593 (mmm) cc_final: 0.8180 (tpp) REVERT: B 152 MET cc_start: 0.8229 (tmm) cc_final: 0.7370 (tmm) REVERT: B 154 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7030 (mmp) REVERT: B 498 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7034 (p0) outliers start: 30 outliers final: 22 residues processed: 60 average time/residue: 0.1587 time to fit residues: 15.8242 Evaluate side-chains 56 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 32 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 0.0470 chunk 29 optimal weight: 5.9990 overall best weight: 1.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9552 Z= 0.261 Angle : 0.626 10.512 12917 Z= 0.314 Chirality : 0.044 0.205 1418 Planarity : 0.004 0.044 1709 Dihedral : 5.013 24.260 1296 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.43 % Favored : 86.57 % Rotamer: Outliers : 2.64 % Allowed : 23.94 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.24), residues: 1206 helix: -1.91 (0.58), residues: 72 sheet: -2.44 (0.44), residues: 140 loop : -1.82 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 176 HIS 0.007 0.001 HIS A 597 PHE 0.008 0.001 PHE B 412 TYR 0.007 0.001 TYR A 586 ARG 0.002 0.000 ARG B 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 34 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7738 (tpt) cc_final: 0.7495 (tpt) REVERT: B 152 MET cc_start: 0.8314 (tmm) cc_final: 0.7511 (tmm) REVERT: B 154 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.7046 (mmp) REVERT: B 498 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.6935 (p0) outliers start: 28 outliers final: 21 residues processed: 58 average time/residue: 0.1602 time to fit residues: 15.5963 Evaluate side-chains 56 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 33 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 96 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 5 optimal weight: 0.0570 chunk 69 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS B 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.047060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.032971 restraints weight = 67395.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.033692 restraints weight = 41421.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.034232 restraints weight = 29986.492| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9552 Z= 0.141 Angle : 0.581 10.351 12917 Z= 0.291 Chirality : 0.044 0.211 1418 Planarity : 0.004 0.039 1709 Dihedral : 4.780 23.665 1296 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 2.36 % Allowed : 24.32 % Favored : 73.33 % 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: -2.60 (0.24), residues: 1206 helix: -2.27 (0.54), residues: 84 sheet: -2.23 (0.44), residues: 140 loop : -1.74 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 386 HIS 0.004 0.001 HIS A 597 PHE 0.008 0.001 PHE C 23 TYR 0.006 0.001 TYR A 292 ARG 0.002 0.000 ARG B 427 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1897.26 seconds wall clock time: 35 minutes 28.06 seconds (2128.06 seconds total)