Starting phenix.real_space_refine on Sun Mar 17 04:40:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs3_34219/03_2024/8gs3_34219.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs3_34219/03_2024/8gs3_34219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs3_34219/03_2024/8gs3_34219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs3_34219/03_2024/8gs3_34219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs3_34219/03_2024/8gs3_34219.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs3_34219/03_2024/8gs3_34219.pdb" } resolution = 3.9 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= 0.002 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 8368 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 38 5.16 5 C 5389 2.51 5 N 1395 2.21 5 O 1554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 344": "OD1" <-> "OD2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 430": "OD1" <-> "OD2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B ASP 220": "OD1" <-> "OD2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B ASP 350": "OD1" <-> "OD2" Residue "B ASP 386": "OD1" <-> "OD2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B ASP 430": "OD1" <-> "OD2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B ASP 465": "OD1" <-> "OD2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B ASP 492": "OD1" <-> "OD2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 577": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8376 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4191 Classifications: {'peptide': 534} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 491} Chain breaks: 2 Chain: "B" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4185 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 490} Chain breaks: 2 Time building chain proxies: 4.60, per 1000 atoms: 0.55 Number of scatterers: 8376 At special positions: 0 Unit cell: (113.67, 108.618, 83.358, 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 38 16.00 O 1554 8.00 N 1395 7.00 C 5389 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 340 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 544 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 141 " distance=2.64 Simple disulfide: pdb=" SG CYS B 340 " - pdb=" SG CYS B 351 " distance=2.05 Simple disulfide: pdb=" SG CYS B 510 " - pdb=" SG CYS B 544 " distance=2.04 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: 2.88 Conformation dependent library (CDL) restraints added in 1.5 seconds 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1962 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 4 sheets defined 46.5% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.549A pdb=" N LYS A 82 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.570A pdb=" N ASN A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 135 removed outlier: 3.640A pdb=" N THR A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 255 through 272 Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 288 through 299 Processing helix chain 'A' and resid 300 through 304 removed outlier: 3.510A pdb=" N GLU A 304 " --> pdb=" O HIS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.873A pdb=" N TYR A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 356 through 363 removed outlier: 3.825A pdb=" N LEU A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 395 through 399 removed outlier: 4.193A pdb=" N ASN A 398 " --> pdb=" O GLU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 4.655A pdb=" N GLY A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 446 through 458 Processing helix chain 'A' and resid 466 through 483 removed outlier: 3.589A pdb=" N ARG A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 495 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 532 through 537 removed outlier: 4.160A pdb=" N VAL A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 568 Processing helix chain 'A' and resid 617 through 626 Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.707A pdb=" N HIS A 630 " --> pdb=" O HIS A 626 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR A 632 " --> pdb=" O VAL A 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.563A pdb=" N ASN B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 135 removed outlier: 3.769A pdb=" N THR B 132 " --> pdb=" O ASP B 128 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 removed outlier: 3.728A pdb=" N MET B 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 255 through 272 Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 288 through 299 removed outlier: 3.501A pdb=" N LEU B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.903A pdb=" N TYR B 330 " --> pdb=" O GLN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 355 removed outlier: 3.876A pdb=" N GLN B 354 " --> pdb=" O ASP B 350 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 355 " --> pdb=" O CYS B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 363 removed outlier: 3.543A pdb=" N GLN B 363 " --> pdb=" O GLU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 395 through 399 removed outlier: 4.051A pdb=" N ASN B 398 " --> pdb=" O GLU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 4.488A pdb=" N GLY B 416 " --> pdb=" O LYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 446 through 458 Processing helix chain 'B' and resid 466 through 483 removed outlier: 3.910A pdb=" N PHE B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 495 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 532 through 537 removed outlier: 3.932A pdb=" N VAL B 536 " --> pdb=" O GLY B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 568 Processing helix chain 'B' and resid 617 through 626 Processing helix chain 'B' and resid 626 through 632 removed outlier: 4.226A pdb=" N HIS B 630 " --> pdb=" O HIS B 626 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR B 632 " --> pdb=" O VAL B 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 626 through 632' Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.991A pdb=" N LYS A 50 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 56 removed outlier: 5.497A pdb=" N GLN A 68 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL A 148 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU A 70 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 146 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 235 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS A 200 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ARG A 280 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL A 202 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE A 282 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL A 204 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A 284 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE A 206 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY A 286 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG A 309 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 282 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE A 311 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 284 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N GLN A 313 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY A 286 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE A 401 " --> pdb=" O TYR A 502 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N TYR A 504 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A 403 " --> pdb=" O TYR A 504 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N PHE A 506 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 405 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU A 602 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE A 503 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 611 " --> pdb=" O HIS A 605 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 46 Processing sheet with id=AA4, first strand: chain 'B' and resid 54 through 56 removed outlier: 5.448A pdb=" N GLN B 68 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 148 " --> pdb=" O GLN B 68 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU B 70 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL B 146 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR B 143 " --> pdb=" O ASN B 236 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 235 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LYS B 200 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG B 280 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL B 202 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE B 282 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL B 204 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL B 284 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE B 206 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY B 286 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG B 309 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE B 282 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ILE B 311 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL B 284 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLN B 313 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY B 286 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 401 " --> pdb=" O TYR B 502 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N TYR B 504 " --> pdb=" O ILE B 401 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU B 403 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N PHE B 506 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 405 " --> pdb=" O PHE B 506 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N THR B 501 " --> pdb=" O LEU B 602 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N LEU B 604 " --> pdb=" O THR B 501 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N PHE B 503 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE B 606 " --> pdb=" O PHE B 503 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA B 505 " --> pdb=" O ILE B 606 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 936 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: 2.19 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.12: 1 1.12 - 1.41: 3654 1.41 - 1.69: 4911 1.69 - 1.98: 60 1.98 - 2.26: 2 Bond restraints: 8628 Sorted by residual: bond pdb=" CG PRO B 201 " pdb=" CD PRO B 201 " ideal model delta sigma weight residual 1.503 0.839 0.664 3.40e-02 8.65e+02 3.81e+02 bond pdb=" CB PRO B 201 " pdb=" CG PRO B 201 " ideal model delta sigma weight residual 1.492 2.264 -0.772 5.00e-02 4.00e+02 2.38e+02 bond pdb=" N PRO B 201 " pdb=" CD PRO B 201 " ideal model delta sigma weight residual 1.473 1.636 -0.163 1.40e-02 5.10e+03 1.36e+02 bond pdb=" CA PRO B 201 " pdb=" CB PRO B 201 " ideal model delta sigma weight residual 1.533 1.420 0.114 1.42e-02 4.96e+03 6.39e+01 bond pdb=" CB CYS B 141 " pdb=" SG CYS B 141 " ideal model delta sigma weight residual 1.808 2.054 -0.246 3.30e-02 9.18e+02 5.54e+01 ... (remaining 8623 not shown) Histogram of bond angle deviations from ideal: 0.04 - 32.13: 1 32.13 - 64.21: 0 64.21 - 96.29: 4 96.29 - 128.38: 11698 128.38 - 160.46: 89 Bond angle restraints: 11792 Sorted by residual: angle pdb=" CB PRO B 201 " pdb=" CG PRO B 201 " pdb=" CD PRO B 201 " ideal model delta sigma weight residual 106.10 0.04 106.06 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO B 201 " pdb=" N PRO B 201 " pdb=" CD PRO B 201 " ideal model delta sigma weight residual 112.00 77.60 34.40 1.40e+00 5.10e-01 6.04e+02 angle pdb=" CA PRO B 201 " pdb=" CB PRO B 201 " pdb=" CG PRO B 201 " ideal model delta sigma weight residual 104.50 84.71 19.79 1.90e+00 2.77e-01 1.08e+02 angle pdb=" CA LYS B 200 " pdb=" C LYS B 200 " pdb=" O LYS B 200 " ideal model delta sigma weight residual 120.60 111.42 9.18 9.00e-01 1.23e+00 1.04e+02 angle pdb=" C LYS B 200 " pdb=" N PRO B 201 " pdb=" CD PRO B 201 " ideal model delta sigma weight residual 125.00 160.46 -35.46 4.10e+00 5.95e-02 7.48e+01 ... (remaining 11787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.65: 4553 19.65 - 39.31: 401 39.31 - 58.96: 98 58.96 - 78.62: 12 78.62 - 98.27: 8 Dihedral angle restraints: 5072 sinusoidal: 1993 harmonic: 3079 Sorted by residual: dihedral pdb=" CB CYS B 106 " pdb=" SG CYS B 106 " pdb=" SG CYS B 141 " pdb=" CB CYS B 141 " ideal model delta sinusoidal sigma weight residual -86.00 -28.48 -57.52 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS B 510 " pdb=" SG CYS B 510 " pdb=" SG CYS B 544 " pdb=" CB CYS B 544 " ideal model delta sinusoidal sigma weight residual -86.00 -37.20 -48.80 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CA PRO B 201 " pdb=" CB PRO B 201 " pdb=" CG PRO B 201 " pdb=" CD PRO B 201 " ideal model delta sinusoidal sigma weight residual -38.00 -136.27 98.27 1 2.00e+01 2.50e-03 2.75e+01 ... (remaining 5069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1114 0.071 - 0.141: 158 0.141 - 0.211: 3 0.211 - 0.282: 1 0.282 - 0.352: 1 Chirality restraints: 1277 Sorted by residual: chirality pdb=" CA LYS B 200 " pdb=" N LYS B 200 " pdb=" C LYS B 200 " pdb=" CB LYS B 200 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA PRO B 201 " pdb=" N PRO B 201 " pdb=" C PRO B 201 " pdb=" CB PRO B 201 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB VAL A 230 " pdb=" CA VAL A 230 " pdb=" CG1 VAL A 230 " pdb=" CG2 VAL A 230 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 1274 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 102 " -0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO B 103 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 102 " 0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO A 103 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 383 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO A 384 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.044 5.00e-02 4.00e+02 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 33 2.43 - 3.05: 5540 3.05 - 3.66: 13549 3.66 - 4.28: 19743 4.28 - 4.90: 32430 Nonbonded interactions: 71295 Sorted by model distance: nonbonded pdb=" O GLN A 250 " pdb=" OE1 GLN A 250 " model vdw 1.810 3.040 nonbonded pdb=" CD1 LEU B 58 " pdb=" CD1 LEU B 63 " model vdw 1.918 3.880 nonbonded pdb=" OD1 ASP B 492 " pdb=" OH TYR B 596 " model vdw 2.182 2.440 nonbonded pdb=" O HIS A 207 " pdb=" OH TYR A 237 " model vdw 2.183 2.440 nonbonded pdb=" O ILE B 389 " pdb=" OE2 GLU B 392 " model vdw 2.198 3.040 ... (remaining 71290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 150 or resid 198 through 633)) selection = chain 'B' } 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 3.820 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.670 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.013 0.772 8628 Z= 0.774 Angle : 1.319 106.059 11792 Z= 0.573 Chirality : 0.047 0.352 1277 Planarity : 0.007 0.089 1539 Dihedral : 15.895 98.273 3092 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 22.50 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.27 (0.25), residues: 1055 helix: 0.93 (0.27), residues: 378 sheet: 0.05 (0.41), residues: 140 loop : -0.25 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 518 HIS 0.008 0.001 HIS B 207 PHE 0.014 0.002 PHE B 546 TYR 0.039 0.002 TYR B 69 ARG 0.008 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 556 VAL cc_start: 0.9006 (t) cc_final: 0.8781 (p) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1687 time to fit residues: 19.8314 Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 61 optimal weight: 0.3980 chunk 96 optimal weight: 10.0000 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 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.772 8628 Z= 0.774 Angle : 1.318 106.099 11792 Z= 0.572 Chirality : 0.047 0.352 1277 Planarity : 0.007 0.089 1539 Dihedral : 4.783 26.199 1157 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 23.16 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.27 (0.25), residues: 1055 helix: 0.93 (0.27), residues: 378 sheet: 0.05 (0.41), residues: 140 loop : -0.25 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 518 HIS 0.008 0.001 HIS B 207 PHE 0.014 0.002 PHE B 546 TYR 0.039 0.002 TYR B 69 ARG 0.008 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 556 VAL cc_start: 0.9008 (t) cc_final: 0.8781 (p) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1624 time to fit residues: 19.1715 Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 32 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.772 8628 Z= 0.774 Angle : 1.318 106.099 11792 Z= 0.572 Chirality : 0.047 0.352 1277 Planarity : 0.007 0.089 1539 Dihedral : 4.783 26.199 1157 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 23.16 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.27 (0.25), residues: 1055 helix: 0.93 (0.27), residues: 378 sheet: 0.05 (0.41), residues: 140 loop : -0.25 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 518 HIS 0.008 0.001 HIS B 207 PHE 0.014 0.002 PHE B 546 TYR 0.039 0.002 TYR B 69 ARG 0.008 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 556 VAL cc_start: 0.9008 (t) cc_final: 0.8781 (p) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1566 time to fit residues: 18.4943 Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 64 optimal weight: 40.0000 chunk 96 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.772 8628 Z= 0.774 Angle : 1.318 106.100 11792 Z= 0.572 Chirality : 0.047 0.352 1277 Planarity : 0.007 0.089 1539 Dihedral : 4.783 26.199 1157 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 23.16 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.27 (0.25), residues: 1055 helix: 0.93 (0.27), residues: 378 sheet: 0.05 (0.41), residues: 140 loop : -0.25 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 518 HIS 0.008 0.001 HIS B 207 PHE 0.014 0.002 PHE B 546 TYR 0.039 0.002 TYR B 69 ARG 0.008 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 556 VAL cc_start: 0.9008 (t) cc_final: 0.8781 (p) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1681 time to fit residues: 19.8585 Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.0770 chunk 1 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 0.0980 chunk 87 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 overall best weight: 2.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.772 8628 Z= 0.774 Angle : 1.318 106.100 11792 Z= 0.572 Chirality : 0.047 0.352 1277 Planarity : 0.007 0.089 1539 Dihedral : 4.783 26.199 1157 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 23.16 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.27 (0.25), residues: 1055 helix: 0.93 (0.27), residues: 378 sheet: 0.05 (0.41), residues: 140 loop : -0.25 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 518 HIS 0.008 0.001 HIS B 207 PHE 0.014 0.002 PHE B 546 TYR 0.039 0.002 TYR B 69 ARG 0.008 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 556 VAL cc_start: 0.9008 (t) cc_final: 0.8781 (p) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1587 time to fit residues: 18.6873 Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.772 8628 Z= 0.774 Angle : 1.318 106.100 11792 Z= 0.572 Chirality : 0.047 0.352 1277 Planarity : 0.007 0.089 1539 Dihedral : 4.783 26.199 1157 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 23.16 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.27 (0.25), residues: 1055 helix: 0.93 (0.27), residues: 378 sheet: 0.05 (0.41), residues: 140 loop : -0.25 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 518 HIS 0.008 0.001 HIS B 207 PHE 0.014 0.002 PHE B 546 TYR 0.039 0.002 TYR B 69 ARG 0.008 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 556 VAL cc_start: 0.9008 (t) cc_final: 0.8781 (p) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1644 time to fit residues: 19.3201 Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 86 optimal weight: 0.0670 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 47 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.772 8628 Z= 0.774 Angle : 1.318 106.100 11792 Z= 0.572 Chirality : 0.047 0.352 1277 Planarity : 0.007 0.089 1539 Dihedral : 4.783 26.199 1157 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 23.16 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.27 (0.25), residues: 1055 helix: 0.93 (0.27), residues: 378 sheet: 0.05 (0.41), residues: 140 loop : -0.25 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 518 HIS 0.008 0.001 HIS B 207 PHE 0.014 0.002 PHE B 546 TYR 0.039 0.002 TYR B 69 ARG 0.008 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 556 VAL cc_start: 0.9008 (t) cc_final: 0.8781 (p) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1583 time to fit residues: 18.2737 Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 64 optimal weight: 40.0000 chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 0.0370 chunk 80 optimal weight: 0.0670 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 chunk 89 optimal weight: 4.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.772 8628 Z= 0.774 Angle : 1.318 106.100 11792 Z= 0.572 Chirality : 0.047 0.352 1277 Planarity : 0.007 0.089 1539 Dihedral : 4.783 26.199 1157 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 23.16 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.27 (0.25), residues: 1055 helix: 0.93 (0.27), residues: 378 sheet: 0.05 (0.41), residues: 140 loop : -0.25 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 518 HIS 0.008 0.001 HIS B 207 PHE 0.014 0.002 PHE B 546 TYR 0.039 0.002 TYR B 69 ARG 0.008 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 556 VAL cc_start: 0.9008 (t) cc_final: 0.8781 (p) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1680 time to fit residues: 19.7081 Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 10.0000 chunk 97 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 29 optimal weight: 0.4980 chunk 86 optimal weight: 0.0470 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.772 8628 Z= 0.774 Angle : 1.318 106.100 11792 Z= 0.572 Chirality : 0.047 0.352 1277 Planarity : 0.007 0.089 1539 Dihedral : 4.783 26.199 1157 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 23.16 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.27 (0.25), residues: 1055 helix: 0.93 (0.27), residues: 378 sheet: 0.05 (0.41), residues: 140 loop : -0.25 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 518 HIS 0.008 0.001 HIS B 207 PHE 0.014 0.002 PHE B 546 TYR 0.039 0.002 TYR B 69 ARG 0.008 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 556 VAL cc_start: 0.9008 (t) cc_final: 0.8781 (p) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1685 time to fit residues: 19.7187 Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.0980 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.772 8628 Z= 0.774 Angle : 1.318 106.100 11792 Z= 0.572 Chirality : 0.047 0.352 1277 Planarity : 0.007 0.089 1539 Dihedral : 4.783 26.199 1157 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 23.16 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.27 (0.25), residues: 1055 helix: 0.93 (0.27), residues: 378 sheet: 0.05 (0.41), residues: 140 loop : -0.25 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 518 HIS 0.008 0.001 HIS B 207 PHE 0.014 0.002 PHE B 546 TYR 0.039 0.002 TYR B 69 ARG 0.008 0.001 ARG B 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 556 VAL cc_start: 0.9008 (t) cc_final: 0.8781 (p) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1576 time to fit residues: 18.5999 Evaluate side-chains 77 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 35 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** 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 = 0.3470 r_free = 0.3470 target = 0.067883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.053844 restraints weight = 38876.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.055465 restraints weight = 24773.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.056423 restraints weight = 18277.872| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.0014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.772 8628 Z= 0.774 Angle : 1.318 106.100 11792 Z= 0.572 Chirality : 0.047 0.352 1277 Planarity : 0.007 0.089 1539 Dihedral : 4.783 26.199 1157 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 23.16 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.27 (0.25), residues: 1055 helix: 0.93 (0.27), residues: 378 sheet: 0.05 (0.41), residues: 140 loop : -0.25 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 518 HIS 0.008 0.001 HIS B 207 PHE 0.014 0.002 PHE B 546 TYR 0.039 0.002 TYR B 69 ARG 0.008 0.001 ARG B 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1462.90 seconds wall clock time: 27 minutes 39.05 seconds (1659.05 seconds total)