Starting phenix.real_space_refine on Thu Mar 14 14:24:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx4_30895/03_2024/7dx4_30895_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx4_30895/03_2024/7dx4_30895.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/7dx4_30895/03_2024/7dx4_30895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx4_30895/03_2024/7dx4_30895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx4_30895/03_2024/7dx4_30895_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx4_30895/03_2024/7dx4_30895_neut.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= 0.002 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 805 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 43 5.16 5 C 5241 2.51 5 N 1364 2.21 5 O 1586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8234 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "E" Number of atoms: 1542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Conformer: "B" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} bond proxies already assigned to first conformer: 1572 Chain: "H" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 939 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 806 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.09, per 1000 atoms: 0.86 Number of scatterers: 8234 At special positions: 0 Unit cell: (144.56, 91.52, 78, 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 43 16.00 O 1586 8.00 N 1364 7.00 C 5241 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 97 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 53 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 2.6 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1902 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 12 sheets defined 43.9% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.988A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.534A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.631A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 4.132A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.936A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.510A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.613A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 193 removed outlier: 3.572A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.627A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.715A pdb=" N HIS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.817A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.558A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.917A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.709A pdb=" N ALA A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.859A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.966A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.392A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.664A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 515 Processing helix chain 'A' and resid 516 through 531 removed outlier: 3.760A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.800A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.682A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.645A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.606A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 370' Processing helix chain 'E' and resid 385 through 390 removed outlier: 3.554A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 408 removed outlier: 3.788A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.653A pdb=" N GLN E 506 " --> pdb=" O VAL E 503 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.760A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.635A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.817A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS E 432 " --> pdb=" O LEU E 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.917A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'H' and resid 6 through 7 removed outlier: 4.157A pdb=" N VAL H 21 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.568A pdb=" N VAL H 38 " --> pdb=" O TYR H 96 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE H 35 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLY H 51 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.794A pdb=" N GLY L 99 " --> pdb=" O ASP L 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 17 through 21 removed outlier: 3.612A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 866 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: 2.33 Time building geometry restraints manager: 3.19 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: 2374 1.33 - 1.45: 1789 1.45 - 1.58: 4226 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 8455 Sorted by residual: bond pdb=" C GLY A 319 " pdb=" N LEU A 320 " ideal model delta sigma weight residual 1.330 1.362 -0.032 1.37e-02 5.33e+03 5.36e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" CB MET A 579 " pdb=" CG MET A 579 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.13e+00 bond pdb=" C1 NAG A 704 " pdb=" O5 NAG A 704 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 ... (remaining 8450 not shown) Histogram of bond angle deviations from ideal: 97.18 - 104.56: 146 104.56 - 111.94: 3843 111.94 - 119.32: 2945 119.32 - 126.70: 4411 126.70 - 134.08: 146 Bond angle restraints: 11491 Sorted by residual: angle pdb=" N ASP H 113 " pdb=" CA ASP H 113 " pdb=" C ASP H 113 " ideal model delta sigma weight residual 114.16 102.73 11.43 1.48e+00 4.57e-01 5.97e+01 angle pdb=" C PHE H 112 " pdb=" N ASP H 113 " pdb=" CA ASP H 113 " ideal model delta sigma weight residual 120.70 131.47 -10.77 1.63e+00 3.76e-01 4.36e+01 angle pdb=" N ASN E 440 " pdb=" CA ASN E 440 " pdb=" CB ASN E 440 " ideal model delta sigma weight residual 110.13 102.65 7.48 1.48e+00 4.57e-01 2.56e+01 angle pdb=" C GLY L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C ILE L 50 " pdb=" N TYR L 51 " pdb=" CA TYR L 51 " ideal model delta sigma weight residual 120.94 128.52 -7.58 1.57e+00 4.06e-01 2.33e+01 ... (remaining 11486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.43: 4892 20.43 - 40.85: 119 40.85 - 61.28: 23 61.28 - 81.71: 4 81.71 - 102.13: 8 Dihedral angle restraints: 5046 sinusoidal: 2058 harmonic: 2988 Sorted by residual: dihedral pdb=" CA PHE H 112 " pdb=" C PHE H 112 " pdb=" N ASP H 113 " pdb=" CA ASP H 113 " ideal model delta harmonic sigma weight residual 180.00 127.40 52.60 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA LEU L 48 " pdb=" C LEU L 48 " pdb=" N LEU L 49 " pdb=" CA LEU L 49 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ALA H 108 " pdb=" C ALA H 108 " pdb=" N ALA H 109 " pdb=" CA ALA H 109 " ideal model delta harmonic sigma weight residual -180.00 -152.19 -27.81 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 5043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1030 0.073 - 0.145: 173 0.145 - 0.218: 16 0.218 - 0.291: 4 0.291 - 0.363: 2 Chirality restraints: 1225 Sorted by residual: chirality pdb=" CG LEU A 558 " pdb=" CB LEU A 558 " pdb=" CD1 LEU A 558 " pdb=" CD2 LEU A 558 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB ILE H 35 " pdb=" CA ILE H 35 " pdb=" CG1 ILE H 35 " pdb=" CG2 ILE H 35 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CG LEU A 333 " pdb=" CB LEU A 333 " pdb=" CD1 LEU A 333 " pdb=" CD2 LEU A 333 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1222 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 440 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" CG ASN E 440 " -0.064 2.00e-02 2.50e+03 pdb=" OD1 ASN E 440 " 0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN E 440 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 497 " 0.019 2.00e-02 2.50e+03 2.14e-02 8.02e+00 pdb=" CG PHE E 497 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE E 497 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE E 497 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE E 497 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE E 497 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE E 497 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.046 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO A 583 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.039 5.00e-02 4.00e+02 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 0.77 - 1.59: 5 1.59 - 2.42: 43 2.42 - 3.25: 8163 3.25 - 4.07: 21544 4.07 - 4.90: 39724 Warning: very small nonbonded interaction distances. Nonbonded interactions: 69479 Sorted by model distance: nonbonded pdb=" C LEU H 4 " pdb=" OG SER H 26 " model vdw 0.766 3.270 nonbonded pdb=" N LEU H 5 " pdb=" OG SER H 26 " model vdw 0.943 2.520 nonbonded pdb=" CA LEU H 5 " pdb=" CB SER H 26 " model vdw 1.145 3.870 nonbonded pdb=" O LEU H 4 " pdb=" OG SER H 26 " model vdw 1.387 2.440 nonbonded pdb=" O THR H 29 " pdb=" NH2 ARG H 99 " model vdw 1.521 2.520 ... (remaining 69474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 5.970 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.740 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 0.062 8455 Z= 0.430 Angle : 1.002 11.433 11491 Z= 0.575 Chirality : 0.057 0.363 1225 Planarity : 0.007 0.069 1484 Dihedral : 11.251 102.133 3117 Min Nonbonded Distance : 0.766 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.99 % Favored : 93.72 % Rotamer: Outliers : 0.23 % Allowed : 1.25 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.20 (0.21), residues: 1021 helix: -3.94 (0.14), residues: 368 sheet: -2.19 (0.43), residues: 137 loop : -1.95 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 302 HIS 0.014 0.002 HIS A 401 PHE 0.049 0.004 PHE E 497 TYR 0.037 0.004 TYR E 495 ARG 0.019 0.002 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ARG cc_start: 0.7610 (mtm-85) cc_final: 0.7292 (mtp180) REVERT: A 255 TYR cc_start: 0.7745 (m-80) cc_final: 0.7154 (m-10) REVERT: E 385 THR cc_start: 0.8294 (p) cc_final: 0.8018 (t) REVERT: E 444 LYS cc_start: 0.8917 (pttt) cc_final: 0.8090 (mttm) REVERT: E 445 VAL cc_start: 0.8876 (t) cc_final: 0.8674 (p) REVERT: E 470 THR cc_start: 0.8507 (p) cc_final: 0.8304 (p) REVERT: H 48 TRP cc_start: 0.8687 (t60) cc_final: 0.8091 (t60) REVERT: L 108 LEU cc_start: 0.8540 (tt) cc_final: 0.7894 (tp) REVERT: L 109 THR cc_start: 0.8894 (p) cc_final: 0.8677 (p) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2119 time to fit residues: 63.6286 Evaluate side-chains 132 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS A 305 GLN A 540 HIS A 572 ASN A 599 ASN E 501 ASN H 40 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8455 Z= 0.223 Angle : 0.692 7.738 11491 Z= 0.362 Chirality : 0.045 0.196 1225 Planarity : 0.006 0.059 1484 Dihedral : 8.135 60.261 1226 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.04 % Allowed : 7.83 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.53 (0.24), residues: 1021 helix: -2.03 (0.21), residues: 391 sheet: -1.63 (0.44), residues: 122 loop : -1.26 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 302 HIS 0.004 0.001 HIS A 374 PHE 0.029 0.002 PHE E 497 TYR 0.023 0.002 TYR E 495 ARG 0.007 0.001 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 TYR cc_start: 0.7619 (m-80) cc_final: 0.7084 (m-10) REVERT: A 366 MET cc_start: 0.8132 (tpp) cc_final: 0.7791 (tpp) REVERT: A 375 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7882 (mm-30) REVERT: A 484 ILE cc_start: 0.8024 (mm) cc_final: 0.7632 (mm) REVERT: E 385 THR cc_start: 0.8459 (p) cc_final: 0.8187 (t) REVERT: E 430 THR cc_start: 0.8359 (p) cc_final: 0.8145 (t) REVERT: E 444 LYS cc_start: 0.9048 (pttt) cc_final: 0.8077 (mttm) REVERT: E 470 THR cc_start: 0.8412 (p) cc_final: 0.8131 (p) REVERT: E 506 GLN cc_start: 0.7755 (mt0) cc_final: 0.7387 (mt0) REVERT: E 508 TYR cc_start: 0.8318 (m-80) cc_final: 0.8116 (m-80) REVERT: H 48 TRP cc_start: 0.8658 (t60) cc_final: 0.7934 (t60) outliers start: 16 outliers final: 13 residues processed: 177 average time/residue: 0.1793 time to fit residues: 45.0528 Evaluate side-chains 134 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 0.0970 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS A 599 ASN H 7 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8455 Z= 0.190 Angle : 0.660 11.639 11491 Z= 0.333 Chirality : 0.047 0.569 1225 Planarity : 0.005 0.049 1484 Dihedral : 6.402 50.823 1226 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.93 % Allowed : 9.31 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.25), residues: 1021 helix: -0.96 (0.24), residues: 390 sheet: -1.30 (0.41), residues: 146 loop : -0.94 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 302 HIS 0.003 0.001 HIS A 535 PHE 0.033 0.002 PHE H 112 TYR 0.018 0.001 TYR E 495 ARG 0.005 0.001 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8280 (t80) cc_final: 0.7940 (t80) REVERT: A 176 LEU cc_start: 0.7285 (mt) cc_final: 0.6962 (mt) REVERT: A 255 TYR cc_start: 0.7507 (m-80) cc_final: 0.6969 (m-10) REVERT: A 323 MET cc_start: 0.8541 (mmm) cc_final: 0.8205 (mmm) REVERT: A 350 ASP cc_start: 0.7672 (t0) cc_final: 0.7458 (t70) REVERT: E 385 THR cc_start: 0.8410 (p) cc_final: 0.8152 (t) REVERT: E 430 THR cc_start: 0.8283 (p) cc_final: 0.8063 (t) REVERT: E 444 LYS cc_start: 0.9051 (pttt) cc_final: 0.7984 (mttm) REVERT: E 470 THR cc_start: 0.8428 (p) cc_final: 0.8165 (p) REVERT: E 472 ILE cc_start: 0.8688 (mm) cc_final: 0.8408 (mt) REVERT: E 506 GLN cc_start: 0.7718 (mt0) cc_final: 0.7429 (mt0) REVERT: H 48 TRP cc_start: 0.8605 (t60) cc_final: 0.7886 (t60) outliers start: 15 outliers final: 10 residues processed: 160 average time/residue: 0.1803 time to fit residues: 41.2651 Evaluate side-chains 130 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 26 optimal weight: 0.0000 chunk 81 optimal weight: 0.8980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 540 HIS H 40 GLN L 40 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8455 Z= 0.193 Angle : 0.651 10.217 11491 Z= 0.328 Chirality : 0.044 0.140 1225 Planarity : 0.004 0.043 1484 Dihedral : 7.204 75.497 1226 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.16 % Allowed : 9.76 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.26), residues: 1021 helix: -0.44 (0.25), residues: 397 sheet: -1.06 (0.43), residues: 146 loop : -0.84 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.030 0.002 PHE H 112 TYR 0.023 0.001 TYR A 521 ARG 0.004 0.001 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8052 (ptm) cc_final: 0.7748 (ptt) REVERT: A 127 TYR cc_start: 0.8310 (t80) cc_final: 0.7988 (t80) REVERT: A 176 LEU cc_start: 0.7374 (mt) cc_final: 0.7104 (mt) REVERT: A 255 TYR cc_start: 0.7468 (m-80) cc_final: 0.6885 (m-10) REVERT: A 323 MET cc_start: 0.8396 (mmm) cc_final: 0.8157 (mmm) REVERT: A 366 MET cc_start: 0.8513 (tpp) cc_final: 0.7872 (tpp) REVERT: E 385 THR cc_start: 0.8449 (p) cc_final: 0.8209 (t) REVERT: E 430 THR cc_start: 0.8255 (p) cc_final: 0.8031 (t) REVERT: E 444 LYS cc_start: 0.9068 (pttt) cc_final: 0.7995 (mttm) REVERT: E 470 THR cc_start: 0.8514 (p) cc_final: 0.8245 (p) REVERT: E 506 GLN cc_start: 0.7882 (mt0) cc_final: 0.7511 (mt0) REVERT: H 48 TRP cc_start: 0.8663 (t60) cc_final: 0.7895 (t60) REVERT: L 93 TYR cc_start: 0.8133 (t80) cc_final: 0.7576 (t80) outliers start: 17 outliers final: 12 residues processed: 147 average time/residue: 0.1611 time to fit residues: 34.9318 Evaluate side-chains 132 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 0.0970 chunk 40 optimal weight: 0.0030 chunk 83 optimal weight: 0.0370 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 0.0770 chunk 32 optimal weight: 0.9990 overall best weight: 0.2224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8455 Z= 0.154 Angle : 0.628 11.323 11491 Z= 0.312 Chirality : 0.043 0.166 1225 Planarity : 0.004 0.038 1484 Dihedral : 7.147 79.814 1226 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.38 % Allowed : 11.35 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.61 (0.27), residues: 1021 helix: -0.01 (0.26), residues: 391 sheet: -0.58 (0.44), residues: 155 loop : -0.54 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 115 HIS 0.004 0.001 HIS A 374 PHE 0.038 0.002 PHE H 112 TYR 0.018 0.001 TYR A 521 ARG 0.004 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7981 (ptm) cc_final: 0.7774 (ptp) REVERT: A 176 LEU cc_start: 0.7169 (mt) cc_final: 0.6921 (mt) REVERT: A 255 TYR cc_start: 0.7504 (m-80) cc_final: 0.6970 (m-10) REVERT: A 366 MET cc_start: 0.8614 (tpp) cc_final: 0.8003 (tpp) REVERT: E 385 THR cc_start: 0.8448 (p) cc_final: 0.8189 (t) REVERT: E 421 TYR cc_start: 0.8399 (m-10) cc_final: 0.8199 (m-10) REVERT: E 430 THR cc_start: 0.8135 (p) cc_final: 0.7903 (t) REVERT: E 444 LYS cc_start: 0.9004 (pttt) cc_final: 0.7926 (mttm) REVERT: E 470 THR cc_start: 0.8468 (p) cc_final: 0.8210 (p) REVERT: E 506 GLN cc_start: 0.7712 (mt0) cc_final: 0.7381 (mt0) REVERT: H 48 TRP cc_start: 0.8580 (t60) cc_final: 0.7811 (t60) REVERT: H 81 TYR cc_start: 0.7763 (m-80) cc_final: 0.7529 (m-80) REVERT: L 81 GLN cc_start: 0.8123 (mp10) cc_final: 0.7896 (mp10) outliers start: 19 outliers final: 9 residues processed: 161 average time/residue: 0.1671 time to fit residues: 38.9812 Evaluate side-chains 135 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 0.3980 chunk 24 optimal weight: 8.9990 chunk 97 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS L 16 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8455 Z= 0.219 Angle : 0.655 10.282 11491 Z= 0.327 Chirality : 0.045 0.207 1225 Planarity : 0.004 0.044 1484 Dihedral : 7.495 86.208 1226 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.82 % Allowed : 12.37 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.44 (0.27), residues: 1021 helix: 0.13 (0.26), residues: 392 sheet: -0.52 (0.44), residues: 156 loop : -0.43 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 163 HIS 0.003 0.001 HIS L 36 PHE 0.033 0.002 PHE H 112 TYR 0.020 0.002 TYR A 521 ARG 0.008 0.001 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7527 (mt) cc_final: 0.7218 (mt) REVERT: A 255 TYR cc_start: 0.7619 (m-80) cc_final: 0.7078 (m-10) REVERT: A 323 MET cc_start: 0.8180 (mmm) cc_final: 0.7129 (mmm) REVERT: E 385 THR cc_start: 0.8503 (p) cc_final: 0.8248 (t) REVERT: E 432 CYS cc_start: 0.4976 (m) cc_final: 0.4638 (m) REVERT: E 444 LYS cc_start: 0.9115 (pttt) cc_final: 0.8006 (mttm) REVERT: E 470 THR cc_start: 0.8629 (p) cc_final: 0.8372 (p) REVERT: E 506 GLN cc_start: 0.7945 (mt0) cc_final: 0.7580 (mt0) outliers start: 14 outliers final: 13 residues processed: 139 average time/residue: 0.1587 time to fit residues: 32.8504 Evaluate side-chains 135 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8455 Z= 0.196 Angle : 0.667 13.979 11491 Z= 0.326 Chirality : 0.044 0.210 1225 Planarity : 0.004 0.034 1484 Dihedral : 7.474 89.090 1226 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.38 % Allowed : 13.17 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.28 (0.27), residues: 1021 helix: 0.29 (0.26), residues: 392 sheet: -0.51 (0.43), residues: 158 loop : -0.33 (0.31), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.034 0.002 PHE H 112 TYR 0.020 0.001 TYR A 521 ARG 0.007 0.001 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7491 (mt) cc_final: 0.7193 (mt) REVERT: A 255 TYR cc_start: 0.7536 (m-80) cc_final: 0.6966 (m-10) REVERT: A 323 MET cc_start: 0.8016 (mmm) cc_final: 0.6802 (mmm) REVERT: A 366 MET cc_start: 0.8593 (tpp) cc_final: 0.8243 (tpt) REVERT: E 385 THR cc_start: 0.8503 (p) cc_final: 0.8257 (t) REVERT: E 444 LYS cc_start: 0.9091 (pttt) cc_final: 0.7960 (mttm) REVERT: E 470 THR cc_start: 0.8604 (p) cc_final: 0.8379 (p) REVERT: H 33 TYR cc_start: 0.8519 (m-80) cc_final: 0.8319 (m-80) outliers start: 19 outliers final: 11 residues processed: 143 average time/residue: 0.1651 time to fit residues: 34.6671 Evaluate side-chains 131 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 66 GLN Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8455 Z= 0.177 Angle : 0.667 13.222 11491 Z= 0.325 Chirality : 0.044 0.209 1225 Planarity : 0.004 0.047 1484 Dihedral : 7.410 89.685 1226 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.36 % Allowed : 14.53 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.09 (0.27), residues: 1021 helix: 0.46 (0.26), residues: 394 sheet: -0.54 (0.42), residues: 164 loop : -0.17 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 115 HIS 0.003 0.001 HIS A 374 PHE 0.030 0.002 PHE H 112 TYR 0.018 0.001 TYR A 521 ARG 0.007 0.001 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7522 (mt) cc_final: 0.7236 (mt) REVERT: A 255 TYR cc_start: 0.7515 (m-80) cc_final: 0.7008 (m-10) REVERT: A 323 MET cc_start: 0.7826 (mmm) cc_final: 0.7025 (mmm) REVERT: A 366 MET cc_start: 0.8602 (tpp) cc_final: 0.8262 (tpt) REVERT: A 512 PHE cc_start: 0.7684 (t80) cc_final: 0.7423 (t80) REVERT: E 385 THR cc_start: 0.8527 (p) cc_final: 0.8284 (t) REVERT: E 432 CYS cc_start: 0.4978 (m) cc_final: 0.4646 (m) REVERT: E 444 LYS cc_start: 0.9111 (pttt) cc_final: 0.7934 (mttm) REVERT: E 470 THR cc_start: 0.8544 (p) cc_final: 0.8308 (p) REVERT: E 506 GLN cc_start: 0.7981 (mt0) cc_final: 0.7606 (mt0) outliers start: 10 outliers final: 10 residues processed: 136 average time/residue: 0.1728 time to fit residues: 34.3813 Evaluate side-chains 128 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8455 Z= 0.187 Angle : 0.683 13.403 11491 Z= 0.330 Chirality : 0.044 0.214 1225 Planarity : 0.004 0.046 1484 Dihedral : 7.395 89.750 1226 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.14 % Allowed : 14.87 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.00 (0.28), residues: 1021 helix: 0.54 (0.27), residues: 394 sheet: -0.46 (0.42), residues: 164 loop : -0.14 (0.32), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 115 HIS 0.004 0.001 HIS A 374 PHE 0.031 0.002 PHE H 112 TYR 0.018 0.001 TYR A 521 ARG 0.007 0.001 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7524 (mt) cc_final: 0.7252 (mt) REVERT: A 255 TYR cc_start: 0.7539 (m-80) cc_final: 0.7034 (m-10) REVERT: A 259 ILE cc_start: 0.8668 (mm) cc_final: 0.8407 (tp) REVERT: A 366 MET cc_start: 0.8614 (tpp) cc_final: 0.8375 (tpt) REVERT: A 512 PHE cc_start: 0.7686 (t80) cc_final: 0.7409 (t80) REVERT: E 385 THR cc_start: 0.8531 (p) cc_final: 0.8290 (t) REVERT: E 432 CYS cc_start: 0.4967 (m) cc_final: 0.4636 (m) REVERT: E 444 LYS cc_start: 0.9129 (pttt) cc_final: 0.7935 (mttm) REVERT: E 470 THR cc_start: 0.8498 (p) cc_final: 0.8281 (t) REVERT: E 506 GLN cc_start: 0.7952 (mt0) cc_final: 0.7559 (mt0) outliers start: 8 outliers final: 8 residues processed: 132 average time/residue: 0.1681 time to fit residues: 32.7788 Evaluate side-chains 124 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 84 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.0870 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8455 Z= 0.183 Angle : 0.678 13.360 11491 Z= 0.328 Chirality : 0.044 0.212 1225 Planarity : 0.004 0.045 1484 Dihedral : 7.340 89.399 1226 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.59 % Allowed : 15.10 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.07 (0.28), residues: 1021 helix: 0.57 (0.27), residues: 394 sheet: -0.39 (0.42), residues: 164 loop : -0.08 (0.32), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 349 HIS 0.003 0.001 HIS A 239 PHE 0.029 0.002 PHE H 112 TYR 0.018 0.001 TYR A 521 ARG 0.006 0.001 ARG E 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.7920 (t80) cc_final: 0.7497 (t80) REVERT: A 176 LEU cc_start: 0.7538 (mt) cc_final: 0.7283 (mt) REVERT: A 255 TYR cc_start: 0.7564 (m-80) cc_final: 0.7039 (m-10) REVERT: A 259 ILE cc_start: 0.8665 (mm) cc_final: 0.8378 (tp) REVERT: A 366 MET cc_start: 0.8563 (tpp) cc_final: 0.8362 (tpt) REVERT: E 385 THR cc_start: 0.8532 (p) cc_final: 0.8296 (t) REVERT: E 432 CYS cc_start: 0.5026 (m) cc_final: 0.4685 (m) REVERT: E 444 LYS cc_start: 0.9134 (pttt) cc_final: 0.7935 (mttm) REVERT: E 506 GLN cc_start: 0.7955 (mt0) cc_final: 0.7570 (mt0) REVERT: H 33 TYR cc_start: 0.8560 (m-80) cc_final: 0.8308 (m-80) outliers start: 12 outliers final: 10 residues processed: 131 average time/residue: 0.1645 time to fit residues: 31.7448 Evaluate side-chains 130 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 84 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.0020 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** 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 = 0.4050 r_free = 0.4050 target = 0.123066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.099850 restraints weight = 27100.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.104957 restraints weight = 13302.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.108092 restraints weight = 6274.267| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3849 r_free = 0.3849 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8455 Z= 0.189 Angle : 0.685 13.337 11491 Z= 0.331 Chirality : 0.043 0.213 1225 Planarity : 0.004 0.045 1484 Dihedral : 7.345 89.723 1226 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.36 % Allowed : 15.66 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.13 (0.28), residues: 1021 helix: 0.61 (0.27), residues: 394 sheet: -0.32 (0.43), residues: 163 loop : -0.06 (0.32), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 115 HIS 0.003 0.001 HIS A 374 PHE 0.028 0.002 PHE H 112 TYR 0.018 0.001 TYR A 50 ARG 0.006 0.001 ARG E 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1996.73 seconds wall clock time: 36 minutes 41.05 seconds (2201.05 seconds total)