Starting phenix.real_space_refine on Thu Feb 13 12:55:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dx4_30895/02_2025/7dx4_30895_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dx4_30895/02_2025/7dx4_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/cci-nas-00/data/ceres_data/7dx4_30895/02_2025/7dx4_30895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dx4_30895/02_2025/7dx4_30895.map" model { file = "/net/cci-nas-00/data/ceres_data/7dx4_30895/02_2025/7dx4_30895_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dx4_30895/02_2025/7dx4_30895_neut.cif" } 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. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 8.35, per 1000 atoms: 1.01 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 2.12 Conformation dependent library (CDL) restraints added in 1.7 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: 0.88 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: 2.39 Time building geometry restraints manager: 2.44 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: 0.00 - 2.29: 11077 2.29 - 4.57: 355 4.57 - 6.86: 40 6.86 - 9.15: 15 9.15 - 11.43: 4 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 3.120 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 3.040 nonbonded pdb=" O THR H 29 " pdb=" NH2 ARG H 99 " model vdw 1.521 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.670 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.250 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.724 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: 0.2180 time to fit residues: 65.5668 Evaluate side-chains 132 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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: 0.9980 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.0050 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 239 HIS A 305 GLN A 540 HIS A 599 ASN E 498 GLN E 501 ASN H 40 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.121303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099146 restraints weight = 28521.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.104357 restraints weight = 11435.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.108170 restraints weight = 5707.798| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8455 Z= 0.214 Angle : 0.707 9.123 11491 Z= 0.373 Chirality : 0.046 0.189 1225 Planarity : 0.006 0.062 1484 Dihedral : 8.364 63.762 1226 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.04 % Allowed : 7.95 % Favored : 90.01 % 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: -2.56 (0.24), residues: 1021 helix: -2.13 (0.21), residues: 392 sheet: -1.54 (0.42), residues: 142 loop : -1.20 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 302 HIS 0.003 0.001 HIS A 378 PHE 0.031 0.002 PHE A 603 TYR 0.024 0.002 TYR E 495 ARG 0.007 0.001 ARG E 454 *********************** 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 182 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 TYR cc_start: 0.7689 (m-80) cc_final: 0.7081 (m-10) REVERT: A 366 MET cc_start: 0.8136 (tpp) cc_final: 0.7790 (tpp) REVERT: A 375 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7976 (mm-30) REVERT: A 484 ILE cc_start: 0.8005 (mm) cc_final: 0.7669 (mm) REVERT: E 385 THR cc_start: 0.8523 (p) cc_final: 0.8240 (t) REVERT: E 444 LYS cc_start: 0.9101 (pttt) cc_final: 0.8115 (mttm) REVERT: E 498 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8124 (mt0) REVERT: E 506 GLN cc_start: 0.7669 (mt0) cc_final: 0.7323 (mt0) REVERT: E 507 PRO cc_start: 0.8745 (Cg_exo) cc_final: 0.8544 (Cg_endo) REVERT: H 48 TRP cc_start: 0.8637 (t60) cc_final: 0.7903 (t60) REVERT: L 34 ASP cc_start: 0.7501 (m-30) cc_final: 0.7189 (m-30) outliers start: 16 outliers final: 12 residues processed: 177 average time/residue: 0.1881 time to fit residues: 46.6279 Evaluate side-chains 130 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 E residue 498 GLN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 94 optimal weight: 0.0470 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 540 HIS A 599 ASN E 498 GLN H 7 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.113237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.090080 restraints weight = 28495.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.095342 restraints weight = 11753.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.098967 restraints weight = 5558.970| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8455 Z= 0.295 Angle : 0.727 11.091 11491 Z= 0.370 Chirality : 0.050 0.582 1225 Planarity : 0.005 0.053 1484 Dihedral : 7.006 54.583 1226 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.27 % Allowed : 9.19 % Favored : 88.54 % 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: -1.80 (0.25), residues: 1021 helix: -1.09 (0.24), residues: 395 sheet: -1.52 (0.40), residues: 149 loop : -1.02 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 302 HIS 0.004 0.001 HIS L 36 PHE 0.033 0.003 PHE H 112 TYR 0.023 0.002 TYR E 453 ARG 0.008 0.001 ARG E 454 *********************** 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 161 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 TYR cc_start: 0.7829 (m-80) cc_final: 0.7227 (m-10) REVERT: A 323 MET cc_start: 0.7958 (tpp) cc_final: 0.7067 (mpp) REVERT: A 366 MET cc_start: 0.8339 (tpp) cc_final: 0.7767 (tpp) REVERT: E 385 THR cc_start: 0.8685 (p) cc_final: 0.8429 (t) REVERT: E 430 THR cc_start: 0.8296 (p) cc_final: 0.8078 (t) REVERT: E 444 LYS cc_start: 0.9185 (pttt) cc_final: 0.8039 (mttm) REVERT: E 470 THR cc_start: 0.8541 (p) cc_final: 0.8245 (p) REVERT: H 82 MET cc_start: 0.8504 (tmm) cc_final: 0.8131 (tmm) REVERT: L 34 ASP cc_start: 0.7244 (m-30) cc_final: 0.6869 (m-30) outliers start: 18 outliers final: 15 residues processed: 155 average time/residue: 0.1757 time to fit residues: 39.3323 Evaluate side-chains 136 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 261 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 498 GLN 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 51 TYR 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 28 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.115703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.093428 restraints weight = 19618.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.097457 restraints weight = 8847.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.100140 restraints weight = 5269.708| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8455 Z= 0.209 Angle : 0.677 9.387 11491 Z= 0.344 Chirality : 0.045 0.188 1225 Planarity : 0.004 0.043 1484 Dihedral : 7.420 75.760 1226 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.82 % Allowed : 10.78 % Favored : 87.40 % 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: -1.23 (0.26), residues: 1021 helix: -0.44 (0.25), residues: 399 sheet: -1.27 (0.42), residues: 148 loop : -0.84 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 302 HIS 0.003 0.001 HIS A 535 PHE 0.039 0.002 PHE H 112 TYR 0.017 0.002 TYR E 495 ARG 0.006 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 158 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8287 (ptm) cc_final: 0.8003 (ptp) REVERT: A 127 TYR cc_start: 0.8326 (t80) cc_final: 0.7960 (t80) REVERT: A 222 LEU cc_start: 0.8607 (tp) cc_final: 0.8391 (tp) REVERT: A 255 TYR cc_start: 0.7641 (m-80) cc_final: 0.7032 (m-10) REVERT: A 366 MET cc_start: 0.8375 (tpp) cc_final: 0.7809 (tpp) REVERT: E 385 THR cc_start: 0.8526 (p) cc_final: 0.8292 (t) REVERT: E 444 LYS cc_start: 0.9112 (pttt) cc_final: 0.7919 (mttm) REVERT: E 470 THR cc_start: 0.8342 (p) cc_final: 0.8011 (p) REVERT: L 34 ASP cc_start: 0.7306 (m-30) cc_final: 0.6911 (m-30) REVERT: L 80 LEU cc_start: 0.9492 (mt) cc_final: 0.9193 (mt) REVERT: L 81 GLN cc_start: 0.8607 (mt0) cc_final: 0.8253 (mp10) outliers start: 14 outliers final: 11 residues processed: 151 average time/residue: 0.1780 time to fit residues: 39.0365 Evaluate side-chains 127 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 51 TYR Chi-restraints excluded: chain L residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 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 = 0.4008 r_free = 0.4008 target = 0.119745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.098268 restraints weight = 29586.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.103803 restraints weight = 12559.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.104521 restraints weight = 6344.630| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8455 Z= 0.247 Angle : 0.686 11.781 11491 Z= 0.349 Chirality : 0.046 0.181 1225 Planarity : 0.004 0.047 1484 Dihedral : 7.652 85.475 1226 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.84 % Allowed : 10.78 % Favored : 86.38 % 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: -0.99 (0.27), residues: 1021 helix: -0.23 (0.25), residues: 399 sheet: -1.13 (0.41), residues: 158 loop : -0.71 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 436 HIS 0.003 0.001 HIS A 540 PHE 0.031 0.002 PHE H 112 TYR 0.019 0.002 TYR E 453 ARG 0.005 0.001 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 155 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8225 (tt) REVERT: A 127 TYR cc_start: 0.8363 (t80) cc_final: 0.8103 (t80) REVERT: A 255 TYR cc_start: 0.7693 (m-80) cc_final: 0.7112 (m-10) REVERT: A 558 LEU cc_start: 0.8647 (mt) cc_final: 0.8429 (mt) REVERT: E 385 THR cc_start: 0.8617 (p) cc_final: 0.8357 (t) REVERT: E 444 LYS cc_start: 0.9171 (pttt) cc_final: 0.8011 (mttm) REVERT: E 470 THR cc_start: 0.8375 (p) cc_final: 0.8114 (p) REVERT: E 472 ILE cc_start: 0.8631 (mm) cc_final: 0.8403 (mt) REVERT: E 506 GLN cc_start: 0.7865 (mt0) cc_final: 0.7411 (mt0) REVERT: H 55 ILE cc_start: 0.8658 (mt) cc_final: 0.8449 (mt) REVERT: L 81 GLN cc_start: 0.8633 (mt0) cc_final: 0.8412 (mp10) outliers start: 23 outliers final: 14 residues processed: 148 average time/residue: 0.1948 time to fit residues: 41.8349 Evaluate side-chains 134 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 149 ASN 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 399 SER 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 11 SER Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 TYR 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 6 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.118979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.095784 restraints weight = 34533.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.100994 restraints weight = 14673.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.103481 restraints weight = 6939.200| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4214 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= 0.220 Angle : 0.672 10.598 11491 Z= 0.340 Chirality : 0.046 0.217 1225 Planarity : 0.004 0.039 1484 Dihedral : 7.721 87.870 1226 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.38 % Allowed : 10.90 % Favored : 86.72 % 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: -0.84 (0.27), residues: 1021 helix: -0.03 (0.26), residues: 399 sheet: -1.06 (0.41), residues: 158 loop : -0.70 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 535 PHE 0.029 0.002 PHE A 603 TYR 0.024 0.002 TYR A 521 ARG 0.004 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 152 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8330 (tt) REVERT: A 127 TYR cc_start: 0.8308 (t80) cc_final: 0.8049 (t80) REVERT: A 255 TYR cc_start: 0.7640 (m-80) cc_final: 0.7008 (m-10) REVERT: A 558 LEU cc_start: 0.8674 (mt) cc_final: 0.8467 (mt) REVERT: E 385 THR cc_start: 0.8609 (p) cc_final: 0.8354 (t) REVERT: E 432 CYS cc_start: 0.5022 (m) cc_final: 0.4728 (m) REVERT: E 444 LYS cc_start: 0.9173 (pttt) cc_final: 0.8029 (mttm) REVERT: E 472 ILE cc_start: 0.8639 (mm) cc_final: 0.8421 (mt) REVERT: E 506 GLN cc_start: 0.7710 (mt0) cc_final: 0.7194 (mt0) REVERT: E 507 PRO cc_start: 0.9051 (Cg_endo) cc_final: 0.8844 (Cg_exo) REVERT: L 81 GLN cc_start: 0.8541 (mt0) cc_final: 0.8339 (mp10) outliers start: 19 outliers final: 16 residues processed: 143 average time/residue: 0.1679 time to fit residues: 35.5586 Evaluate side-chains 137 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 149 ASN 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 340 GLU Chi-restraints excluded: chain E residue 399 SER 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 11 SER Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 51 TYR 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 78 optimal weight: 0.0040 chunk 64 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 70 optimal weight: 0.0770 chunk 89 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.4550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.122525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.099088 restraints weight = 28850.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.104973 restraints weight = 11609.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.108832 restraints weight = 5377.225| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8455 Z= 0.172 Angle : 0.661 10.214 11491 Z= 0.330 Chirality : 0.044 0.212 1225 Planarity : 0.004 0.037 1484 Dihedral : 7.523 89.610 1226 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.04 % Allowed : 12.15 % 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: -0.56 (0.27), residues: 1021 helix: 0.16 (0.26), residues: 399 sheet: -0.86 (0.41), residues: 169 loop : -0.50 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 115 HIS 0.003 0.001 HIS A 378 PHE 0.031 0.002 PHE A 603 TYR 0.020 0.001 TYR A 521 ARG 0.004 0.000 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 159 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8176 (tt) REVERT: A 255 TYR cc_start: 0.7630 (m-80) cc_final: 0.7038 (m-10) REVERT: A 375 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8155 (mm-30) REVERT: A 508 ASN cc_start: 0.8354 (m-40) cc_final: 0.8086 (t0) REVERT: A 558 LEU cc_start: 0.8591 (mt) cc_final: 0.8389 (mt) REVERT: E 385 THR cc_start: 0.8531 (p) cc_final: 0.8282 (t) REVERT: E 432 CYS cc_start: 0.4925 (m) cc_final: 0.4639 (m) REVERT: E 444 LYS cc_start: 0.9166 (pttt) cc_final: 0.7935 (mttm) REVERT: E 466 ARG cc_start: 0.8332 (ttm110) cc_final: 0.8081 (ttm-80) REVERT: E 506 GLN cc_start: 0.7673 (mt0) cc_final: 0.7204 (mt0) REVERT: E 508 TYR cc_start: 0.8437 (m-80) cc_final: 0.8224 (m-80) REVERT: L 34 ASP cc_start: 0.7334 (m-30) cc_final: 0.7024 (m-30) outliers start: 16 outliers final: 11 residues processed: 152 average time/residue: 0.1634 time to fit residues: 36.4503 Evaluate side-chains 139 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain E residue 333 THR 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 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 51 TYR 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 3 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.117402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.093900 restraints weight = 32837.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.099110 restraints weight = 13097.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.103224 restraints weight = 6623.164| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8455 Z= 0.275 Angle : 0.717 9.978 11491 Z= 0.359 Chirality : 0.047 0.223 1225 Planarity : 0.004 0.037 1484 Dihedral : 7.874 93.201 1226 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.38 % Allowed : 13.28 % Favored : 84.34 % 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: -0.50 (0.27), residues: 1021 helix: 0.22 (0.26), residues: 399 sheet: -0.89 (0.41), residues: 158 loop : -0.47 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 115 HIS 0.003 0.001 HIS A 540 PHE 0.030 0.002 PHE A 603 TYR 0.023 0.002 TYR A 521 ARG 0.004 0.001 ARG L 63 *********************** 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 144 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8282 (tt) REVERT: A 255 TYR cc_start: 0.7769 (m-80) cc_final: 0.7114 (m-10) REVERT: A 375 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8063 (mm-30) REVERT: A 376 MET cc_start: 0.8755 (tpp) cc_final: 0.8509 (tpp) REVERT: A 558 LEU cc_start: 0.8743 (mt) cc_final: 0.8536 (mt) REVERT: E 385 THR cc_start: 0.8659 (p) cc_final: 0.8436 (t) REVERT: E 432 CYS cc_start: 0.5118 (m) cc_final: 0.4790 (m) REVERT: E 444 LYS cc_start: 0.9177 (pttt) cc_final: 0.7950 (mttm) REVERT: E 508 TYR cc_start: 0.8575 (m-80) cc_final: 0.8343 (m-80) outliers start: 19 outliers final: 17 residues processed: 136 average time/residue: 0.1641 time to fit residues: 33.3831 Evaluate side-chains 137 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 222 LEU 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 340 GLU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 468 ILE 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 11 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 77 optimal weight: 0.0040 chunk 22 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.120920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.097353 restraints weight = 30318.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.103087 restraints weight = 12213.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.106353 restraints weight = 5650.599| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4748 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= 0.189 Angle : 0.690 11.621 11491 Z= 0.339 Chirality : 0.045 0.218 1225 Planarity : 0.004 0.037 1484 Dihedral : 7.610 91.205 1226 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.04 % Allowed : 13.85 % 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: -0.36 (0.27), residues: 1021 helix: 0.30 (0.26), residues: 396 sheet: -0.87 (0.40), residues: 171 loop : -0.30 (0.32), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 115 HIS 0.002 0.001 HIS A 378 PHE 0.031 0.002 PHE A 603 TYR 0.020 0.001 TYR A 521 ARG 0.004 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 149 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8196 (tt) REVERT: A 127 TYR cc_start: 0.7969 (t80) cc_final: 0.7558 (t80) REVERT: A 255 TYR cc_start: 0.7745 (m-80) cc_final: 0.7097 (m-10) REVERT: A 323 MET cc_start: 0.6399 (ptp) cc_final: 0.6171 (ptp) REVERT: A 375 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8100 (mm-30) REVERT: A 558 LEU cc_start: 0.8606 (mt) cc_final: 0.8396 (mt) REVERT: E 385 THR cc_start: 0.8633 (p) cc_final: 0.8394 (t) REVERT: E 432 CYS cc_start: 0.5061 (m) cc_final: 0.4742 (m) REVERT: E 444 LYS cc_start: 0.9201 (pttt) cc_final: 0.7963 (mttm) REVERT: E 466 ARG cc_start: 0.8307 (ttm110) cc_final: 0.7628 (ptm160) REVERT: E 508 TYR cc_start: 0.8475 (m-80) cc_final: 0.8214 (m-80) REVERT: L 34 ASP cc_start: 0.7430 (m-30) cc_final: 0.7071 (m-30) outliers start: 16 outliers final: 14 residues processed: 141 average time/residue: 0.1636 time to fit residues: 33.9973 Evaluate side-chains 135 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain E residue 333 THR 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 11 SER 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 51 TYR Chi-restraints excluded: chain L residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.121186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.098048 restraints weight = 27032.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.103619 restraints weight = 11318.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.107493 restraints weight = 5456.156| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8455 Z= 0.196 Angle : 0.702 13.054 11491 Z= 0.347 Chirality : 0.045 0.219 1225 Planarity : 0.004 0.036 1484 Dihedral : 7.589 90.917 1226 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.04 % Allowed : 14.30 % Favored : 83.65 % 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: -0.26 (0.27), residues: 1021 helix: 0.37 (0.26), residues: 396 sheet: -0.75 (0.41), residues: 170 loop : -0.26 (0.32), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.002 0.001 HIS A 535 PHE 0.033 0.002 PHE A 603 TYR 0.020 0.001 TYR A 521 ARG 0.004 0.001 ARG E 466 ********************** 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 146 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8212 (tt) REVERT: A 127 TYR cc_start: 0.7932 (t80) cc_final: 0.7576 (t80) REVERT: A 255 TYR cc_start: 0.7704 (m-80) cc_final: 0.7106 (m-10) REVERT: A 323 MET cc_start: 0.6321 (ptp) cc_final: 0.6118 (ptp) REVERT: A 375 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8152 (mm-30) REVERT: A 558 LEU cc_start: 0.8623 (mt) cc_final: 0.8410 (mt) REVERT: E 385 THR cc_start: 0.8580 (p) cc_final: 0.8370 (t) REVERT: E 432 CYS cc_start: 0.5072 (m) cc_final: 0.4762 (m) REVERT: E 444 LYS cc_start: 0.9174 (pttt) cc_final: 0.7974 (mttm) REVERT: E 486 PHE cc_start: 0.7647 (t80) cc_final: 0.7302 (t80) REVERT: E 508 TYR cc_start: 0.8437 (m-80) cc_final: 0.8170 (m-80) REVERT: H 55 ILE cc_start: 0.8384 (mp) cc_final: 0.8049 (mm) REVERT: L 34 ASP cc_start: 0.7442 (m-30) cc_final: 0.7207 (m-30) outliers start: 16 outliers final: 14 residues processed: 140 average time/residue: 0.1766 time to fit residues: 35.9211 Evaluate side-chains 138 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain H residue 4 LEU 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 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 0.0000 chunk 26 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.121883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.099814 restraints weight = 31230.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.105162 restraints weight = 12577.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.108544 restraints weight = 6095.156| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8455 Z= 0.223 Angle : 0.712 13.513 11491 Z= 0.353 Chirality : 0.046 0.225 1225 Planarity : 0.004 0.050 1484 Dihedral : 7.642 91.276 1226 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.27 % Allowed : 14.30 % Favored : 83.43 % 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: -0.23 (0.28), residues: 1021 helix: 0.37 (0.26), residues: 396 sheet: -0.69 (0.42), residues: 163 loop : -0.24 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 115 HIS 0.002 0.001 HIS L 36 PHE 0.032 0.002 PHE A 603 TYR 0.019 0.002 TYR A 521 ARG 0.006 0.001 ARG H 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3451.78 seconds wall clock time: 62 minutes 16.24 seconds (3736.24 seconds total)