Starting phenix.real_space_refine on Tue Jan 21 02:29:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsf_38618/01_2025/8xsf_38618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsf_38618/01_2025/8xsf_38618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xsf_38618/01_2025/8xsf_38618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsf_38618/01_2025/8xsf_38618.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsf_38618/01_2025/8xsf_38618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsf_38618/01_2025/8xsf_38618.cif" } resolution = 2.16 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= 0.001 sd= 0.018 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 7990 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 50 5.16 5 C 6189 2.51 5 N 1618 2.21 5 O 1878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9736 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 1549 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Conformer: "B" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} bond proxies already assigned to first conformer: 1580 Chain: "H" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Chain: "L" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1612 Classifications: {'peptide': 211} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 199} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.20, per 1000 atoms: 0.74 Number of scatterers: 9736 At special positions: 0 Unit cell: (74.8, 84.15, 179.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 50 16.00 O 1878 8.00 N 1618 7.00 C 6189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 109 " distance=2.04 Simple disulfide: pdb=" SG CYS H 153 " - pdb=" SG CYS H 209 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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 901 " - " ASN A 53 " " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 322 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 904 " - pdb=" NE2 HIS A 378 " 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 16 sheets defined 39.8% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.945A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.824A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.963A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix 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 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.621A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.841A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.722A 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 413 removed outlier: 3.938A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 removed outlier: 3.543A pdb=" N LEU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.509A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.209A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (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: 3.579A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (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 513 through 533 removed outlier: 3.635A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.618A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.755A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.543A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.928A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.544A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.362A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.759A pdb=" N ARG H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.894A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 171 No H-bonds generated for 'chain 'H' and resid 169 through 171' Processing helix chain 'H' and resid 198 through 202 Processing helix chain 'L' and resid 121 through 127 removed outlier: 3.893A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.769A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.562A 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 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.268A pdb=" N GLY H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.268A pdb=" N GLY H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 133 through 137 removed outlier: 6.037A pdb=" N TYR H 189 " --> pdb=" O ASP H 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 133 through 137 removed outlier: 6.037A pdb=" N TYR H 189 " --> pdb=" O ASP H 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 164 through 167 removed outlier: 4.548A pdb=" N TYR H 207 " --> pdb=" O VAL H 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.889A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 20 through 24 removed outlier: 4.198A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.056A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 153 through 154 452 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3122 1.35 - 1.47: 2629 1.47 - 1.60: 4167 1.60 - 1.72: 0 1.72 - 1.84: 74 Bond restraints: 9992 Sorted by residual: bond pdb=" CB PRO A 258 " pdb=" CG PRO A 258 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.84e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.93e+00 bond pdb=" C1 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.44e+00 ... (remaining 9987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 13421 2.29 - 4.57: 154 4.57 - 6.86: 9 6.86 - 9.14: 0 9.14 - 11.43: 1 Bond angle restraints: 13585 Sorted by residual: angle pdb=" C PRO L 44 " pdb=" N LYS L 45 " pdb=" CA LYS L 45 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C CYS A 498 " pdb=" N ASP A 499 " pdb=" CA ASP A 499 " ideal model delta sigma weight residual 120.58 125.03 -4.45 1.32e+00 5.74e-01 1.14e+01 angle pdb=" CA LEU A 450 " pdb=" CB LEU A 450 " pdb=" CG LEU A 450 " ideal model delta sigma weight residual 116.30 127.73 -11.43 3.50e+00 8.16e-02 1.07e+01 angle pdb=" CA PRO A 258 " pdb=" N PRO A 258 " pdb=" CD PRO A 258 " ideal model delta sigma weight residual 112.00 107.58 4.42 1.40e+00 5.10e-01 9.95e+00 angle pdb=" C ILE A 544 " pdb=" CA ILE A 544 " pdb=" CB ILE A 544 " ideal model delta sigma weight residual 112.19 108.59 3.60 1.15e+00 7.56e-01 9.79e+00 ... (remaining 13580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 5478 17.19 - 34.38: 389 34.38 - 51.56: 77 51.56 - 68.75: 24 68.75 - 85.94: 7 Dihedral angle restraints: 5975 sinusoidal: 2409 harmonic: 3566 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 46.13 46.87 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CA GLU A 483 " pdb=" C GLU A 483 " pdb=" N ILE A 484 " pdb=" CA ILE A 484 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA CYS H 104 " pdb=" CB CYS H 104 " pdb=" SG CYS H 104 " pdb=" SG CYS H 109 " ideal model delta sinusoidal sigma weight residual -73.00 -11.00 -62.00 1 2.00e+01 2.50e-03 1.27e+01 ... (remaining 5972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 881 0.030 - 0.060: 385 0.060 - 0.090: 107 0.090 - 0.120: 82 0.120 - 0.150: 11 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CA CYS H 109 " pdb=" N CYS H 109 " pdb=" C CYS H 109 " pdb=" CB CYS H 109 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA GLU A 35 " pdb=" N GLU A 35 " pdb=" C GLU A 35 " pdb=" CB GLU A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CG LEU A 450 " pdb=" CB LEU A 450 " pdb=" CD1 LEU A 450 " pdb=" CD2 LEU A 450 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 1463 not shown) Planarity restraints: 1754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " -0.069 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO A 258 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 468 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO A 469 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 48 " 0.014 2.00e-02 2.50e+03 1.30e-02 4.21e+00 pdb=" CG TRP A 48 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 48 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 48 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 48 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 48 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 48 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 48 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 48 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 48 " 0.002 2.00e-02 2.50e+03 ... (remaining 1751 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 169 2.69 - 3.24: 9066 3.24 - 3.80: 14987 3.80 - 4.35: 20133 4.35 - 4.90: 33826 Nonbonded interactions: 78181 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 904 " model vdw 2.140 2.230 nonbonded pdb=" OH TYR B 396 " pdb=" OE2 GLU H 100 " model vdw 2.151 3.040 nonbonded pdb=" OD2 ASP H 54 " pdb=" OG SER H 56 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR A 276 " pdb=" OG1 THR A 445 " model vdw 2.233 3.040 nonbonded pdb=" OD1 ASP A 494 " pdb=" OG1 THR A 496 " model vdw 2.238 3.040 ... (remaining 78176 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.120 Process input model: 28.110 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:17.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 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 : 0.003 0.084 9992 Z= 0.184 Angle : 0.591 11.428 13585 Z= 0.332 Chirality : 0.042 0.150 1466 Planarity : 0.005 0.102 1750 Dihedral : 12.918 85.939 3660 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1212 helix: 1.26 (0.28), residues: 396 sheet: 1.64 (0.32), residues: 256 loop : -0.21 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 48 HIS 0.007 0.001 HIS A 401 PHE 0.021 0.001 PHE A 504 TYR 0.014 0.001 TYR H 80 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: B 477 SER cc_start: 0.6359 (p) cc_final: 0.6048 (m) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.9917 time to fit residues: 192.5127 Evaluate side-chains 159 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.0370 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 0.0570 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 49 ASN A 98 GLN A 394 ASN A 401 HIS A 522 GLN A 601 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN H 77 ASN H 99 GLN L 34 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.187753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.160936 restraints weight = 20177.015| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 2.61 r_work: 0.4087 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4087 r_free = 0.4087 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4087 r_free = 0.4087 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9992 Z= 0.219 Angle : 0.570 6.936 13585 Z= 0.302 Chirality : 0.043 0.143 1466 Planarity : 0.005 0.070 1750 Dihedral : 4.854 59.465 1409 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 1.69 % Allowed : 8.55 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1212 helix: 1.31 (0.27), residues: 396 sheet: 1.44 (0.31), residues: 275 loop : -0.30 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 48 HIS 0.007 0.001 HIS A 401 PHE 0.025 0.002 PHE A 28 TYR 0.018 0.002 TYR A 385 ARG 0.004 0.001 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.993 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 173 average time/residue: 1.0106 time to fit residues: 191.0485 Evaluate side-chains 163 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 434 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 0.8980 chunk 91 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 601 ASN B 448 ASN B 501 ASN H 3 GLN L 6 GLN L 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.184718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.157026 restraints weight = 21549.081| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.84 r_work: 0.4011 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4013 r_free = 0.4013 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4013 r_free = 0.4013 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9992 Z= 0.257 Angle : 0.600 18.539 13585 Z= 0.312 Chirality : 0.044 0.302 1466 Planarity : 0.005 0.061 1750 Dihedral : 4.785 59.085 1409 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 1.22 % Allowed : 11.75 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.24), residues: 1212 helix: 1.20 (0.26), residues: 397 sheet: 1.41 (0.31), residues: 271 loop : -0.45 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.008 0.001 HIS A 401 PHE 0.014 0.001 PHE A 28 TYR 0.017 0.002 TYR A 385 ARG 0.003 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 1.075 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 163 average time/residue: 1.0471 time to fit residues: 186.8276 Evaluate side-chains 159 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 50 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 556 ASN A 601 ASN B 354 ASN B 450 ASN B 487 ASN H 3 GLN H 77 ASN L 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.182869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.156794 restraints weight = 18109.811| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 2.37 r_work: 0.4040 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 9992 Z= 0.303 Angle : 0.622 14.897 13585 Z= 0.324 Chirality : 0.045 0.290 1466 Planarity : 0.005 0.059 1750 Dihedral : 4.974 58.821 1409 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 2.54 % Allowed : 12.88 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1212 helix: 1.00 (0.26), residues: 396 sheet: 1.42 (0.31), residues: 275 loop : -0.59 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 165 HIS 0.006 0.001 HIS A 401 PHE 0.017 0.002 PHE A 28 TYR 0.019 0.002 TYR A 385 ARG 0.008 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 1.037 Fit side-chains REVERT: A 401 HIS cc_start: 0.8336 (OUTLIER) cc_final: 0.8099 (t-90) REVERT: L 11 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8202 (tp) outliers start: 25 outliers final: 9 residues processed: 171 average time/residue: 0.9889 time to fit residues: 184.9702 Evaluate side-chains 162 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.0070 chunk 86 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 96 GLN A 277 ASN A 556 ASN A 601 ASN B 450 ASN H 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.182499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.154960 restraints weight = 23102.226| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.79 r_work: 0.4010 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4012 r_free = 0.4012 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4012 r_free = 0.4012 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9992 Z= 0.284 Angle : 0.610 14.710 13585 Z= 0.318 Chirality : 0.045 0.260 1466 Planarity : 0.005 0.059 1750 Dihedral : 4.926 59.228 1409 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 2.82 % Allowed : 13.35 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1212 helix: 1.01 (0.26), residues: 396 sheet: 1.41 (0.31), residues: 270 loop : -0.62 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.007 0.001 HIS A 401 PHE 0.017 0.002 PHE A 28 TYR 0.022 0.002 TYR H 110 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.002 Fit side-chains REVERT: A 154 ASN cc_start: 0.5948 (m110) cc_final: 0.5648 (m110) outliers start: 28 outliers final: 12 residues processed: 167 average time/residue: 0.9828 time to fit residues: 179.5002 Evaluate side-chains 161 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 104 optimal weight: 3.9990 chunk 73 optimal weight: 0.0000 chunk 95 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 556 ASN A 601 ASN B 450 ASN H 3 GLN L 124 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.183034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.155103 restraints weight = 23160.711| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.57 r_work: 0.4025 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9992 Z= 0.233 Angle : 0.579 14.002 13585 Z= 0.302 Chirality : 0.043 0.248 1466 Planarity : 0.005 0.058 1750 Dihedral : 4.871 59.127 1409 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 2.63 % Allowed : 14.38 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1212 helix: 1.23 (0.26), residues: 387 sheet: 1.42 (0.30), residues: 276 loop : -0.60 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 PHE 0.021 0.001 PHE A 504 TYR 0.016 0.002 TYR A 385 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.055 Fit side-chains REVERT: A 474 MET cc_start: 0.5683 (mpp) cc_final: 0.5306 (mpm) outliers start: 26 outliers final: 17 residues processed: 165 average time/residue: 1.0571 time to fit residues: 189.9219 Evaluate side-chains 161 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 0.0470 chunk 44 optimal weight: 0.4980 chunk 54 optimal weight: 0.0060 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A 601 ASN B 450 ASN H 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.184348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.157218 restraints weight = 19042.986| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 2.29 r_work: 0.4060 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9992 Z= 0.190 Angle : 0.557 13.619 13585 Z= 0.290 Chirality : 0.043 0.243 1466 Planarity : 0.005 0.058 1750 Dihedral : 5.064 58.341 1409 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.97 % Favored : 96.94 % Rotamer: Outliers : 2.54 % Allowed : 14.94 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1212 helix: 1.37 (0.26), residues: 387 sheet: 1.45 (0.31), residues: 276 loop : -0.57 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.001 PHE A 504 TYR 0.013 0.001 TYR A 516 ARG 0.005 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.025 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 167 average time/residue: 1.0880 time to fit residues: 197.8446 Evaluate side-chains 165 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 91 optimal weight: 0.0170 chunk 116 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 526 GLN A 556 ASN A 601 ASN B 354 ASN B 450 ASN B 474 GLN H 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.183608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.156211 restraints weight = 18766.834| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 2.30 r_work: 0.4053 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3917 r_free = 0.3917 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3917 r_free = 0.3917 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9992 Z= 0.225 Angle : 0.574 13.271 13585 Z= 0.298 Chirality : 0.043 0.239 1466 Planarity : 0.005 0.057 1750 Dihedral : 4.937 59.247 1409 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 2.35 % Allowed : 15.79 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1212 helix: 1.29 (0.26), residues: 388 sheet: 1.41 (0.30), residues: 276 loop : -0.59 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 PHE 0.019 0.001 PHE A 504 TYR 0.016 0.002 TYR A 385 ARG 0.005 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.3944 (OUTLIER) cc_final: 0.3176 (pp-130) REVERT: H 3 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6945 (mp10) outliers start: 23 outliers final: 17 residues processed: 163 average time/residue: 1.0193 time to fit residues: 181.2341 Evaluate side-chains 166 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 0.0270 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 chunk 101 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 chunk 64 optimal weight: 6.9990 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A 601 ASN B 354 ASN H 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.184987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.158497 restraints weight = 15889.756| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.07 r_work: 0.4085 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3957 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3960 r_free = 0.3960 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3960 r_free = 0.3960 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9992 Z= 0.174 Angle : 0.547 13.087 13585 Z= 0.283 Chirality : 0.042 0.229 1466 Planarity : 0.005 0.057 1750 Dihedral : 4.803 57.579 1409 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 2.16 % Allowed : 16.26 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.24), residues: 1212 helix: 1.51 (0.26), residues: 385 sheet: 1.42 (0.31), residues: 271 loop : -0.51 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.003 0.001 HIS H 35 PHE 0.018 0.001 PHE A 504 TYR 0.012 0.001 TYR A 516 ARG 0.008 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.3929 (OUTLIER) cc_final: 0.2971 (pp-130) outliers start: 21 outliers final: 15 residues processed: 165 average time/residue: 1.0335 time to fit residues: 185.3736 Evaluate side-chains 168 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 59 optimal weight: 0.3980 chunk 97 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 73 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 111 optimal weight: 0.0170 chunk 1 optimal weight: 0.9980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 GLN A 556 ASN A 601 ASN B 354 ASN B 474 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.184588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.157897 restraints weight = 16275.533| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.11 r_work: 0.4080 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3950 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9992 Z= 0.193 Angle : 0.558 12.953 13585 Z= 0.288 Chirality : 0.042 0.230 1466 Planarity : 0.005 0.056 1750 Dihedral : 4.823 59.081 1409 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.53 % Rotamer: Outliers : 2.07 % Allowed : 16.54 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.24), residues: 1212 helix: 1.50 (0.26), residues: 385 sheet: 1.40 (0.31), residues: 271 loop : -0.51 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS H 35 PHE 0.018 0.001 PHE A 28 TYR 0.014 0.001 TYR A 385 ARG 0.004 0.000 ARG A 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.966 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 16 residues processed: 160 average time/residue: 0.9836 time to fit residues: 171.9345 Evaluate side-chains 163 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 5 optimal weight: 0.4980 chunk 99 optimal weight: 0.0050 chunk 25 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 73 optimal weight: 0.0870 chunk 77 optimal weight: 0.0270 chunk 95 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 overall best weight: 0.2030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 GLN A 556 ASN A 601 ASN B 354 ASN H 3 GLN L 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.186467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.160264 restraints weight = 18646.512| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.38 r_work: 0.4094 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3961 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3960 r_free = 0.3960 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3960 r_free = 0.3960 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 9992 Z= 0.154 Angle : 0.532 12.860 13585 Z= 0.273 Chirality : 0.042 0.220 1466 Planarity : 0.005 0.056 1750 Dihedral : 4.620 55.830 1409 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.89 % Favored : 97.03 % Rotamer: Outliers : 1.50 % Allowed : 17.20 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.24), residues: 1212 helix: 1.58 (0.26), residues: 390 sheet: 1.49 (0.31), residues: 261 loop : -0.44 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.003 0.001 HIS H 35 PHE 0.018 0.001 PHE A 504 TYR 0.013 0.001 TYR A 516 ARG 0.003 0.000 ARG A 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11442.87 seconds wall clock time: 203 minutes 1.61 seconds (12181.61 seconds total)