Starting phenix.real_space_refine on Sat Jun 14 13:00:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsf_38618/06_2025/8xsf_38618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsf_38618/06_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_38618/06_2025/8xsf_38618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsf_38618/06_2025/8xsf_38618.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsf_38618/06_2025/8xsf_38618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsf_38618/06_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-5710/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: 7.60, per 1000 atoms: 0.78 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: 2.39 Conformation dependent library (CDL) restraints added in 1.6 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: 1.20 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: 3.44 Time building geometry restraints manager: 2.86 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: 2.590 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.230 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.140 ------------------------------------------------------------------------------- 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 10009 Z= 0.139 Angle : 0.594 11.428 13619 Z= 0.333 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 4) link_NAG-ASN : angle 1.21642 ( 12) hydrogen bonds : bond 0.12749 ( 433) hydrogen bonds : angle 5.74869 ( 1227) metal coordination : bond 0.00055 ( 2) SS BOND : bond 0.00312 ( 11) SS BOND : angle 1.36409 ( 22) covalent geometry : bond 0.00277 ( 9992) covalent geometry : angle 0.59078 (13585) *********************** 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 : 0.916 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: 1.0380 time to fit residues: 202.5838 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 : 1.230 ------------------------------------------------------------------------------- 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 = 0.187751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.160982 restraints weight = 20177.926| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.60 r_work: 0.4087 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4093 r_free = 0.4093 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 = 0.4093 r_free = 0.4093 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 10009 Z= 0.151 Angle : 0.575 6.938 13619 Z= 0.303 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 4) link_NAG-ASN : angle 2.03685 ( 12) hydrogen bonds : bond 0.04936 ( 433) hydrogen bonds : angle 4.73441 ( 1227) metal coordination : bond 0.00173 ( 2) SS BOND : bond 0.00419 ( 11) SS BOND : angle 1.20046 ( 22) covalent geometry : bond 0.00336 ( 9992) covalent geometry : angle 0.57036 (13585) *********************** 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 : 1.184 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 173 average time/residue: 1.2993 time to fit residues: 246.1311 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 : 2.036 ------------------------------------------------------------------------------- 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: 0.7980 chunk 91 optimal weight: 0.0570 chunk 32 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 77 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 474 GLN B 501 ASN H 3 GLN L 6 GLN L 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.186437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.159376 restraints weight = 21676.088| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.69 r_work: 0.4060 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4063 r_free = 0.4063 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4063 r_free = 0.4063 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10009 Z= 0.139 Angle : 0.570 18.669 13619 Z= 0.295 Chirality : 0.043 0.322 1466 Planarity : 0.005 0.060 1750 Dihedral : 4.599 58.564 1409 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 1.13 % Allowed : 12.12 % Favored : 86.75 % 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: 0.92 (0.24), residues: 1212 helix: 1.37 (0.26), residues: 396 sheet: 1.45 (0.31), residues: 271 loop : -0.35 (0.27), residues: 545 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 0.014 0.001 PHE A 28 TYR 0.014 0.001 TYR A 385 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 4) link_NAG-ASN : angle 2.30924 ( 12) hydrogen bonds : bond 0.04749 ( 433) hydrogen bonds : angle 4.60644 ( 1227) metal coordination : bond 0.00143 ( 2) SS BOND : bond 0.00567 ( 11) SS BOND : angle 1.84625 ( 22) covalent geometry : bond 0.00313 ( 9992) covalent geometry : angle 0.56176 (13585) *********************** 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 162 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 1.073 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 158 average time/residue: 1.0129 time to fit residues: 174.4660 Evaluate side-chains 157 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 151 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 50 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 L 37 GLN L 124 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.182618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.156662 restraints weight = 18239.966| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.33 r_work: 0.4039 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 10009 Z= 0.211 Angle : 0.650 14.855 13619 Z= 0.338 Chirality : 0.046 0.289 1466 Planarity : 0.005 0.059 1750 Dihedral : 5.007 57.914 1409 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 2.26 % Allowed : 12.50 % Favored : 85.24 % 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: 0.58 (0.24), residues: 1212 helix: 0.99 (0.26), residues: 396 sheet: 1.41 (0.31), residues: 276 loop : -0.59 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 116 HIS 0.007 0.002 HIS A 401 PHE 0.019 0.002 PHE A 28 TYR 0.021 0.002 TYR A 385 ARG 0.007 0.001 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 4) link_NAG-ASN : angle 2.27414 ( 12) hydrogen bonds : bond 0.05843 ( 433) hydrogen bonds : angle 4.86539 ( 1227) metal coordination : bond 0.00250 ( 2) SS BOND : bond 0.00809 ( 11) SS BOND : angle 2.14985 ( 22) covalent geometry : bond 0.00495 ( 9992) covalent geometry : angle 0.64173 (13585) *********************** 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: 22 poor density : 161 time to evaluate : 1.005 Fit side-chains REVERT: L 11 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8207 (tp) outliers start: 22 outliers final: 10 residues processed: 173 average time/residue: 1.0140 time to fit residues: 191.4268 Evaluate side-chains 164 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 434 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 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: 0.3980 chunk 86 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 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 277 ASN A 556 ASN A 601 ASN B 354 ASN B 450 ASN B 474 GLN H 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.182432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.154300 restraints weight = 23094.117| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.58 r_work: 0.4019 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10009 Z= 0.192 Angle : 0.625 14.666 13619 Z= 0.323 Chirality : 0.045 0.262 1466 Planarity : 0.005 0.059 1750 Dihedral : 4.945 59.082 1409 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 2.73 % Allowed : 13.16 % Favored : 84.12 % 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: 0.52 (0.24), residues: 1212 helix: 0.99 (0.26), residues: 392 sheet: 1.40 (0.31), residues: 270 loop : -0.65 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 165 HIS 0.004 0.001 HIS A 374 PHE 0.013 0.002 PHE A 28 TYR 0.020 0.002 TYR A 385 ARG 0.004 0.001 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 4) link_NAG-ASN : angle 2.34486 ( 12) hydrogen bonds : bond 0.05474 ( 433) hydrogen bonds : angle 4.82807 ( 1227) metal coordination : bond 0.00184 ( 2) SS BOND : bond 0.00771 ( 11) SS BOND : angle 1.87335 ( 22) covalent geometry : bond 0.00449 ( 9992) covalent geometry : angle 0.61690 (13585) *********************** 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 179 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.993 Fit side-chains REVERT: A 41 TYR cc_start: 0.7660 (t80) cc_final: 0.7300 (t80) outliers start: 27 outliers final: 9 residues processed: 167 average time/residue: 0.9821 time to fit residues: 178.5545 Evaluate side-chains 158 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 434 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 341 VAL 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: 2.9990 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 62 optimal weight: 0.0030 chunk 74 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.0370 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.4668 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.183753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.155771 restraints weight = 23252.955| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.59 r_work: 0.4032 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4036 r_free = 0.4036 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4036 r_free = 0.4036 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10009 Z= 0.141 Angle : 0.574 13.899 13619 Z= 0.297 Chirality : 0.043 0.245 1466 Planarity : 0.005 0.057 1750 Dihedral : 4.805 59.511 1409 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 2.16 % Allowed : 14.38 % Favored : 83.46 % 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: 0.70 (0.24), residues: 1212 helix: 1.22 (0.26), residues: 389 sheet: 1.41 (0.30), residues: 277 loop : -0.58 (0.26), residues: 546 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 0.017 0.001 PHE A 28 TYR 0.015 0.001 TYR H 110 ARG 0.004 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 4) link_NAG-ASN : angle 2.19226 ( 12) hydrogen bonds : bond 0.04772 ( 433) hydrogen bonds : angle 4.65914 ( 1227) metal coordination : bond 0.00131 ( 2) SS BOND : bond 0.00679 ( 11) SS BOND : angle 1.81872 ( 22) covalent geometry : bond 0.00321 ( 9992) covalent geometry : angle 0.56662 (13585) *********************** 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 171 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.006 Fit side-chains REVERT: A 41 TYR cc_start: 0.7613 (t80) cc_final: 0.7245 (t80) REVERT: A 401 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7848 (m-70) outliers start: 21 outliers final: 14 residues processed: 164 average time/residue: 0.9705 time to fit residues: 173.7796 Evaluate side-chains 160 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 401 HIS 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 B residue 341 VAL 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 33 LEU 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: 7.9990 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A 601 ASN B 354 ASN H 77 ASN L 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.182529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.155302 restraints weight = 18960.511| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.28 r_work: 0.4035 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3897 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10009 Z= 0.172 Angle : 0.643 21.117 13619 Z= 0.321 Chirality : 0.045 0.252 1466 Planarity : 0.005 0.058 1750 Dihedral : 5.233 59.915 1409 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.37 % Rotamer: Outliers : 2.44 % Allowed : 15.23 % Favored : 82.33 % 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: 0.57 (0.24), residues: 1212 helix: 1.12 (0.26), residues: 387 sheet: 1.35 (0.31), residues: 271 loop : -0.64 (0.26), residues: 554 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 0.023 0.001 PHE A 504 TYR 0.018 0.002 TYR A 385 ARG 0.004 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.01034 ( 4) link_NAG-ASN : angle 7.31140 ( 12) hydrogen bonds : bond 0.05234 ( 433) hydrogen bonds : angle 4.72292 ( 1227) metal coordination : bond 0.00174 ( 2) SS BOND : bond 0.00719 ( 11) SS BOND : angle 1.90130 ( 22) covalent geometry : bond 0.00398 ( 9992) covalent geometry : angle 0.60097 (13585) *********************** 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 166 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7781 (t80) cc_final: 0.7428 (t80) REVERT: A 401 HIS cc_start: 0.8360 (OUTLIER) cc_final: 0.7997 (m-70) outliers start: 24 outliers final: 15 residues processed: 157 average time/residue: 0.9667 time to fit residues: 165.5952 Evaluate side-chains 156 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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 522 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 341 VAL 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 33 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: 0.6980 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 91 optimal weight: 0.0000 chunk 116 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 B 450 ASN B 474 GLN H 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.183590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.156201 restraints weight = 18707.349| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.31 r_work: 0.4054 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10009 Z= 0.145 Angle : 0.624 20.194 13619 Z= 0.310 Chirality : 0.044 0.238 1466 Planarity : 0.005 0.058 1750 Dihedral : 4.978 59.756 1409 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 2.63 % Allowed : 15.13 % Favored : 82.24 % 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: 0.66 (0.24), residues: 1212 helix: 1.24 (0.26), residues: 388 sheet: 1.38 (0.30), residues: 276 loop : -0.64 (0.26), residues: 548 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 0.024 0.001 PHE A 504 TYR 0.015 0.001 TYR A 385 ARG 0.008 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.01043 ( 4) link_NAG-ASN : angle 7.26641 ( 12) hydrogen bonds : bond 0.04788 ( 433) hydrogen bonds : angle 4.64762 ( 1227) metal coordination : bond 0.00130 ( 2) SS BOND : bond 0.00669 ( 11) SS BOND : angle 1.75840 ( 22) covalent geometry : bond 0.00329 ( 9992) covalent geometry : angle 0.58223 (13585) *********************** 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: 26 poor density : 147 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7741 (t80) cc_final: 0.7381 (t80) REVERT: A 401 HIS cc_start: 0.8286 (OUTLIER) cc_final: 0.7859 (m-70) outliers start: 26 outliers final: 16 residues processed: 164 average time/residue: 0.9374 time to fit residues: 168.0246 Evaluate side-chains 162 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 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 522 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 58 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 56 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.0040 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 91 optimal weight: 0.0060 chunk 101 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 30 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 overall best weight: 0.1608 ------------------------------------------------------------------------------- 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 B 450 ASN H 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.186994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.160657 restraints weight = 15931.748| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 2.07 r_work: 0.4113 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3989 r_free = 0.3989 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3989 r_free = 0.3989 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 10009 Z= 0.106 Angle : 0.579 18.866 13619 Z= 0.286 Chirality : 0.042 0.222 1466 Planarity : 0.005 0.057 1750 Dihedral : 4.647 55.121 1409 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.81 % Favored : 97.11 % Rotamer: Outliers : 1.60 % Allowed : 16.82 % 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: 0.85 (0.24), residues: 1212 helix: 1.45 (0.26), residues: 397 sheet: 1.49 (0.31), residues: 261 loop : -0.54 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 PHE 0.023 0.001 PHE A 504 TYR 0.015 0.001 TYR A 516 ARG 0.005 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.01120 ( 4) link_NAG-ASN : angle 6.75079 ( 12) hydrogen bonds : bond 0.03821 ( 433) hydrogen bonds : angle 4.41242 ( 1227) metal coordination : bond 0.00044 ( 2) SS BOND : bond 0.00604 ( 11) SS BOND : angle 1.56240 ( 22) covalent geometry : bond 0.00226 ( 9992) covalent geometry : angle 0.54024 (13585) *********************** 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 171 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 401 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7635 (m-70) outliers start: 15 outliers final: 8 residues processed: 167 average time/residue: 1.0189 time to fit residues: 186.4823 Evaluate side-chains 165 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 59 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.0000 chunk 62 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.183708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.156931 restraints weight = 16254.051| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.11 r_work: 0.4071 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10009 Z= 0.157 Angle : 0.638 19.079 13619 Z= 0.314 Chirality : 0.044 0.230 1466 Planarity : 0.005 0.057 1750 Dihedral : 4.912 58.720 1409 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 1.41 % Allowed : 17.29 % 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: 0.71 (0.24), residues: 1212 helix: 1.34 (0.26), residues: 393 sheet: 1.35 (0.30), residues: 270 loop : -0.62 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 PHE 0.028 0.002 PHE A 28 TYR 0.017 0.002 TYR A 385 ARG 0.005 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.01067 ( 4) link_NAG-ASN : angle 6.88732 ( 12) hydrogen bonds : bond 0.04818 ( 433) hydrogen bonds : angle 4.53468 ( 1227) metal coordination : bond 0.00167 ( 2) SS BOND : bond 0.00673 ( 11) SS BOND : angle 1.74048 ( 22) covalent geometry : bond 0.00363 ( 9992) covalent geometry : angle 0.60131 (13585) ********************** 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 166 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 401 HIS cc_start: 0.8286 (OUTLIER) cc_final: 0.7855 (m-70) REVERT: H 3 GLN cc_start: 0.7107 (mp-120) cc_final: 0.6888 (mp10) outliers start: 13 outliers final: 8 residues processed: 163 average time/residue: 0.9630 time to fit residues: 171.5110 Evaluate side-chains 162 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 43 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 99 optimal weight: 0.0270 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 73 optimal weight: 0.0040 chunk 77 optimal weight: 0.0470 chunk 95 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 overall best weight: 0.2548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 556 ASN A 601 ASN B 354 ASN B 450 ASN B 474 GLN H 77 ASN H 205 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.186471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.160303 restraints weight = 18591.260| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.34 r_work: 0.4088 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3957 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 10009 Z= 0.111 Angle : 0.582 18.482 13619 Z= 0.288 Chirality : 0.042 0.221 1466 Planarity : 0.005 0.057 1750 Dihedral : 4.702 56.672 1409 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 1.41 % Allowed : 17.29 % 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: 0.81 (0.24), residues: 1212 helix: 1.48 (0.26), residues: 390 sheet: 1.51 (0.31), residues: 259 loop : -0.60 (0.26), residues: 563 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 0.022 0.001 PHE A 504 TYR 0.012 0.001 TYR H 158 ARG 0.009 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.01098 ( 4) link_NAG-ASN : angle 6.68067 ( 12) hydrogen bonds : bond 0.04074 ( 433) hydrogen bonds : angle 4.38886 ( 1227) metal coordination : bond 0.00057 ( 2) SS BOND : bond 0.00605 ( 11) SS BOND : angle 1.61583 ( 22) covalent geometry : bond 0.00241 ( 9992) covalent geometry : angle 0.54363 (13585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12014.79 seconds wall clock time: 207 minutes 53.32 seconds (12473.32 seconds total)