Starting phenix.real_space_refine on Sat May 17 21:26:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsf_38618/05_2025/8xsf_38618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsf_38618/05_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_38618/05_2025/8xsf_38618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsf_38618/05_2025/8xsf_38618.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsf_38618/05_2025/8xsf_38618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsf_38618/05_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-5687/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: 7.08, per 1000 atoms: 0.73 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: 2.22 Conformation dependent library (CDL) restraints added in 1.4 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: 1.15 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: 3.37 Time building geometry restraints manager: 2.60 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: 9.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.100 Process input model: 27.730 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.650 ------------------------------------------------------------------------------- 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 : 1.060 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: 0.9048 time to fit residues: 176.2483 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 : 1.098 ------------------------------------------------------------------------------- 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 10009 Z= 0.151 Angle : 0.575 6.936 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 0.00268 ( 4) link_NAG-ASN : angle 2.03580 ( 12) hydrogen bonds : bond 0.04936 ( 433) hydrogen bonds : angle 4.73442 ( 1227) metal coordination : bond 0.00172 ( 2) SS BOND : bond 0.00417 ( 11) SS BOND : angle 1.20080 ( 22) covalent geometry : bond 0.00336 ( 9992) covalent geometry : angle 0.57035 (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 : 1.132 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 173 average time/residue: 0.9303 time to fit residues: 176.0155 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 : 1.021 ------------------------------------------------------------------------------- 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 10009 Z= 0.168 Angle : 0.609 18.539 13619 Z= 0.315 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 4) link_NAG-ASN : angle 2.35927 ( 12) hydrogen bonds : bond 0.05300 ( 433) hydrogen bonds : angle 4.74191 ( 1227) metal coordination : bond 0.00198 ( 2) SS BOND : bond 0.00506 ( 11) SS BOND : angle 2.12665 ( 22) covalent geometry : bond 0.00388 ( 9992) covalent geometry : angle 0.59970 (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 168 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 1.031 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 163 average time/residue: 0.9474 time to fit residues: 168.8659 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 : 1.012 ------------------------------------------------------------------------------- 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 10009 Z= 0.195 Angle : 0.631 14.897 13619 Z= 0.327 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 4) link_NAG-ASN : angle 2.38624 ( 12) hydrogen bonds : bond 0.05588 ( 433) hydrogen bonds : angle 4.83161 ( 1227) metal coordination : bond 0.00231 ( 2) SS BOND : bond 0.00762 ( 11) SS BOND : angle 2.13112 ( 22) covalent geometry : bond 0.00459 ( 9992) covalent geometry : angle 0.62210 (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: 25 poor density : 158 time to evaluate : 0.963 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: 0.9405 time to fit residues: 176.1621 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 : 1.277 ------------------------------------------------------------------------------- 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 10009 Z= 0.185 Angle : 0.618 14.710 13619 Z= 0.320 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 4) link_NAG-ASN : angle 2.44106 ( 12) hydrogen bonds : bond 0.05395 ( 433) hydrogen bonds : angle 4.81934 ( 1227) metal coordination : bond 0.00232 ( 2) SS BOND : bond 0.00760 ( 11) SS BOND : angle 1.85122 ( 22) covalent geometry : bond 0.00432 ( 9992) covalent geometry : angle 0.61037 (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 178 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.018 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: 0.9321 time to fit residues: 170.5435 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 : 0.964 ------------------------------------------------------------------------------- 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: 0.9980 chunk 95 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 74 optimal weight: 0.4980 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: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4432 r_free = 0.4432 target = 0.182375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.154393 restraints weight = 23129.730| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.58 r_work: 0.4016 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 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 = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10009 Z= 0.171 Angle : 0.605 14.013 13619 Z= 0.313 Chirality : 0.044 0.252 1466 Planarity : 0.005 0.059 1750 Dihedral : 4.940 59.625 1409 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % 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: 0.61 (0.24), residues: 1212 helix: 1.18 (0.26), residues: 385 sheet: 1.39 (0.31), residues: 270 loop : -0.64 (0.26), residues: 557 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 0.022 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 0.00085 ( 4) link_NAG-ASN : angle 2.40730 ( 12) hydrogen bonds : bond 0.05229 ( 433) hydrogen bonds : angle 4.75941 ( 1227) metal coordination : bond 0.00188 ( 2) SS BOND : bond 0.00734 ( 11) SS BOND : angle 1.96170 ( 22) covalent geometry : bond 0.00396 ( 9992) covalent geometry : angle 0.59597 (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 176 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.136 Fit side-chains REVERT: A 474 MET cc_start: 0.5699 (mpp) cc_final: 0.5262 (mpm) outliers start: 26 outliers final: 16 residues processed: 167 average time/residue: 0.9465 time to fit residues: 172.6940 Evaluate side-chains 162 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4435 r_free = 0.4435 target = 0.182672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.155505 restraints weight = 18968.529| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.29 r_work: 0.4042 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3904 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3903 r_free = 0.3903 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3903 r_free = 0.3903 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10009 Z= 0.161 Angle : 0.633 21.232 13619 Z= 0.317 Chirality : 0.044 0.247 1466 Planarity : 0.005 0.059 1750 Dihedral : 5.243 58.731 1409 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 2.63 % Allowed : 15.04 % 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: 0.60 (0.24), residues: 1212 helix: 1.16 (0.26), residues: 387 sheet: 1.39 (0.31), residues: 270 loop : -0.64 (0.26), residues: 555 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 0.020 0.001 PHE A 504 TYR 0.016 0.002 TYR A 385 ARG 0.004 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00966 ( 4) link_NAG-ASN : angle 7.35613 ( 12) hydrogen bonds : bond 0.05077 ( 433) hydrogen bonds : angle 4.71781 ( 1227) metal coordination : bond 0.00153 ( 2) SS BOND : bond 0.00708 ( 11) SS BOND : angle 1.89039 ( 22) covalent geometry : bond 0.00370 ( 9992) covalent geometry : angle 0.58988 (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 174 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 401 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.8019 (m-70) outliers start: 26 outliers final: 17 residues processed: 163 average time/residue: 0.9583 time to fit residues: 171.1100 Evaluate side-chains 165 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 91 optimal weight: 0.0050 chunk 116 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.181683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.154120 restraints weight = 18700.661| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.64 r_work: 0.4006 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- 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 = 0.15 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 = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4558 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= 0.184 Angle : 0.665 20.553 13619 Z= 0.332 Chirality : 0.045 0.248 1466 Planarity : 0.005 0.059 1750 Dihedral : 5.143 59.217 1409 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 2.82 % Allowed : 15.32 % 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: 0.52 (0.24), residues: 1212 helix: 1.13 (0.26), residues: 384 sheet: 1.34 (0.31), residues: 270 loop : -0.71 (0.26), residues: 558 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 0.022 0.002 PHE A 504 TYR 0.018 0.002 TYR A 385 ARG 0.005 0.001 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00980 ( 4) link_NAG-ASN : angle 7.46800 ( 12) hydrogen bonds : bond 0.05431 ( 433) hydrogen bonds : angle 4.80168 ( 1227) metal coordination : bond 0.00204 ( 2) SS BOND : bond 0.00731 ( 11) SS BOND : angle 1.90548 ( 22) covalent geometry : bond 0.00428 ( 9992) covalent geometry : angle 0.62292 (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: 28 poor density : 145 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 401 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.7821 (m-70) REVERT: A 559 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7394 (ptm160) outliers start: 28 outliers final: 18 residues processed: 160 average time/residue: 0.9347 time to fit residues: 163.6557 Evaluate side-chains 163 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 559 ARG 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 58 LYS 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: 0.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 91 optimal weight: 0.0670 chunk 101 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A 601 ASN B 354 ASN B 450 ASN H 3 GLN H 77 ASN L 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.183289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.156635 restraints weight = 15745.163| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 2.09 r_work: 0.4066 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3938 r_free = 0.3938 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3938 r_free = 0.3938 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4604 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= 0.149 Angle : 0.627 19.423 13619 Z= 0.312 Chirality : 0.044 0.239 1466 Planarity : 0.005 0.059 1750 Dihedral : 5.056 59.767 1409 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 2.54 % Allowed : 16.07 % 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: 0.62 (0.24), residues: 1212 helix: 1.25 (0.26), residues: 385 sheet: 1.35 (0.30), residues: 276 loop : -0.68 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.004 0.001 HIS H 35 PHE 0.021 0.001 PHE A 504 TYR 0.017 0.001 TYR A 237 ARG 0.008 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.01111 ( 4) link_NAG-ASN : angle 7.00710 ( 12) hydrogen bonds : bond 0.04858 ( 433) hydrogen bonds : angle 4.63715 ( 1227) metal coordination : bond 0.00129 ( 2) SS BOND : bond 0.00670 ( 11) SS BOND : angle 1.78096 ( 22) covalent geometry : bond 0.00340 ( 9992) covalent geometry : angle 0.58838 (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 174 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.4270 (OUTLIER) cc_final: 0.3578 (pp-130) REVERT: A 401 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.7824 (m-70) outliers start: 25 outliers final: 17 residues processed: 164 average time/residue: 0.9383 time to fit residues: 168.9556 Evaluate side-chains 168 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 59 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.0370 chunk 62 optimal weight: 0.0270 chunk 116 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 73 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.2694 ------------------------------------------------------------------------------- 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 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.185141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.158445 restraints weight = 16148.373| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.12 r_work: 0.4086 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10009 Z= 0.114 Angle : 0.595 18.821 13619 Z= 0.294 Chirality : 0.042 0.228 1466 Planarity : 0.005 0.059 1750 Dihedral : 4.826 57.146 1409 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.86 % Rotamer: Outliers : 2.26 % Allowed : 16.35 % 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: 0.78 (0.24), residues: 1212 helix: 1.46 (0.26), residues: 387 sheet: 1.38 (0.31), residues: 271 loop : -0.60 (0.26), residues: 554 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 0.020 0.001 PHE A 504 TYR 0.014 0.001 TYR A 516 ARG 0.007 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.01092 ( 4) link_NAG-ASN : angle 6.79582 ( 12) hydrogen bonds : bond 0.04220 ( 433) hydrogen bonds : angle 4.47853 ( 1227) metal coordination : bond 0.00069 ( 2) SS BOND : bond 0.00602 ( 11) SS BOND : angle 1.64302 ( 22) covalent geometry : bond 0.00249 ( 9992) covalent geometry : angle 0.55613 (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 173 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.4169 (OUTLIER) cc_final: 0.3934 (pmt) REVERT: A 401 HIS cc_start: 0.8194 (OUTLIER) cc_final: 0.7694 (m-70) REVERT: A 559 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7498 (ptm160) REVERT: H 3 GLN cc_start: 0.7134 (mp10) cc_final: 0.6877 (mp10) outliers start: 22 outliers final: 12 residues processed: 163 average time/residue: 0.9275 time to fit residues: 165.5626 Evaluate side-chains 164 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 401 HIS Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 559 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 99 optimal weight: 0.0030 chunk 25 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 111 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.0470 chunk 95 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 overall best weight: 0.2888 ------------------------------------------------------------------------------- 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 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 = 0.4465 r_free = 0.4465 target = 0.185442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.158392 restraints weight = 18475.618| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 2.47 r_work: 0.4061 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4064 r_free = 0.4064 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4064 r_free = 0.4064 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10009 Z= 0.117 Angle : 0.591 18.347 13619 Z= 0.291 Chirality : 0.042 0.226 1466 Planarity : 0.005 0.058 1750 Dihedral : 4.774 58.003 1409 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.86 % Rotamer: Outliers : 1.97 % Allowed : 16.82 % Favored : 81.20 % 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: 0.84 (0.24), residues: 1212 helix: 1.53 (0.26), residues: 388 sheet: 1.44 (0.31), residues: 261 loop : -0.56 (0.26), residues: 563 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 0.020 0.001 PHE A 504 TYR 0.012 0.001 TYR A 516 ARG 0.005 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.01129 ( 4) link_NAG-ASN : angle 6.63222 ( 12) hydrogen bonds : bond 0.04222 ( 433) hydrogen bonds : angle 4.41026 ( 1227) metal coordination : bond 0.00068 ( 2) SS BOND : bond 0.00623 ( 11) SS BOND : angle 1.65811 ( 22) covalent geometry : bond 0.00257 ( 9992) covalent geometry : angle 0.55425 (13585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10674.16 seconds wall clock time: 183 minutes 55.41 seconds (11035.41 seconds total)