Starting phenix.real_space_refine on Thu Sep 18 10:43:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsf_38618/09_2025/8xsf_38618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsf_38618/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xsf_38618/09_2025/8xsf_38618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsf_38618/09_2025/8xsf_38618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xsf_38618/09_2025/8xsf_38618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsf_38618/09_2025/8xsf_38618.map" } resolution = 2.16 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.01, per 1000 atoms: 0.31 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: 0.82 Conformation dependent library (CDL) restraints added in 445.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.39 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: 1.56 Time building geometry restraints manager: 1.12 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.320 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.720 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 357 TYR 0.014 0.001 TYR H 80 PHE 0.021 0.001 PHE A 504 TRP 0.034 0.001 TRP A 48 HIS 0.007 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9992) covalent geometry : angle 0.59078 (13585) SS BOND : bond 0.00312 ( 11) SS BOND : angle 1.36409 ( 22) hydrogen bonds : bond 0.12749 ( 433) hydrogen bonds : angle 5.74869 ( 1227) metal coordination : bond 0.00055 ( 2) link_NAG-ASN : bond 0.00186 ( 4) link_NAG-ASN : angle 1.21642 ( 12) *********************** 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 : 0.346 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: 0.4369 time to fit residues: 84.9616 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 : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 = 0.4460 r_free = 0.4460 target = 0.185410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.156579 restraints weight = 27323.531| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.87 r_work: 0.4030 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10009 Z= 0.201 Angle : 0.635 8.626 13619 Z= 0.334 Chirality : 0.045 0.159 1466 Planarity : 0.006 0.073 1750 Dihedral : 5.160 59.295 1409 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 1.60 % Allowed : 8.74 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.24), residues: 1212 helix: 1.04 (0.26), residues: 397 sheet: 1.42 (0.31), residues: 277 loop : -0.45 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 460 TYR 0.019 0.002 TYR A 385 PHE 0.026 0.002 PHE A 28 TRP 0.027 0.002 TRP A 48 HIS 0.006 0.002 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 9992) covalent geometry : angle 0.62913 (13585) SS BOND : bond 0.00477 ( 11) SS BOND : angle 1.50005 ( 22) hydrogen bonds : bond 0.05808 ( 433) hydrogen bonds : angle 4.97890 ( 1227) metal coordination : bond 0.00267 ( 2) link_NAG-ASN : bond 0.00684 ( 4) link_NAG-ASN : angle 2.21996 ( 12) *********************** 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 180 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7702 (t80) cc_final: 0.7429 (t80) outliers start: 15 outliers final: 3 residues processed: 169 average time/residue: 0.4477 time to fit residues: 82.4790 Evaluate side-chains 157 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 154 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 101 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 108 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 487 ASN B 501 ASN 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 = 0.4459 r_free = 0.4459 target = 0.185217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.159875 restraints weight = 17125.293| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.26 r_work: 0.4076 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3944 r_free = 0.3944 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 = 0.3944 r_free = 0.3944 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10009 Z= 0.153 Angle : 0.585 18.079 13619 Z= 0.304 Chirality : 0.044 0.308 1466 Planarity : 0.005 0.061 1750 Dihedral : 4.730 59.569 1409 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.86 % Rotamer: Outliers : 1.13 % Allowed : 11.28 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.24), residues: 1212 helix: 1.19 (0.26), residues: 397 sheet: 1.42 (0.31), residues: 277 loop : -0.46 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.016 0.001 TYR A 385 PHE 0.013 0.001 PHE A 28 TRP 0.016 0.001 TRP A 165 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9992) covalent geometry : angle 0.57519 (13585) SS BOND : bond 0.00615 ( 11) SS BOND : angle 2.06042 ( 22) hydrogen bonds : bond 0.04939 ( 433) hydrogen bonds : angle 4.74004 ( 1227) metal coordination : bond 0.00142 ( 2) link_NAG-ASN : bond 0.00548 ( 4) link_NAG-ASN : angle 2.47396 ( 12) *********************** 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 163 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.376 Fit side-chains REVERT: A 231 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7418 (mm-30) outliers start: 10 outliers final: 7 residues processed: 158 average time/residue: 0.4683 time to fit residues: 80.2363 Evaluate side-chains 157 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 579 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 98 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 25 optimal weight: 0.0670 chunk 97 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 64 ASN A 556 ASN A 601 ASN B 450 ASN B 474 GLN H 77 ASN L 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.183082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.154290 restraints weight = 27071.231| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.84 r_work: 0.4007 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4008 r_free = 0.4008 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4008 r_free = 0.4008 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 10009 Z= 0.184 Angle : 0.620 15.910 13619 Z= 0.322 Chirality : 0.045 0.268 1466 Planarity : 0.005 0.060 1750 Dihedral : 4.955 59.396 1409 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 2.35 % Allowed : 12.88 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.24), residues: 1212 helix: 1.05 (0.26), residues: 396 sheet: 1.36 (0.31), residues: 276 loop : -0.56 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.019 0.002 TYR A 385 PHE 0.016 0.002 PHE A 28 TRP 0.014 0.002 TRP A 165 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 9992) covalent geometry : angle 0.61136 (13585) SS BOND : bond 0.00785 ( 11) SS BOND : angle 2.01998 ( 22) hydrogen bonds : bond 0.05470 ( 433) hydrogen bonds : angle 4.80835 ( 1227) metal coordination : bond 0.00206 ( 2) link_NAG-ASN : bond 0.00181 ( 4) link_NAG-ASN : angle 2.39500 ( 12) *********************** 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 171 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.357 Fit side-chains REVERT: A 231 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7315 (mm-30) outliers start: 23 outliers final: 10 residues processed: 160 average time/residue: 0.4262 time to fit residues: 74.1413 Evaluate side-chains 152 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 455 MET 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 L residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 83 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 74 optimal weight: 0.0770 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 51 optimal weight: 0.0970 chunk 99 optimal weight: 2.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 64 ASN A 556 ASN A 601 ASN B 354 ASN B 450 ASN L 89 GLN L 124 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.185102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.157418 restraints weight = 23115.325| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.57 r_work: 0.4049 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10009 Z= 0.125 Angle : 0.556 15.014 13619 Z= 0.288 Chirality : 0.042 0.226 1466 Planarity : 0.005 0.057 1750 Dihedral : 4.657 58.650 1409 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.86 % Rotamer: Outliers : 2.16 % Allowed : 13.16 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.24), residues: 1212 helix: 1.31 (0.26), residues: 396 sheet: 1.46 (0.31), residues: 271 loop : -0.45 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.013 0.001 TYR A 516 PHE 0.016 0.001 PHE A 28 TRP 0.014 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9992) covalent geometry : angle 0.54839 (13585) SS BOND : bond 0.00712 ( 11) SS BOND : angle 1.77098 ( 22) hydrogen bonds : bond 0.04500 ( 433) hydrogen bonds : angle 4.59824 ( 1227) metal coordination : bond 0.00124 ( 2) link_NAG-ASN : bond 0.00216 ( 4) link_NAG-ASN : angle 2.28536 ( 12) *********************** 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 166 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.369 Fit side-chains REVERT: A 85 LEU cc_start: 0.7334 (tp) cc_final: 0.7114 (tp) outliers start: 21 outliers final: 11 residues processed: 158 average time/residue: 0.5115 time to fit residues: 87.6412 Evaluate side-chains 153 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 434 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 4 optimal weight: 0.4980 chunk 0 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 74 optimal weight: 0.0570 chunk 49 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 114 optimal weight: 0.9980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 96 GLN A 556 ASN A 601 ASN B 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.185618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.157973 restraints weight = 23995.348| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.92 r_work: 0.4038 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4038 r_free = 0.4038 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4038 r_free = 0.4038 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10009 Z= 0.120 Angle : 0.545 14.369 13619 Z= 0.283 Chirality : 0.042 0.213 1466 Planarity : 0.005 0.057 1750 Dihedral : 4.579 58.094 1409 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 1.97 % Allowed : 13.72 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.24), residues: 1212 helix: 1.47 (0.26), residues: 395 sheet: 1.53 (0.31), residues: 269 loop : -0.41 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 19 TYR 0.012 0.001 TYR A 385 PHE 0.016 0.001 PHE A 28 TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9992) covalent geometry : angle 0.53755 (13585) SS BOND : bond 0.00683 ( 11) SS BOND : angle 1.64522 ( 22) hydrogen bonds : bond 0.04315 ( 433) hydrogen bonds : angle 4.49537 ( 1227) metal coordination : bond 0.00131 ( 2) link_NAG-ASN : bond 0.00165 ( 4) link_NAG-ASN : angle 2.13021 ( 12) *********************** 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 162 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.371 Fit side-chains REVERT: A 401 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7775 (m-70) outliers start: 19 outliers final: 13 residues processed: 155 average time/residue: 0.4904 time to fit residues: 82.6748 Evaluate side-chains 155 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain 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 105 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 0.0020 chunk 110 optimal weight: 0.9980 chunk 77 optimal weight: 0.0000 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 118 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 H 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.185256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.159711 restraints weight = 17147.877| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.28 r_work: 0.4072 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3939 r_free = 0.3939 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3939 r_free = 0.3939 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4111 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= 0.125 Angle : 0.587 20.867 13619 Z= 0.293 Chirality : 0.043 0.232 1466 Planarity : 0.005 0.056 1750 Dihedral : 4.912 58.540 1409 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 2.16 % Allowed : 14.76 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.24), residues: 1212 helix: 1.47 (0.26), residues: 396 sheet: 1.52 (0.31), residues: 269 loop : -0.43 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 19 TYR 0.013 0.001 TYR A 385 PHE 0.017 0.001 PHE A 28 TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9992) covalent geometry : angle 0.54229 (13585) SS BOND : bond 0.00680 ( 11) SS BOND : angle 1.59222 ( 22) hydrogen bonds : bond 0.04359 ( 433) hydrogen bonds : angle 4.50246 ( 1227) metal coordination : bond 0.00114 ( 2) link_NAG-ASN : bond 0.01019 ( 4) link_NAG-ASN : angle 7.27318 ( 12) *********************** 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 168 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 401 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.7819 (m-70) outliers start: 21 outliers final: 15 residues processed: 159 average time/residue: 0.4323 time to fit residues: 75.2153 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 : 0.343 ------------------------------------------------------------------------------- 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 522 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain L residue 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 96 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 91 optimal weight: 0.0470 chunk 93 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.182313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.156295 restraints weight = 17666.363| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.38 r_work: 0.4035 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3894 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4292 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 : 0.654 20.240 13619 Z= 0.329 Chirality : 0.045 0.219 1466 Planarity : 0.005 0.056 1750 Dihedral : 5.041 58.557 1409 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.79 % Rotamer: Outliers : 2.07 % Allowed : 14.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.24), residues: 1212 helix: 1.18 (0.26), residues: 394 sheet: 1.37 (0.30), residues: 270 loop : -0.54 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 19 TYR 0.019 0.002 TYR A 385 PHE 0.020 0.002 PHE A 28 TRP 0.012 0.002 TRP A 566 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 9992) covalent geometry : angle 0.61339 (13585) SS BOND : bond 0.00776 ( 11) SS BOND : angle 1.79853 ( 22) hydrogen bonds : bond 0.05349 ( 433) hydrogen bonds : angle 4.71968 ( 1227) metal coordination : bond 0.00258 ( 2) link_NAG-ASN : bond 0.00968 ( 4) link_NAG-ASN : angle 7.31615 ( 12) *********************** 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 165 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 154 ASN cc_start: 0.6123 (m110) cc_final: 0.5779 (m110) REVERT: A 401 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.7989 (m-70) REVERT: A 474 MET cc_start: 0.5703 (mpp) cc_final: 0.5225 (mpm) outliers start: 20 outliers final: 14 residues processed: 157 average time/residue: 0.4255 time to fit residues: 73.2462 Evaluate side-chains 157 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 522 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 24 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 58 optimal weight: 0.0270 chunk 104 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 overall best weight: 0.3216 ------------------------------------------------------------------------------- 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 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.184975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.158535 restraints weight = 15901.420| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.09 r_work: 0.4089 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3961 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3961 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10009 Z= 0.120 Angle : 0.586 19.240 13619 Z= 0.293 Chirality : 0.042 0.203 1466 Planarity : 0.005 0.056 1750 Dihedral : 4.806 57.473 1409 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.86 % Rotamer: Outliers : 1.88 % Allowed : 15.51 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.24), residues: 1212 helix: 1.43 (0.26), residues: 393 sheet: 1.47 (0.31), residues: 269 loop : -0.47 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 19 TYR 0.012 0.001 TYR A 516 PHE 0.016 0.001 PHE A 504 TRP 0.014 0.001 TRP A 165 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9992) covalent geometry : angle 0.54657 (13585) SS BOND : bond 0.00672 ( 11) SS BOND : angle 1.50665 ( 22) hydrogen bonds : bond 0.04288 ( 433) hydrogen bonds : angle 4.50817 ( 1227) metal coordination : bond 0.00105 ( 2) link_NAG-ASN : bond 0.01071 ( 4) link_NAG-ASN : angle 6.91289 ( 12) *********************** 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 167 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.3769 (OUTLIER) cc_final: 0.3034 (ppp) REVERT: A 401 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7758 (m-70) outliers start: 18 outliers final: 12 residues processed: 161 average time/residue: 0.4705 time to fit residues: 82.6740 Evaluate side-chains 161 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 4 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 110 optimal weight: 0.0270 chunk 75 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 56 optimal weight: 0.0870 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.185453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.156020 restraints weight = 27167.669| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 3.34 r_work: 0.4009 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10009 Z= 0.126 Angle : 0.601 18.742 13619 Z= 0.299 Chirality : 0.042 0.203 1466 Planarity : 0.005 0.056 1750 Dihedral : 4.811 58.835 1409 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 1.50 % Allowed : 16.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.24), residues: 1212 helix: 1.48 (0.26), residues: 391 sheet: 1.39 (0.31), residues: 271 loop : -0.47 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.014 0.001 TYR A 385 PHE 0.019 0.001 PHE A 28 TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9992) covalent geometry : angle 0.56332 (13585) SS BOND : bond 0.00680 ( 11) SS BOND : angle 1.54062 ( 22) hydrogen bonds : bond 0.04383 ( 433) hydrogen bonds : angle 4.48190 ( 1227) metal coordination : bond 0.00100 ( 2) link_NAG-ASN : bond 0.01119 ( 4) link_NAG-ASN : angle 6.76730 ( 12) ********************** 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 162 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.3936 (OUTLIER) cc_final: 0.3711 (pmt) REVERT: A 401 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.7759 (m-70) outliers start: 14 outliers final: 13 residues processed: 159 average time/residue: 0.4878 time to fit residues: 84.5333 Evaluate side-chains 163 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain 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 H residue 77 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 0.0060 chunk 32 optimal weight: 0.0030 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 76 optimal weight: 0.0770 overall best weight: 0.2764 ------------------------------------------------------------------------------- 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 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.185880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.158012 restraints weight = 23933.068| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.94 r_work: 0.4053 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.4446 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 : 0.575 18.301 13619 Z= 0.287 Chirality : 0.042 0.198 1466 Planarity : 0.005 0.056 1750 Dihedral : 4.709 57.206 1409 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 1.69 % Allowed : 16.17 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.24), residues: 1212 helix: 1.53 (0.26), residues: 394 sheet: 1.38 (0.31), residues: 271 loop : -0.39 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 19 TYR 0.012 0.001 TYR A 516 PHE 0.018 0.001 PHE A 28 TRP 0.014 0.001 TRP A 165 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9992) covalent geometry : angle 0.53718 (13585) SS BOND : bond 0.00657 ( 11) SS BOND : angle 1.46671 ( 22) hydrogen bonds : bond 0.04095 ( 433) hydrogen bonds : angle 4.42138 ( 1227) metal coordination : bond 0.00075 ( 2) link_NAG-ASN : bond 0.01074 ( 4) link_NAG-ASN : angle 6.63402 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5435.81 seconds wall clock time: 92 minutes 44.49 seconds (5564.49 seconds total)