Starting phenix.real_space_refine on Tue Aug 6 10:34:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xsf_38618/08_2024/8xsf_38618.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xsf_38618/08_2024/8xsf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xsf_38618/08_2024/8xsf_38618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xsf_38618/08_2024/8xsf_38618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xsf_38618/08_2024/8xsf_38618.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xsf_38618/08_2024/8xsf_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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 8.03, per 1000 atoms: 0.82 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 - 3.50 Amino acid : False - 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: 3.64 Conformation dependent library (CDL) restraints added in 2.1 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: 1.06 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: 2.81 Time building geometry restraints manager: 4.05 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: 98.49 - 105.59: 208 105.59 - 112.69: 5130 112.69 - 119.79: 3271 119.79 - 126.89: 4821 126.89 - 133.98: 155 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: 6.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 33.160 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 9992 Z= 0.184 Angle : 0.591 11.428 13585 Z= 0.332 Chirality : 0.042 0.150 1466 Planarity : 0.005 0.102 1750 Dihedral : 12.918 85.939 3660 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1212 helix: 1.26 (0.28), residues: 396 sheet: 1.64 (0.32), residues: 256 loop : -0.21 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 48 HIS 0.007 0.001 HIS A 401 PHE 0.021 0.001 PHE A 504 TYR 0.014 0.001 TYR H 80 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.009 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: 0.9571 time to fit residues: 186.2980 Evaluate side-chains 159 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9992 Z= 0.219 Angle : 0.570 6.936 13585 Z= 0.302 Chirality : 0.043 0.143 1466 Planarity : 0.005 0.070 1750 Dihedral : 4.854 59.465 1409 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 1.69 % Allowed : 8.55 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1212 helix: 1.31 (0.27), residues: 396 sheet: 1.44 (0.31), residues: 275 loop : -0.30 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 48 HIS 0.007 0.001 HIS A 401 PHE 0.025 0.002 PHE A 28 TYR 0.018 0.002 TYR A 385 ARG 0.004 0.001 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 169 time to evaluate : 1.125 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 173 average time/residue: 0.9008 time to fit residues: 170.7936 Evaluate side-chains 163 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. 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 60 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 37 GLN L 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9992 Z= 0.310 Angle : 0.640 18.448 13585 Z= 0.333 Chirality : 0.046 0.327 1466 Planarity : 0.005 0.063 1750 Dihedral : 4.946 59.141 1409 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.12 % Rotamer: Outliers : 1.69 % Allowed : 11.56 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1212 helix: 1.01 (0.26), residues: 397 sheet: 1.39 (0.31), residues: 276 loop : -0.57 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 165 HIS 0.008 0.001 HIS A 401 PHE 0.016 0.002 PHE A 28 TYR 0.020 0.002 TYR A 385 ARG 0.005 0.001 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 1.052 Fit side-chains REVERT: A 231 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6711 (mm-30) REVERT: L 11 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7862 (tp) outliers start: 16 outliers final: 9 residues processed: 172 average time/residue: 0.9181 time to fit residues: 173.6287 Evaluate side-chains 165 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 LEU 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 107 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 0.0870 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 474 GLN B 487 ASN H 3 GLN L 124 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9992 Z= 0.283 Angle : 0.603 15.206 13585 Z= 0.315 Chirality : 0.045 0.288 1466 Planarity : 0.005 0.059 1750 Dihedral : 4.949 59.810 1409 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.61 % 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 (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: 1.06 (0.26), residues: 395 sheet: 1.37 (0.31), residues: 276 loop : -0.60 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 PHE 0.016 0.002 PHE A 28 TYR 0.019 0.002 TYR A 385 ARG 0.007 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 0.969 Fit side-chains REVERT: A 41 TYR cc_start: 0.7740 (t80) cc_final: 0.7377 (t80) REVERT: A 231 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6760 (mm-30) REVERT: L 11 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7900 (tp) outliers start: 23 outliers final: 10 residues processed: 163 average time/residue: 0.9407 time to fit residues: 168.3261 Evaluate side-chains 158 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU 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 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 96 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 556 ASN A 601 ASN B 354 ASN B 450 ASN H 3 GLN H 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9992 Z= 0.268 Angle : 0.601 14.679 13585 Z= 0.313 Chirality : 0.044 0.260 1466 Planarity : 0.005 0.059 1750 Dihedral : 4.905 59.993 1409 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 2.44 % Allowed : 13.72 % 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: 0.58 (0.24), residues: 1212 helix: 1.06 (0.26), residues: 394 sheet: 1.36 (0.31), residues: 271 loop : -0.59 (0.26), residues: 547 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 0.016 0.001 PHE A 28 TYR 0.018 0.002 TYR A 385 ARG 0.006 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 1.017 Fit side-chains REVERT: A 41 TYR cc_start: 0.7737 (t80) cc_final: 0.7311 (t80) REVERT: A 154 ASN cc_start: 0.5827 (m110) cc_final: 0.5455 (m110) REVERT: A 401 HIS cc_start: 0.8260 (OUTLIER) cc_final: 0.7893 (m-70) outliers start: 24 outliers final: 14 residues processed: 162 average time/residue: 0.9324 time to fit residues: 165.5842 Evaluate side-chains 159 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 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 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 39 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 0.2980 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 277 ASN A 556 ASN A 601 ASN B 450 ASN B 474 GLN H 3 GLN H 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9992 Z= 0.250 Angle : 0.585 13.975 13585 Z= 0.305 Chirality : 0.044 0.251 1466 Planarity : 0.005 0.059 1750 Dihedral : 4.916 59.007 1409 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 2.73 % Allowed : 14.00 % Favored : 83.27 % 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: 0.63 (0.24), residues: 1212 helix: 1.23 (0.26), residues: 385 sheet: 1.34 (0.31), residues: 271 loop : -0.61 (0.26), residues: 556 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 0.017 0.001 PHE A 28 TYR 0.017 0.002 TYR A 385 ARG 0.007 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.081 Fit side-chains REVERT: A 41 TYR cc_start: 0.7731 (t80) cc_final: 0.7307 (t80) REVERT: A 401 HIS cc_start: 0.8231 (OUTLIER) cc_final: 0.7764 (m-70) REVERT: A 474 MET cc_start: 0.5507 (mpp) cc_final: 0.5028 (mpm) outliers start: 27 outliers final: 14 residues processed: 165 average time/residue: 0.9230 time to fit residues: 166.8282 Evaluate side-chains 162 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 354 ASN H 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9992 Z= 0.305 Angle : 0.624 13.720 13585 Z= 0.325 Chirality : 0.046 0.254 1466 Planarity : 0.005 0.059 1750 Dihedral : 5.389 58.646 1409 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 2.54 % Allowed : 15.04 % Favored : 82.42 % 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: 0.47 (0.24), residues: 1212 helix: 0.95 (0.26), residues: 394 sheet: 1.33 (0.30), residues: 270 loop : -0.66 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 165 HIS 0.005 0.001 HIS A 374 PHE 0.025 0.002 PHE A 504 TYR 0.020 0.002 TYR A 385 ARG 0.007 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7760 (t80) cc_final: 0.7362 (t80) REVERT: A 401 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7828 (m-70) REVERT: A 474 MET cc_start: 0.5534 (mpp) cc_final: 0.5292 (mpm) REVERT: A 559 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7092 (ptm160) outliers start: 25 outliers final: 16 residues processed: 156 average time/residue: 0.9837 time to fit residues: 168.1948 Evaluate side-chains 159 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 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 71 optimal weight: 0.0670 chunk 46 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 556 ASN A 601 ASN B 354 ASN B 450 ASN B 474 GLN H 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9992 Z= 0.201 Angle : 0.567 13.343 13585 Z= 0.295 Chirality : 0.043 0.241 1466 Planarity : 0.005 0.058 1750 Dihedral : 4.969 58.554 1409 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.97 % Favored : 96.94 % 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: 0.67 (0.24), residues: 1212 helix: 1.30 (0.26), residues: 387 sheet: 1.34 (0.30), residues: 276 loop : -0.65 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 PHE 0.025 0.001 PHE A 504 TYR 0.014 0.001 TYR A 385 ARG 0.007 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6758 (mm-30) REVERT: A 401 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7683 (m-70) REVERT: A 474 MET cc_start: 0.5479 (mpp) cc_final: 0.5270 (mpm) outliers start: 26 outliers final: 13 residues processed: 163 average time/residue: 0.9247 time to fit residues: 164.8542 Evaluate side-chains 160 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 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 74 ASN Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 10 SER 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 110 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 84 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 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 354 ASN B 450 ASN B 474 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9992 Z= 0.245 Angle : 0.596 13.145 13585 Z= 0.309 Chirality : 0.044 0.242 1466 Planarity : 0.005 0.058 1750 Dihedral : 5.092 59.516 1409 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 2.35 % Allowed : 15.88 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.24), residues: 1212 helix: 1.24 (0.26), residues: 385 sheet: 1.26 (0.31), residues: 269 loop : -0.67 (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 0.024 0.002 PHE A 504 TYR 0.017 0.002 TYR A 385 ARG 0.007 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7730 (t80) cc_final: 0.7312 (t80) REVERT: A 152 MET cc_start: 0.3945 (OUTLIER) cc_final: 0.3040 (pp-130) REVERT: A 401 HIS cc_start: 0.8230 (OUTLIER) cc_final: 0.7746 (m-70) REVERT: A 474 MET cc_start: 0.5400 (mpp) cc_final: 0.5145 (mpm) REVERT: B 356 LYS cc_start: 0.7084 (ttpp) cc_final: 0.6841 (tmtm) REVERT: H 3 GLN cc_start: 0.6561 (mp-120) cc_final: 0.6335 (mp10) outliers start: 23 outliers final: 15 residues processed: 159 average time/residue: 0.9223 time to fit residues: 160.6142 Evaluate side-chains 162 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 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 151 LEU Chi-restraints excluded: chain L residue 10 SER 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 54 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 110 optimal weight: 0.0870 chunk 95 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9992 Z= 0.273 Angle : 0.613 13.166 13585 Z= 0.318 Chirality : 0.045 0.246 1466 Planarity : 0.005 0.058 1750 Dihedral : 5.171 59.787 1409 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 2.35 % Allowed : 15.98 % Favored : 81.67 % 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: 0.48 (0.24), residues: 1212 helix: 1.13 (0.26), residues: 385 sheet: 1.23 (0.30), residues: 269 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 H 35 PHE 0.024 0.002 PHE A 504 TYR 0.019 0.002 TYR A 385 ARG 0.007 0.001 ARG H 19 ********************** 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 170 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7744 (t80) cc_final: 0.7396 (t80) REVERT: A 152 MET cc_start: 0.4169 (OUTLIER) cc_final: 0.2720 (mmt) REVERT: A 401 HIS cc_start: 0.8234 (OUTLIER) cc_final: 0.7764 (m-70) REVERT: B 356 LYS cc_start: 0.7112 (ttpp) cc_final: 0.6883 (tmtm) REVERT: H 3 GLN cc_start: 0.6573 (mp-120) cc_final: 0.6348 (mp10) outliers start: 23 outliers final: 16 residues processed: 161 average time/residue: 0.9040 time to fit residues: 159.8353 Evaluate side-chains 164 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 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 H residue 151 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 26 optimal weight: 0.3980 chunk 95 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.182293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.154371 restraints weight = 21467.167| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.75 r_work: 0.4016 rms_B_bonded: 3.05 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) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9992 Z= 0.243 Angle : 0.656 21.685 13585 Z= 0.352 Chirality : 0.045 0.386 1466 Planarity : 0.006 0.093 1750 Dihedral : 5.151 59.161 1409 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 2.54 % Allowed : 15.70 % Favored : 81.77 % Cbeta Deviations : 0.09 % 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: 0.51 (0.24), residues: 1212 helix: 1.17 (0.26), residues: 385 sheet: 1.22 (0.30), residues: 269 loop : -0.69 (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 0.024 0.001 PHE A 504 TYR 0.017 0.002 TYR A 385 ARG 0.007 0.001 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3998.23 seconds wall clock time: 71 minutes 0.06 seconds (4260.06 seconds total)