Starting phenix.real_space_refine on Wed Mar 12 21:02:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vlv_43345/03_2025/8vlv_43345.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vlv_43345/03_2025/8vlv_43345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vlv_43345/03_2025/8vlv_43345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vlv_43345/03_2025/8vlv_43345.map" model { file = "/net/cci-nas-00/data/ceres_data/8vlv_43345/03_2025/8vlv_43345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vlv_43345/03_2025/8vlv_43345.cif" } resolution = 3.49 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= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 5452 2.51 5 N 1340 2.21 5 O 1438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8265 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4104 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 542, 4079 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 25, 'TRANS': 516} Chain breaks: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 130 Conformer: "B" Number of residues, atoms: 542, 4079 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 25, 'TRANS': 516} Chain breaks: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 130 bond proxies already assigned to first conformer: 4163 Chain: "B" Number of atoms: 4035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4035 Classifications: {'peptide': 543} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 24, 'TRANS': 518} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 152 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATRP A 344 " occ=0.52 ... (26 atoms not shown) pdb=" CH2BTRP A 344 " occ=0.48 residue: pdb=" N AARG A 412 " occ=0.42 ... (20 atoms not shown) pdb=" NH2BARG A 412 " occ=0.58 Time building chain proxies: 8.06, per 1000 atoms: 0.98 Number of scatterers: 8265 At special positions: 0 Unit cell: (108.42, 95.91, 104.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1438 8.00 N 1340 7.00 C 5452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 107 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 443 " - pdb=" SG CYS B 462 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 701 " - " ASN A 94 " " NAG A 702 " - " ASN A 162 " " NAG A 703 " - " ASN A 461 " " NAG B 701 " - " ASN B 94 " " NAG B 702 " - " ASN B 142 " " NAG B 703 " - " ASN B 162 " " NAG B 704 " - " ASN B 461 " " NAG C 1 " - " ASN A 142 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.5 seconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 54.1% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 194 through 202 removed outlier: 3.964A pdb=" N ILE A 200 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 223 removed outlier: 3.694A pdb=" N ASP A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 287 Processing helix chain 'A' and resid 288 through 292 removed outlier: 3.707A pdb=" N TYR A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 332 removed outlier: 3.527A pdb=" N PHE A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 357 Processing helix chain 'A' and resid 375 through 394 removed outlier: 3.566A pdb=" N PHE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.650A pdb=" N THR A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 438 Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.523A pdb=" N LYS A 458 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 476 removed outlier: 3.544A pdb=" N ILE A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASP A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 removed outlier: 4.036A pdb=" N VAL A 488 " --> pdb=" O SER A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 524 removed outlier: 3.607A pdb=" N ILE A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 551 removed outlier: 4.323A pdb=" N ILE A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 590 Proline residue: A 587 - end of helix Processing helix chain 'A' and resid 602 through 605 removed outlier: 3.655A pdb=" N MET A 605 " --> pdb=" O TYR A 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 602 through 605' Processing helix chain 'A' and resid 606 through 617 Processing helix chain 'A' and resid 632 through 657 Processing helix chain 'B' and resid 195 through 228 Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 288 through 292 removed outlier: 3.778A pdb=" N TYR B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 308 through 331 removed outlier: 3.810A pdb=" N TRP B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 357 Processing helix chain 'B' and resid 375 through 394 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 417 through 438 removed outlier: 3.526A pdb=" N TRP B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.734A pdb=" N PHE B 456 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 475 removed outlier: 3.524A pdb=" N ASP B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 491 Processing helix chain 'B' and resid 503 through 524 removed outlier: 3.750A pdb=" N TYR B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 551 Processing helix chain 'B' and resid 567 through 590 Proline residue: B 587 - end of helix Processing helix chain 'B' and resid 600 through 606 removed outlier: 3.607A pdb=" N ASN B 606 " --> pdb=" O TYR B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 617 Processing helix chain 'B' and resid 632 through 657 removed outlier: 3.584A pdb=" N HIS B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 642 " --> pdb=" O THR B 638 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 132 removed outlier: 3.695A pdb=" N SER A 125 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A 165 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU A 85 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL A 167 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS A 87 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 166 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115 removed outlier: 3.725A pdb=" N GLN A 110 " --> pdb=" O TRP A 99 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 97 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASN A 114 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU A 95 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N CYS A 151 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP A 143 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU A 149 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 127 through 132 removed outlier: 7.555A pdb=" N LEU B 165 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU B 85 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL B 167 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N HIS B 87 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ASN B 169 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 115 removed outlier: 3.881A pdb=" N LEU B 112 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL B 97 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASN B 114 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU B 95 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 96 " --> pdb=" O ASN B 142 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N CYS B 151 " --> pdb=" O LEU B 141 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1342 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: 2.15 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2522 1.34 - 1.46: 2110 1.46 - 1.58: 3814 1.58 - 1.70: 0 1.70 - 1.81: 46 Bond restraints: 8492 Sorted by residual: bond pdb=" C1 NAG B 702 " pdb=" O5 NAG B 702 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 NAG B 703 " pdb=" O5 NAG B 703 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 ... (remaining 8487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 11187 1.28 - 2.56: 345 2.56 - 3.84: 74 3.84 - 5.12: 18 5.12 - 6.40: 8 Bond angle restraints: 11632 Sorted by residual: angle pdb=" C GLY B 613 " pdb=" N HIS B 614 " pdb=" CA HIS B 614 " ideal model delta sigma weight residual 121.14 116.35 4.79 1.75e+00 3.27e-01 7.51e+00 angle pdb=" N TRP A 418 " pdb=" CA TRP A 418 " pdb=" C TRP A 418 " ideal model delta sigma weight residual 109.81 115.81 -6.00 2.21e+00 2.05e-01 7.38e+00 angle pdb=" C GLY A 613 " pdb=" N HIS A 614 " pdb=" CA HIS A 614 " ideal model delta sigma weight residual 121.14 116.55 4.59 1.75e+00 3.27e-01 6.87e+00 angle pdb=" C PHE A 600 " pdb=" N PHE A 601 " pdb=" CA PHE A 601 " ideal model delta sigma weight residual 122.06 117.79 4.27 1.86e+00 2.89e-01 5.27e+00 angle pdb=" C GLY A 452 " pdb=" N ILE A 453 " pdb=" CA ILE A 453 " ideal model delta sigma weight residual 121.97 125.90 -3.93 1.80e+00 3.09e-01 4.76e+00 ... (remaining 11627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 4639 22.75 - 45.49: 276 45.49 - 68.24: 33 68.24 - 90.99: 17 90.99 - 113.73: 6 Dihedral angle restraints: 4971 sinusoidal: 1831 harmonic: 3140 Sorted by residual: dihedral pdb=" CB CYS B 443 " pdb=" SG CYS B 443 " pdb=" SG CYS B 462 " pdb=" CB CYS B 462 " ideal model delta sinusoidal sigma weight residual 93.00 151.90 -58.90 1 1.00e+01 1.00e-02 4.64e+01 dihedral pdb=" CA ASN B 94 " pdb=" C ASN B 94 " pdb=" N LEU B 95 " pdb=" CA LEU B 95 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C3 NAG B 702 " pdb=" C1 NAG B 702 " pdb=" C2 NAG B 702 " pdb=" O5 NAG B 702 " ideal model delta sinusoidal sigma weight residual -55.55 58.18 -113.73 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 4968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1267 0.069 - 0.138: 117 0.138 - 0.208: 4 0.208 - 0.277: 0 0.277 - 0.346: 1 Chirality restraints: 1389 Sorted by residual: chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 94 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" N2 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 142 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.27e-01 ... (remaining 1386 not shown) Planarity restraints: 1434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 92 " 0.010 2.00e-02 2.50e+03 1.35e-02 4.54e+00 pdb=" CG TRP B 92 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP B 92 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 92 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 92 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 92 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 92 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 92 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 92 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 606 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C ASN A 606 " 0.025 2.00e-02 2.50e+03 pdb=" O ASN A 606 " -0.009 2.00e-02 2.50e+03 pdb=" N SER A 607 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 322 " -0.014 2.00e-02 2.50e+03 1.09e-02 2.08e+00 pdb=" CG PHE B 322 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE B 322 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 322 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 322 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 322 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 322 " -0.004 2.00e-02 2.50e+03 ... (remaining 1431 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 476 2.73 - 3.27: 8561 3.27 - 3.82: 13773 3.82 - 4.36: 14986 4.36 - 4.90: 27138 Nonbonded interactions: 64934 Sorted by model distance: nonbonded pdb=" OE1 GLU B 391 " pdb=" NE2 GLN B 420 " model vdw 2.192 3.120 nonbonded pdb=" NH1 ARG A 275 " pdb=" O GLY A 604 " model vdw 2.271 3.120 nonbonded pdb=" O TYR B 105 " pdb=" ND1 HIS B 106 " model vdw 2.280 3.120 nonbonded pdb=" ND2 ASN A 506 " pdb=" O TRP A 566 " model vdw 2.281 3.120 nonbonded pdb=" O ARG A 269 " pdb=" OG1 THR A 273 " model vdw 2.285 3.040 ... (remaining 64929 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 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 76 and (name N or name CA or name C or name O or name CB \ )) or resid 77 through 90 or (resid 91 through 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 118 or (resid 119 through 121 and \ (name N or name CA or name C or name O or name CB )) or resid 122 through 146 o \ r (resid 147 through 150 and (name N or name CA or name C or name O or name CB ) \ ) or resid 151 through 169 or (resid 170 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 175 through 176 and (name N or name CA or name C or \ name O or name CB )) or resid 177 through 179 or (resid 180 and (name N or name \ CA or name C or name O or name CB )) or resid 181 through 192 or (resid 194 thro \ ugh 200 and (name N or name CA or name C or name O or name CB )) or resid 201 or \ (resid 202 through 223 and (name N or name CA or name C or name O or name CB )) \ or resid 266 or (resid 267 and (name N or name CA or name C or name O or name C \ B )) or resid 268 through 329 or (resid 330 through 331 and (name N or name CA o \ r name C or name O or name CB )) or resid 332 through 343 or resid 345 through 4 \ 11 or resid 413 through 492 or (resid 493 and (name N or name CA or name C or na \ me O or name CB )) or resid 494 through 552 or (resid 553 through 554 and (name \ N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 and (n \ ame N or name CA or name C or name O or name CB )) or resid 557 through 589 or ( \ resid 590 and (name N or name CA or name C or name O or name CB )) or resid 591 \ or (resid 592 and (name N or name CA or name C or name O or name CB )) or resid \ 593 through 597 or (resid 598 and (name N or name CA or name C or name O or name \ CB )) or resid 599 through 604 or (resid 605 and (name N or name CA or name C o \ r name O or name CB )) or resid 606 through 625 or (resid 626 and (name N or nam \ e CA or name C or name O or name CB )) or resid 627 through 628 or (resid 629 an \ d (name N or name CA or name C or name O or name CB )) or resid 630 through 633 \ or (resid 634 through 635 and (name N or name CA or name C or name O or name CB \ )) or resid 636 through 654 or (resid 655 and (name N or name CA or name C or na \ me O or name CB )) or resid 656 through 661 or resid 701 through 703)) selection = (chain 'B' and (resid 76 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 101 or (resid 102 and (name N or n \ ame CA or name C or name O or name CB )) or resid 103 through 116 or (resid 117 \ and (name N or name CA or name C or name O or name CB )) or resid 118 through 14 \ 3 or (resid 144 through 150 and (name N or name CA or name C or name O or name C \ B )) or resid 151 through 167 or (resid 168 and (name N or name CA or name C or \ name O or name CB )) or resid 169 through 184 or (resid 185 through 186 and (nam \ e N or name CA or name C or name O or name CB )) or resid 187 through 192 or (re \ sid 194 through 200 and (name N or name CA or name C or name O or name CB )) or \ resid 201 through 223 or resid 266 through 336 or (resid 337 and (name N or name \ CA or name C or name O or name CB )) or resid 338 through 343 or resid 345 thro \ ugh 362 or (resid 363 and (name N or name CA or name C or name O or name CB )) o \ r resid 364 through 395 or (resid 396 and (name N or name CA or name C or name O \ or name CB )) or resid 397 through 400 or (resid 401 through 402 and (name N or \ name CA or name C or name O or name CB )) or (resid 408 through 410 and (name N \ or name CA or name C or name O or name CB )) or resid 411 or resid 413 through \ 454 or (resid 455 and (name N or name CA or name C or name O or name CB )) or re \ sid 456 through 661 or resid 702 through 704)) } 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=0.42 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: 5.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.140 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 0.070 8492 Z= 0.211 Angle : 0.564 6.404 11632 Z= 0.288 Chirality : 0.042 0.346 1389 Planarity : 0.004 0.036 1426 Dihedral : 15.449 113.732 2941 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.12 % Allowed : 0.25 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.27), residues: 1075 helix: 2.48 (0.22), residues: 521 sheet: -0.63 (0.56), residues: 113 loop : -1.76 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 92 HIS 0.003 0.001 HIS B 614 PHE 0.024 0.001 PHE B 322 TYR 0.016 0.001 TYR B 570 ARG 0.005 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.880 Fit side-chains REVERT: A 159 GLU cc_start: 0.8479 (tt0) cc_final: 0.8133 (tt0) REVERT: B 341 LYS cc_start: 0.7443 (tttt) cc_final: 0.7240 (mtpt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1705 time to fit residues: 22.4951 Evaluate side-chains 70 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.0770 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 HIS ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115081 restraints weight = 31220.376| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.48 r_work: 0.3192 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8492 Z= 0.236 Angle : 0.581 9.224 11632 Z= 0.293 Chirality : 0.043 0.320 1389 Planarity : 0.004 0.058 1426 Dihedral : 9.351 96.596 1344 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.62 % Allowed : 5.99 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1075 helix: 2.36 (0.22), residues: 524 sheet: -0.58 (0.54), residues: 113 loop : -1.70 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 92 HIS 0.005 0.001 HIS B 483 PHE 0.024 0.001 PHE B 322 TYR 0.018 0.001 TYR B 570 ARG 0.006 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.932 Fit side-chains REVERT: A 159 GLU cc_start: 0.8494 (tt0) cc_final: 0.8289 (tt0) REVERT: B 325 MET cc_start: 0.8320 (ttm) cc_final: 0.8043 (ttt) outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 0.1630 time to fit residues: 18.7788 Evaluate side-chains 70 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 627 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 0.0050 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.140295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116444 restraints weight = 32574.136| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.69 r_work: 0.3195 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8492 Z= 0.170 Angle : 0.530 9.324 11632 Z= 0.267 Chirality : 0.042 0.407 1389 Planarity : 0.004 0.038 1426 Dihedral : 7.809 93.399 1344 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.75 % Allowed : 8.86 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.27), residues: 1075 helix: 2.53 (0.22), residues: 522 sheet: -0.24 (0.56), residues: 111 loop : -1.67 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 92 HIS 0.002 0.001 HIS A 614 PHE 0.020 0.001 PHE A 322 TYR 0.016 0.001 TYR B 570 ARG 0.005 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.712 Fit side-chains REVERT: A 159 GLU cc_start: 0.8484 (tt0) cc_final: 0.8271 (tt0) REVERT: B 325 MET cc_start: 0.8312 (ttm) cc_final: 0.8035 (ttt) REVERT: B 510 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8025 (ttp) outliers start: 5 outliers final: 4 residues processed: 78 average time/residue: 0.1720 time to fit residues: 19.8716 Evaluate side-chains 79 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 510 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.137975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113645 restraints weight = 38904.807| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.62 r_work: 0.3148 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8492 Z= 0.198 Angle : 0.537 9.316 11632 Z= 0.271 Chirality : 0.042 0.355 1389 Planarity : 0.004 0.037 1426 Dihedral : 7.596 91.621 1344 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.00 % Allowed : 10.49 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.27), residues: 1075 helix: 2.48 (0.22), residues: 526 sheet: -0.26 (0.55), residues: 113 loop : -1.61 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 92 HIS 0.002 0.001 HIS B 633 PHE 0.021 0.001 PHE B 322 TYR 0.017 0.001 TYR B 570 ARG 0.008 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.850 Fit side-chains REVERT: A 159 GLU cc_start: 0.8585 (tt0) cc_final: 0.8349 (tt0) REVERT: B 325 MET cc_start: 0.8439 (ttm) cc_final: 0.8164 (ttt) REVERT: B 510 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8161 (ttp) outliers start: 7 outliers final: 5 residues processed: 79 average time/residue: 0.1640 time to fit residues: 19.8271 Evaluate side-chains 78 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 545 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 104 optimal weight: 0.0000 chunk 96 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.137470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113802 restraints weight = 32778.288| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.70 r_work: 0.3184 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8492 Z= 0.200 Angle : 0.541 9.407 11632 Z= 0.270 Chirality : 0.042 0.337 1389 Planarity : 0.003 0.036 1426 Dihedral : 7.407 89.843 1344 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.25 % Allowed : 11.49 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.27), residues: 1075 helix: 2.52 (0.22), residues: 525 sheet: -0.25 (0.54), residues: 113 loop : -1.56 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 647 HIS 0.002 0.001 HIS B 135 PHE 0.022 0.001 PHE B 322 TYR 0.017 0.001 TYR B 570 ARG 0.007 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.875 Fit side-chains REVERT: B 325 MET cc_start: 0.8404 (ttm) cc_final: 0.8105 (ttt) REVERT: B 510 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8057 (ttp) outliers start: 9 outliers final: 6 residues processed: 79 average time/residue: 0.1565 time to fit residues: 19.1835 Evaluate side-chains 76 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 545 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107516 restraints weight = 25426.920| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.92 r_work: 0.3129 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 8492 Z= 0.436 Angle : 0.676 9.169 11632 Z= 0.343 Chirality : 0.046 0.307 1389 Planarity : 0.004 0.040 1426 Dihedral : 7.765 91.109 1344 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.87 % Allowed : 12.61 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.26), residues: 1075 helix: 1.99 (0.22), residues: 527 sheet: -0.63 (0.53), residues: 115 loop : -1.84 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.005 0.001 HIS B 135 PHE 0.036 0.002 PHE B 322 TYR 0.024 0.002 TYR B 570 ARG 0.006 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.975 Fit side-chains REVERT: A 159 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: B 510 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8192 (ttp) outliers start: 14 outliers final: 11 residues processed: 74 average time/residue: 0.1574 time to fit residues: 17.7909 Evaluate side-chains 74 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111319 restraints weight = 32384.402| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.81 r_work: 0.3132 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8492 Z= 0.254 Angle : 0.582 9.289 11632 Z= 0.293 Chirality : 0.043 0.302 1389 Planarity : 0.004 0.041 1426 Dihedral : 7.610 89.834 1344 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.75 % Allowed : 13.73 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1075 helix: 2.21 (0.22), residues: 527 sheet: -0.51 (0.53), residues: 114 loop : -1.74 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.002 0.001 HIS B 135 PHE 0.030 0.001 PHE B 322 TYR 0.019 0.001 TYR B 570 ARG 0.006 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.841 Fit side-chains REVERT: A 159 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: B 510 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8192 (ttp) outliers start: 13 outliers final: 11 residues processed: 77 average time/residue: 0.1568 time to fit residues: 18.4668 Evaluate side-chains 77 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 85 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.127567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102806 restraints weight = 39569.352| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 4.94 r_work: 0.2989 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8492 Z= 0.366 Angle : 0.638 9.212 11632 Z= 0.323 Chirality : 0.045 0.297 1389 Planarity : 0.004 0.042 1426 Dihedral : 7.670 89.814 1344 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.12 % Allowed : 13.86 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.26), residues: 1075 helix: 2.01 (0.22), residues: 527 sheet: -0.61 (0.53), residues: 114 loop : -1.85 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.004 0.001 HIS B 135 PHE 0.026 0.002 PHE B 322 TYR 0.022 0.002 TYR B 570 ARG 0.006 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.865 Fit side-chains REVERT: A 159 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: A 294 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: B 510 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8338 (ttp) outliers start: 16 outliers final: 13 residues processed: 74 average time/residue: 0.1559 time to fit residues: 17.7627 Evaluate side-chains 75 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 39 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 75 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 14 optimal weight: 20.0000 chunk 98 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113000 restraints weight = 36991.923| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 4.36 r_work: 0.3148 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8492 Z= 0.177 Angle : 0.552 9.339 11632 Z= 0.277 Chirality : 0.042 0.303 1389 Planarity : 0.004 0.040 1426 Dihedral : 7.400 89.359 1344 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.75 % Allowed : 14.61 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.27), residues: 1075 helix: 2.41 (0.22), residues: 527 sheet: -0.45 (0.53), residues: 115 loop : -1.69 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.002 0.000 HIS A 297 PHE 0.025 0.001 PHE B 322 TYR 0.016 0.001 TYR B 570 ARG 0.006 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.924 Fit side-chains REVERT: A 159 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: B 510 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8162 (ttp) outliers start: 13 outliers final: 11 residues processed: 79 average time/residue: 0.1755 time to fit residues: 21.0271 Evaluate side-chains 79 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 101 optimal weight: 0.0040 chunk 68 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.134429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110591 restraints weight = 31776.900| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.80 r_work: 0.3121 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8492 Z= 0.297 Angle : 0.597 9.277 11632 Z= 0.300 Chirality : 0.043 0.299 1389 Planarity : 0.004 0.041 1426 Dihedral : 7.396 88.943 1344 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.00 % Allowed : 14.11 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.26), residues: 1075 helix: 2.26 (0.22), residues: 527 sheet: -0.51 (0.52), residues: 115 loop : -1.74 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.003 0.001 HIS B 135 PHE 0.032 0.002 PHE B 322 TYR 0.020 0.002 TYR B 570 ARG 0.006 0.000 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.946 Fit side-chains REVERT: A 159 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: A 294 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.8060 (m-80) REVERT: B 510 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8226 (ttp) outliers start: 15 outliers final: 12 residues processed: 78 average time/residue: 0.1636 time to fit residues: 19.3555 Evaluate side-chains 82 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.135869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112068 restraints weight = 33767.246| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 4.09 r_work: 0.3137 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8492 Z= 0.223 Angle : 0.570 9.320 11632 Z= 0.285 Chirality : 0.042 0.300 1389 Planarity : 0.004 0.040 1426 Dihedral : 7.331 88.325 1344 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.12 % Allowed : 14.36 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.27), residues: 1075 helix: 2.36 (0.22), residues: 527 sheet: -0.47 (0.52), residues: 115 loop : -1.68 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.002 0.001 HIS B 135 PHE 0.032 0.001 PHE B 322 TYR 0.018 0.001 TYR B 570 ARG 0.006 0.000 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4045.47 seconds wall clock time: 71 minutes 4.70 seconds (4264.70 seconds total)