Starting phenix.real_space_refine on Tue May 13 02:46:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w4a_37264/05_2025/8w4a_37264.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w4a_37264/05_2025/8w4a_37264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w4a_37264/05_2025/8w4a_37264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w4a_37264/05_2025/8w4a_37264.map" model { file = "/net/cci-nas-00/data/ceres_data/8w4a_37264/05_2025/8w4a_37264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w4a_37264/05_2025/8w4a_37264.cif" } resolution = 2.69 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= 0.035 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 40 5.16 5 C 6612 2.51 5 N 1382 2.21 5 O 1548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9588 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 506} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 506} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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: "D" 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: "E" 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: "F" 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: "B" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 508 Unusual residues: {'ACO': 1, 'C14': 12, 'CLR': 2, 'D10': 1, 'D12': 3, 'HP6': 1, 'NAG': 1, 'OCT': 16, 'R16': 1, 'UV6': 1} Classifications: {'undetermined': 39} Link IDs: {None: 38} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ACO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 508 Unusual residues: {'ACO': 1, 'C14': 12, 'CLR': 2, 'D10': 1, 'D12': 3, 'HP6': 1, 'NAG': 1, 'OCT': 16, 'R16': 1, 'UV6': 1} Classifications: {'undetermined': 39} Link IDs: {None: 38} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ACO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 7.42, per 1000 atoms: 0.77 Number of scatterers: 9588 At special positions: 0 Unit cell: (108.73, 87.98, 107.07, 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) S 40 16.00 P 6 15.00 O 1548 8.00 N 1382 7.00 C 6612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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 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=2.04 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 804 " - " ASN A 94 " " NAG B 803 " - " ASN B 94 " " NAG C 1 " - " ASN B 142 " " NAG D 1 " - " ASN B 162 " " NAG E 1 " - " ASN A 142 " " NAG F 1 " - " ASN A 162 " Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.2 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 4 sheets defined 55.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'B' and resid 191 through 215 Processing helix chain 'B' and resid 268 through 287 removed outlier: 3.517A pdb=" N ASP B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.577A pdb=" N TYR B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP B 293 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 332 removed outlier: 3.522A pdb=" N TRP B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 356 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 375 through 394 Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.697A pdb=" N SER B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 438 removed outlier: 3.561A pdb=" N LEU B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 Processing helix chain 'B' and resid 465 through 475 removed outlier: 3.540A pdb=" N ASP B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.941A pdb=" N VAL B 488 " --> pdb=" O SER B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 524 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 605 Processing helix chain 'B' and resid 606 through 617 Processing helix chain 'B' and resid 632 through 657 Processing helix chain 'A' and resid 191 through 215 Processing helix chain 'A' and resid 268 through 287 removed outlier: 3.501A pdb=" N ASP A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.503A pdb=" N TYR A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TRP A 293 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR A 294 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 308 through 332 removed outlier: 3.607A pdb=" N TRP A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 375 through 394 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.694A pdb=" N SER A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 438 removed outlier: 3.638A pdb=" N LEU A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 465 through 475 Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.947A pdb=" N VAL A 488 " --> pdb=" O SER A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 524 Processing helix chain 'A' and resid 527 through 551 removed outlier: 3.539A pdb=" N ILE A 531 " --> pdb=" O ARG A 527 " (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 600 through 605 Processing helix chain 'A' and resid 606 through 617 Processing helix chain 'A' and resid 632 through 657 Processing sheet with id=AA1, first strand: chain 'B' and resid 125 through 132 removed outlier: 9.013A pdb=" N TYR B 163 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU B 83 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU B 165 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 85 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL B 167 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS B 87 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ASN B 169 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN B 162 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 110 through 115 removed outlier: 6.893A pdb=" N VAL B 97 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASN B 114 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B 95 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER B 137 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU B 154 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 139 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG B 152 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU B 141 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 148 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 132 removed outlier: 8.947A pdb=" N TYR A 163 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 83 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU A 165 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU A 85 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL A 167 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N HIS A 87 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ASN A 169 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN A 162 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 115 removed outlier: 6.906A pdb=" N VAL A 97 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN A 114 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 95 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER A 137 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU A 154 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU A 139 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ARG A 152 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU A 141 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 148 " --> pdb=" O ASP A 143 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1353 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: 2.63 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1302 1.32 - 1.44: 2594 1.44 - 1.57: 5821 1.57 - 1.70: 11 1.70 - 1.82: 52 Bond restraints: 9780 Sorted by residual: bond pdb=" C4' UV6 B 801 " pdb=" O5 UV6 B 801 " ideal model delta sigma weight residual 1.419 1.560 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C4' UV6 A 802 " pdb=" O5 UV6 A 802 " ideal model delta sigma weight residual 1.419 1.560 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C8 UV6 B 801 " pdb=" N9 UV6 B 801 " ideal model delta sigma weight residual 1.351 1.477 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C8 UV6 A 802 " pdb=" N9 UV6 A 802 " ideal model delta sigma weight residual 1.351 1.476 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C4' UV6 B 801 " pdb=" C5' UV6 B 801 " ideal model delta sigma weight residual 1.527 1.419 0.108 2.00e-02 2.50e+03 2.91e+01 ... (remaining 9775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 12806 1.60 - 3.21: 205 3.21 - 4.81: 42 4.81 - 6.42: 9 6.42 - 8.02: 4 Bond angle restraints: 13066 Sorted by residual: angle pdb=" C9 UV6 B 801 " pdb=" OP3 UV6 B 801 " pdb=" CAA UV6 B 801 " ideal model delta sigma weight residual 119.59 111.57 8.02 3.00e+00 1.11e-01 7.15e+00 angle pdb=" C LYS A 551 " pdb=" N VAL A 552 " pdb=" CA VAL A 552 " ideal model delta sigma weight residual 121.97 126.63 -4.66 1.80e+00 3.09e-01 6.69e+00 angle pdb=" C9 UV6 A 802 " pdb=" OP3 UV6 A 802 " pdb=" CAA UV6 A 802 " ideal model delta sigma weight residual 119.59 111.91 7.68 3.00e+00 1.11e-01 6.55e+00 angle pdb=" C LYS B 551 " pdb=" N VAL B 552 " pdb=" CA VAL B 552 " ideal model delta sigma weight residual 121.97 126.57 -4.60 1.80e+00 3.09e-01 6.53e+00 angle pdb=" C2' UV6 A 802 " pdb=" C1' UV6 A 802 " pdb=" N9 UV6 A 802 " ideal model delta sigma weight residual 112.50 105.68 6.82 3.00e+00 1.11e-01 5.16e+00 ... (remaining 13061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 5355 16.05 - 32.09: 618 32.09 - 48.14: 158 48.14 - 64.18: 61 64.18 - 80.23: 12 Dihedral angle restraints: 6204 sinusoidal: 3132 harmonic: 3072 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 93.00 169.66 -76.66 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS A 443 " pdb=" SG CYS A 443 " pdb=" SG CYS A 462 " pdb=" CB CYS A 462 " ideal model delta sinusoidal sigma weight residual 93.00 168.30 -75.30 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CA LEU A 308 " pdb=" C LEU A 308 " pdb=" N VAL A 309 " pdb=" CA VAL A 309 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1348 0.070 - 0.141: 114 0.141 - 0.211: 0 0.211 - 0.282: 2 0.282 - 0.352: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C4' UV6 A 802 " pdb=" C3' UV6 A 802 " pdb=" C5' UV6 A 802 " pdb=" O5 UV6 A 802 " both_signs ideal model delta sigma weight residual False -2.25 -2.60 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C4' UV6 B 801 " pdb=" C3' UV6 B 801 " pdb=" C5' UV6 B 801 " pdb=" O5 UV6 B 801 " both_signs ideal model delta sigma weight residual False -2.25 -2.59 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" C17 UV6 A 802 " pdb=" C12 UV6 A 802 " pdb=" C18 UV6 A 802 " pdb=" C5 UV6 A 802 " both_signs ideal model delta sigma weight residual False 2.54 2.79 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1463 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 265 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO B 266 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 266 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 266 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 265 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO A 266 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 266 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 266 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 481 " 0.014 2.00e-02 2.50e+03 1.07e-02 2.28e+00 pdb=" CG TYR B 481 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 481 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 481 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 481 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 481 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 481 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 481 " 0.001 2.00e-02 2.50e+03 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 929 2.75 - 3.29: 8399 3.29 - 3.82: 15220 3.82 - 4.36: 19875 4.36 - 4.90: 33489 Nonbonded interactions: 77912 Sorted by model distance: nonbonded pdb=" OH TYR A 652 " pdb=" NH2 ARG A 656 " model vdw 2.212 3.120 nonbonded pdb=" ND2 ASN A 506 " pdb=" O TRP A 566 " model vdw 2.267 3.120 nonbonded pdb=" OH TYR B 652 " pdb=" NH2 ARG B 656 " model vdw 2.312 3.120 nonbonded pdb=" OH TYR A 447 " pdb=" OD2 ASP A 455 " model vdw 2.315 3.040 nonbonded pdb=" O ILE B 355 " pdb=" OH TYR B 361 " model vdw 2.332 3.040 ... (remaining 77907 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 663 or resid 805 through 807 or resid 814 or re \ sid 819 through 820 or resid 824 or resid 829 through 830 or resid 832 or resid \ 835 through 838)) selection = (chain 'B' and (resid 75 through 663 or resid 805 through 807 or resid 814 or re \ sid 819 through 820 or resid 824 or resid 829 through 830 or resid 832 or resid \ 835 through 838)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.010 Find NCS groups from input model: 0.480 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 : 0.006 0.141 9796 Z= 0.295 Angle : 0.575 8.020 13108 Z= 0.264 Chirality : 0.043 0.352 1466 Planarity : 0.004 0.071 1468 Dihedral : 14.929 80.225 4222 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.30 (0.25), residues: 1054 helix: 1.47 (0.22), residues: 506 sheet: 1.29 (0.44), residues: 128 loop : 0.08 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 418 HIS 0.007 0.001 HIS B 614 PHE 0.020 0.001 PHE B 274 TYR 0.026 0.001 TYR B 481 ARG 0.005 0.001 ARG B 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00051 ( 6) link_NAG-ASN : angle 1.78339 ( 18) link_BETA1-4 : bond 0.00430 ( 4) link_BETA1-4 : angle 0.84279 ( 12) hydrogen bonds : bond 0.18678 ( 476) hydrogen bonds : angle 5.94964 ( 1353) SS BOND : bond 0.00307 ( 6) SS BOND : angle 1.05544 ( 12) covalent geometry : bond 0.00612 ( 9780) covalent geometry : angle 0.57020 (13066) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.974 Fit side-chains REVERT: B 471 ASP cc_start: 0.8312 (m-30) cc_final: 0.7991 (m-30) REVERT: B 628 LYS cc_start: 0.8068 (tttp) cc_final: 0.7804 (tttp) REVERT: A 125 SER cc_start: 0.8571 (m) cc_final: 0.8357 (m) REVERT: A 471 ASP cc_start: 0.7679 (m-30) cc_final: 0.7419 (m-30) REVERT: A 546 SER cc_start: 0.8313 (m) cc_final: 0.8059 (m) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 1.2117 time to fit residues: 139.7668 Evaluate side-chains 94 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.0980 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.0060 chunk 96 optimal weight: 0.9980 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN B 358 ASN B 624 GLN A 114 ASN A 286 ASN A 330 GLN A 358 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.141178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108564 restraints weight = 10290.060| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.61 r_work: 0.3166 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9796 Z= 0.163 Angle : 0.540 6.531 13108 Z= 0.274 Chirality : 0.042 0.137 1466 Planarity : 0.004 0.054 1468 Dihedral : 12.809 72.066 2312 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.41 % Allowed : 7.03 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.97 (0.25), residues: 1054 helix: 2.49 (0.22), residues: 496 sheet: 1.49 (0.42), residues: 126 loop : -0.14 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.007 0.001 HIS B 614 PHE 0.022 0.001 PHE B 274 TYR 0.024 0.002 TYR B 481 ARG 0.004 0.000 ARG B 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 6) link_NAG-ASN : angle 1.61426 ( 18) link_BETA1-4 : bond 0.00442 ( 4) link_BETA1-4 : angle 1.11813 ( 12) hydrogen bonds : bond 0.05737 ( 476) hydrogen bonds : angle 4.13831 ( 1353) SS BOND : bond 0.00215 ( 6) SS BOND : angle 0.78807 ( 12) covalent geometry : bond 0.00387 ( 9780) covalent geometry : angle 0.53568 (13066) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.989 Fit side-chains REVERT: B 471 ASP cc_start: 0.8191 (m-30) cc_final: 0.7902 (m-30) REVERT: B 556 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6693 (mm-30) REVERT: A 471 ASP cc_start: 0.7781 (m-30) cc_final: 0.7499 (m-30) REVERT: A 546 SER cc_start: 0.8279 (m) cc_final: 0.7995 (m) outliers start: 13 outliers final: 4 residues processed: 99 average time/residue: 1.0840 time to fit residues: 116.5475 Evaluate side-chains 91 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 618 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 61 optimal weight: 0.0470 chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 82 optimal weight: 3.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 GLN A 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108650 restraints weight = 10417.384| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.61 r_work: 0.3162 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9796 Z= 0.160 Angle : 0.524 6.351 13108 Z= 0.264 Chirality : 0.041 0.127 1466 Planarity : 0.004 0.047 1468 Dihedral : 12.278 73.201 2312 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.41 % Allowed : 9.20 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.10 (0.25), residues: 1054 helix: 2.70 (0.22), residues: 496 sheet: 1.45 (0.42), residues: 126 loop : -0.20 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 647 HIS 0.007 0.001 HIS A 614 PHE 0.016 0.001 PHE B 274 TYR 0.017 0.002 TYR B 481 ARG 0.003 0.000 ARG A 267 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 6) link_NAG-ASN : angle 1.60684 ( 18) link_BETA1-4 : bond 0.00415 ( 4) link_BETA1-4 : angle 1.20934 ( 12) hydrogen bonds : bond 0.05224 ( 476) hydrogen bonds : angle 3.94297 ( 1353) SS BOND : bond 0.00185 ( 6) SS BOND : angle 0.69414 ( 12) covalent geometry : bond 0.00384 ( 9780) covalent geometry : angle 0.51939 (13066) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.905 Fit side-chains REVERT: B 471 ASP cc_start: 0.8227 (m-30) cc_final: 0.7928 (m-30) REVERT: B 556 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6679 (mm-30) REVERT: A 546 SER cc_start: 0.8272 (m) cc_final: 0.8013 (m) outliers start: 13 outliers final: 5 residues processed: 93 average time/residue: 1.0666 time to fit residues: 107.8797 Evaluate side-chains 90 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 618 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.0170 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.143297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111040 restraints weight = 10296.950| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.60 r_work: 0.3210 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9796 Z= 0.106 Angle : 0.457 6.427 13108 Z= 0.233 Chirality : 0.039 0.127 1466 Planarity : 0.003 0.039 1468 Dihedral : 11.377 73.930 2312 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.08 % Allowed : 10.61 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.41 (0.25), residues: 1054 helix: 3.02 (0.22), residues: 498 sheet: 1.62 (0.43), residues: 126 loop : -0.16 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 PHE 0.014 0.001 PHE A 315 TYR 0.013 0.001 TYR B 570 ARG 0.004 0.000 ARG A 412 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 6) link_NAG-ASN : angle 1.45539 ( 18) link_BETA1-4 : bond 0.00424 ( 4) link_BETA1-4 : angle 1.09253 ( 12) hydrogen bonds : bond 0.04166 ( 476) hydrogen bonds : angle 3.66594 ( 1353) SS BOND : bond 0.00162 ( 6) SS BOND : angle 0.48975 ( 12) covalent geometry : bond 0.00236 ( 9780) covalent geometry : angle 0.45317 (13066) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.913 Fit side-chains REVERT: B 471 ASP cc_start: 0.8237 (m-30) cc_final: 0.7965 (m-30) REVERT: A 546 SER cc_start: 0.8227 (m) cc_final: 0.7970 (m) outliers start: 10 outliers final: 0 residues processed: 95 average time/residue: 0.9703 time to fit residues: 100.7507 Evaluate side-chains 87 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 0.0000 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 GLN A 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.139718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107098 restraints weight = 10399.425| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.61 r_work: 0.3136 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9796 Z= 0.234 Angle : 0.600 6.834 13108 Z= 0.296 Chirality : 0.045 0.152 1466 Planarity : 0.004 0.039 1468 Dihedral : 12.182 72.431 2312 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.97 % Allowed : 12.55 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.91 (0.25), residues: 1054 helix: 2.48 (0.22), residues: 500 sheet: 1.34 (0.43), residues: 126 loop : -0.23 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 647 HIS 0.010 0.001 HIS B 614 PHE 0.018 0.002 PHE A 322 TYR 0.017 0.002 TYR B 570 ARG 0.005 0.001 ARG A 267 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 6) link_NAG-ASN : angle 1.84845 ( 18) link_BETA1-4 : bond 0.00429 ( 4) link_BETA1-4 : angle 1.32056 ( 12) hydrogen bonds : bond 0.05783 ( 476) hydrogen bonds : angle 3.98436 ( 1353) SS BOND : bond 0.00418 ( 6) SS BOND : angle 1.16439 ( 12) covalent geometry : bond 0.00582 ( 9780) covalent geometry : angle 0.59485 (13066) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.907 Fit side-chains REVERT: B 471 ASP cc_start: 0.8292 (m-30) cc_final: 0.8028 (m-30) REVERT: B 556 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6739 (mm-30) outliers start: 9 outliers final: 3 residues processed: 91 average time/residue: 1.0124 time to fit residues: 100.3894 Evaluate side-chains 88 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain A residue 614 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 3 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.140894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108389 restraints weight = 10342.049| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.60 r_work: 0.3158 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9796 Z= 0.167 Angle : 0.531 6.378 13108 Z= 0.265 Chirality : 0.042 0.127 1466 Planarity : 0.004 0.038 1468 Dihedral : 11.854 73.450 2312 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.19 % Allowed : 12.77 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.01 (0.25), residues: 1054 helix: 2.65 (0.22), residues: 498 sheet: 1.34 (0.43), residues: 126 loop : -0.26 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 647 HIS 0.008 0.001 HIS B 614 PHE 0.018 0.001 PHE A 315 TYR 0.015 0.002 TYR B 570 ARG 0.004 0.000 ARG A 412 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 6) link_NAG-ASN : angle 1.77555 ( 18) link_BETA1-4 : bond 0.00426 ( 4) link_BETA1-4 : angle 1.22938 ( 12) hydrogen bonds : bond 0.05034 ( 476) hydrogen bonds : angle 3.84204 ( 1353) SS BOND : bond 0.00214 ( 6) SS BOND : angle 1.15220 ( 12) covalent geometry : bond 0.00406 ( 9780) covalent geometry : angle 0.52542 (13066) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.923 Fit side-chains REVERT: B 471 ASP cc_start: 0.8224 (m-30) cc_final: 0.7962 (m-30) REVERT: B 556 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6685 (mm-30) REVERT: A 546 SER cc_start: 0.8260 (m) cc_final: 0.8041 (m) outliers start: 11 outliers final: 4 residues processed: 91 average time/residue: 1.0252 time to fit residues: 101.6830 Evaluate side-chains 90 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 614 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 0.0470 chunk 77 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 GLN A 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107825 restraints weight = 10455.590| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.61 r_work: 0.3157 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9796 Z= 0.176 Angle : 0.542 6.967 13108 Z= 0.269 Chirality : 0.042 0.127 1466 Planarity : 0.004 0.036 1468 Dihedral : 11.847 73.675 2312 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.97 % Allowed : 13.20 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.99 (0.25), residues: 1054 helix: 2.64 (0.22), residues: 498 sheet: 1.25 (0.43), residues: 128 loop : -0.25 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 647 HIS 0.008 0.001 HIS B 614 PHE 0.017 0.001 PHE A 315 TYR 0.015 0.002 TYR B 570 ARG 0.005 0.000 ARG A 412 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 6) link_NAG-ASN : angle 1.78625 ( 18) link_BETA1-4 : bond 0.00449 ( 4) link_BETA1-4 : angle 1.25655 ( 12) hydrogen bonds : bond 0.05127 ( 476) hydrogen bonds : angle 3.84969 ( 1353) SS BOND : bond 0.00177 ( 6) SS BOND : angle 0.87592 ( 12) covalent geometry : bond 0.00429 ( 9780) covalent geometry : angle 0.53642 (13066) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.908 Fit side-chains REVERT: B 471 ASP cc_start: 0.8225 (m-30) cc_final: 0.7961 (m-30) REVERT: B 556 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6696 (mm-30) REVERT: A 605 MET cc_start: 0.9024 (mtp) cc_final: 0.8761 (mtt) outliers start: 9 outliers final: 5 residues processed: 93 average time/residue: 0.9734 time to fit residues: 99.1484 Evaluate side-chains 89 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 614 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.142863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110297 restraints weight = 10483.317| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.62 r_work: 0.3195 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9796 Z= 0.108 Angle : 0.470 7.178 13108 Z= 0.238 Chirality : 0.039 0.136 1466 Planarity : 0.003 0.034 1468 Dihedral : 11.112 74.412 2312 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.43 % Allowed : 13.85 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.34 (0.25), residues: 1054 helix: 2.99 (0.22), residues: 498 sheet: 1.38 (0.43), residues: 128 loop : -0.17 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 PHE 0.015 0.001 PHE A 315 TYR 0.013 0.001 TYR B 570 ARG 0.005 0.000 ARG A 412 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 6) link_NAG-ASN : angle 1.56752 ( 18) link_BETA1-4 : bond 0.00441 ( 4) link_BETA1-4 : angle 1.12312 ( 12) hydrogen bonds : bond 0.04124 ( 476) hydrogen bonds : angle 3.64872 ( 1353) SS BOND : bond 0.00391 ( 6) SS BOND : angle 0.69280 ( 12) covalent geometry : bond 0.00240 ( 9780) covalent geometry : angle 0.46540 (13066) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 1.002 Fit side-chains REVERT: B 471 ASP cc_start: 0.8276 (m-30) cc_final: 0.8030 (m-30) REVERT: B 556 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6658 (mm-30) outliers start: 4 outliers final: 0 residues processed: 88 average time/residue: 1.0173 time to fit residues: 97.7983 Evaluate side-chains 83 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 556 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 80 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109645 restraints weight = 10336.140| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.59 r_work: 0.3186 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9796 Z= 0.132 Angle : 0.498 7.256 13108 Z= 0.250 Chirality : 0.040 0.137 1466 Planarity : 0.004 0.033 1468 Dihedral : 11.112 73.877 2312 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.65 % Allowed : 13.53 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.29 (0.25), residues: 1054 helix: 2.90 (0.22), residues: 500 sheet: 1.39 (0.43), residues: 128 loop : -0.14 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.005 0.001 HIS A 614 PHE 0.015 0.001 PHE B 315 TYR 0.014 0.001 TYR B 570 ARG 0.005 0.000 ARG A 412 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 6) link_NAG-ASN : angle 1.62703 ( 18) link_BETA1-4 : bond 0.00454 ( 4) link_BETA1-4 : angle 1.17213 ( 12) hydrogen bonds : bond 0.04483 ( 476) hydrogen bonds : angle 3.69358 ( 1353) SS BOND : bond 0.00352 ( 6) SS BOND : angle 0.98920 ( 12) covalent geometry : bond 0.00309 ( 9780) covalent geometry : angle 0.49256 (13066) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 1.121 Fit side-chains REVERT: B 471 ASP cc_start: 0.8205 (m-30) cc_final: 0.7939 (m-30) REVERT: B 556 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6704 (mm-30) outliers start: 6 outliers final: 3 residues processed: 92 average time/residue: 1.0115 time to fit residues: 101.9954 Evaluate side-chains 88 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain A residue 488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107303 restraints weight = 10532.011| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.61 r_work: 0.3141 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9796 Z= 0.246 Angle : 0.604 7.265 13108 Z= 0.298 Chirality : 0.045 0.145 1466 Planarity : 0.004 0.034 1468 Dihedral : 11.803 73.779 2312 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.76 % Allowed : 13.85 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.93 (0.25), residues: 1054 helix: 2.50 (0.22), residues: 500 sheet: 1.33 (0.42), residues: 126 loop : -0.21 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 647 HIS 0.008 0.001 HIS B 614 PHE 0.018 0.002 PHE A 322 TYR 0.016 0.002 TYR B 570 ARG 0.005 0.001 ARG A 412 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 6) link_NAG-ASN : angle 1.93120 ( 18) link_BETA1-4 : bond 0.00459 ( 4) link_BETA1-4 : angle 1.32065 ( 12) hydrogen bonds : bond 0.05692 ( 476) hydrogen bonds : angle 3.93180 ( 1353) SS BOND : bond 0.00325 ( 6) SS BOND : angle 1.35492 ( 12) covalent geometry : bond 0.00611 ( 9780) covalent geometry : angle 0.59772 (13066) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.968 Fit side-chains REVERT: B 471 ASP cc_start: 0.8281 (m-30) cc_final: 0.8020 (m-30) REVERT: B 556 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6813 (mm-30) REVERT: A 471 ASP cc_start: 0.8207 (m-30) cc_final: 0.7961 (OUTLIER) REVERT: A 618 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8237 (pt0) outliers start: 7 outliers final: 3 residues processed: 85 average time/residue: 1.0401 time to fit residues: 96.4365 Evaluate side-chains 82 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 618 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108906 restraints weight = 10434.061| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.60 r_work: 0.3173 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9796 Z= 0.134 Angle : 0.508 7.374 13108 Z= 0.254 Chirality : 0.040 0.138 1466 Planarity : 0.004 0.033 1468 Dihedral : 11.381 73.944 2312 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.43 % Allowed : 13.96 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.17 (0.25), residues: 1054 helix: 2.79 (0.22), residues: 498 sheet: 1.30 (0.43), residues: 128 loop : -0.16 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.005 0.001 HIS A 614 PHE 0.016 0.001 PHE A 315 TYR 0.014 0.001 TYR B 570 ARG 0.005 0.000 ARG A 412 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 6) link_NAG-ASN : angle 1.74735 ( 18) link_BETA1-4 : bond 0.00464 ( 4) link_BETA1-4 : angle 1.20412 ( 12) hydrogen bonds : bond 0.04657 ( 476) hydrogen bonds : angle 3.75914 ( 1353) SS BOND : bond 0.00260 ( 6) SS BOND : angle 1.01263 ( 12) covalent geometry : bond 0.00314 ( 9780) covalent geometry : angle 0.50205 (13066) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5935.25 seconds wall clock time: 103 minutes 5.19 seconds (6185.19 seconds total)