Starting phenix.real_space_refine on Sat Aug 23 04:11:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w4a_37264/08_2025/8w4a_37264.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w4a_37264/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8w4a_37264/08_2025/8w4a_37264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w4a_37264/08_2025/8w4a_37264.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w4a_37264/08_2025/8w4a_37264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w4a_37264/08_2025/8w4a_37264.map" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.97, per 1000 atoms: 0.31 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: 1.11 Conformation dependent library (CDL) restraints added in 363.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.34 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: 1.67 Time building geometry restraints manager: 1.38 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: 0.01 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: 6.270 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.400 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.690 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.005 0.001 ARG B 337 TYR 0.026 0.001 TYR B 481 PHE 0.020 0.001 PHE B 274 TRP 0.011 0.001 TRP B 418 HIS 0.007 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00612 ( 9780) covalent geometry : angle 0.57020 (13066) SS BOND : bond 0.00307 ( 6) SS BOND : angle 1.05544 ( 12) hydrogen bonds : bond 0.18678 ( 476) hydrogen bonds : angle 5.94964 ( 1353) link_BETA1-4 : bond 0.00430 ( 4) link_BETA1-4 : angle 0.84279 ( 12) link_NAG-ASN : bond 0.00051 ( 6) link_NAG-ASN : angle 1.78339 ( 18) *********************** 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 : 0.361 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: 0.6214 time to fit residues: 71.2935 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 : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.139803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107293 restraints weight = 10414.604| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.61 r_work: 0.3136 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9796 Z= 0.232 Angle : 0.611 6.499 13108 Z= 0.305 Chirality : 0.045 0.162 1466 Planarity : 0.005 0.054 1468 Dihedral : 13.176 73.538 2312 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.73 % Allowed : 6.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.25), residues: 1054 helix: 2.23 (0.22), residues: 496 sheet: 1.39 (0.42), residues: 126 loop : -0.19 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 267 TYR 0.028 0.002 TYR B 481 PHE 0.026 0.002 PHE B 274 TRP 0.016 0.002 TRP A 647 HIS 0.010 0.002 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 9780) covalent geometry : angle 0.60616 (13066) SS BOND : bond 0.00247 ( 6) SS BOND : angle 0.99134 ( 12) hydrogen bonds : bond 0.06203 ( 476) hydrogen bonds : angle 4.24099 ( 1353) link_BETA1-4 : bond 0.00474 ( 4) link_BETA1-4 : angle 1.23408 ( 12) link_NAG-ASN : bond 0.00262 ( 6) link_NAG-ASN : angle 1.82419 ( 18) *********************** 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 100 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.406 Fit side-chains REVERT: B 471 ASP cc_start: 0.8265 (m-30) cc_final: 0.7964 (m-30) REVERT: B 556 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6760 (mm-30) REVERT: A 556 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6836 (mm-30) outliers start: 16 outliers final: 5 residues processed: 95 average time/residue: 0.5812 time to fit residues: 59.5560 Evaluate side-chains 89 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 A 330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110611 restraints weight = 10436.673| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.22 r_work: 0.3170 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1131 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= 0.234 Angle : 0.605 6.762 13108 Z= 0.301 Chirality : 0.045 0.149 1466 Planarity : 0.005 0.048 1468 Dihedral : 12.906 73.385 2312 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.95 % Allowed : 10.39 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.25), residues: 1054 helix: 2.31 (0.22), residues: 496 sheet: 1.31 (0.42), residues: 126 loop : -0.29 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 267 TYR 0.021 0.002 TYR B 481 PHE 0.019 0.002 PHE A 315 TRP 0.017 0.002 TRP B 647 HIS 0.009 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 9780) covalent geometry : angle 0.60021 (13066) SS BOND : bond 0.00210 ( 6) SS BOND : angle 0.96937 ( 12) hydrogen bonds : bond 0.06024 ( 476) hydrogen bonds : angle 4.11577 ( 1353) link_BETA1-4 : bond 0.00403 ( 4) link_BETA1-4 : angle 1.36752 ( 12) link_NAG-ASN : bond 0.00205 ( 6) link_NAG-ASN : angle 1.87809 ( 18) *********************** 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 99 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.378 Fit side-chains REVERT: B 471 ASP cc_start: 0.8210 (m-30) cc_final: 0.7896 (m-30) REVERT: B 556 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6635 (mm-30) REVERT: A 556 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6664 (mm-30) outliers start: 18 outliers final: 6 residues processed: 92 average time/residue: 0.5581 time to fit residues: 55.5496 Evaluate side-chains 88 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 614 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.141494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112287 restraints weight = 10423.455| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.28 r_work: 0.3209 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9796 Z= 0.120 Angle : 0.491 6.665 13108 Z= 0.248 Chirality : 0.040 0.126 1466 Planarity : 0.004 0.041 1468 Dihedral : 11.990 73.114 2312 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.08 % Allowed : 12.12 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.25), residues: 1054 helix: 2.78 (0.22), residues: 498 sheet: 1.42 (0.43), residues: 126 loop : -0.18 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 412 TYR 0.014 0.001 TYR B 570 PHE 0.016 0.001 PHE A 315 TRP 0.013 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9780) covalent geometry : angle 0.48623 (13066) SS BOND : bond 0.00171 ( 6) SS BOND : angle 0.54910 ( 12) hydrogen bonds : bond 0.04573 ( 476) hydrogen bonds : angle 3.80322 ( 1353) link_BETA1-4 : bond 0.00425 ( 4) link_BETA1-4 : angle 1.21736 ( 12) link_NAG-ASN : bond 0.00241 ( 6) link_NAG-ASN : angle 1.65637 ( 18) *********************** 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 93 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.249 Fit side-chains REVERT: B 471 ASP cc_start: 0.8143 (m-30) cc_final: 0.7849 (m-30) REVERT: B 556 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6544 (mm-30) REVERT: A 546 SER cc_start: 0.8187 (m) cc_final: 0.7960 (m) outliers start: 10 outliers final: 2 residues processed: 89 average time/residue: 0.5265 time to fit residues: 50.6969 Evaluate side-chains 86 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN B 624 GLN A 330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.139212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110543 restraints weight = 10509.960| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.27 r_work: 0.3165 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9796 Z= 0.225 Angle : 0.596 6.677 13108 Z= 0.294 Chirality : 0.044 0.145 1466 Planarity : 0.004 0.039 1468 Dihedral : 12.435 73.661 2312 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.19 % Allowed : 12.55 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.25), residues: 1054 helix: 2.46 (0.22), residues: 498 sheet: 1.24 (0.42), residues: 126 loop : -0.27 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 267 TYR 0.016 0.002 TYR B 570 PHE 0.017 0.002 PHE A 322 TRP 0.017 0.002 TRP A 647 HIS 0.010 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 9780) covalent geometry : angle 0.59076 (13066) SS BOND : bond 0.00160 ( 6) SS BOND : angle 0.91276 ( 12) hydrogen bonds : bond 0.05745 ( 476) hydrogen bonds : angle 3.99920 ( 1353) link_BETA1-4 : bond 0.00432 ( 4) link_BETA1-4 : angle 1.38970 ( 12) link_NAG-ASN : bond 0.00226 ( 6) link_NAG-ASN : angle 1.86658 ( 18) *********************** 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 90 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.328 Fit side-chains REVERT: B 471 ASP cc_start: 0.8188 (m-30) cc_final: 0.7876 (m-30) REVERT: B 556 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6664 (mm-30) outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 0.5346 time to fit residues: 50.3156 Evaluate side-chains 88 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 618 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 9 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 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 A 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108724 restraints weight = 10440.090| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.61 r_work: 0.3161 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9796 Z= 0.132 Angle : 0.499 6.658 13108 Z= 0.251 Chirality : 0.040 0.126 1466 Planarity : 0.004 0.036 1468 Dihedral : 11.760 73.879 2312 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.08 % Allowed : 13.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.25), residues: 1054 helix: 2.77 (0.22), residues: 498 sheet: 1.35 (0.43), residues: 126 loop : -0.20 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 412 TYR 0.014 0.001 TYR B 570 PHE 0.017 0.001 PHE A 315 TRP 0.013 0.001 TRP B 647 HIS 0.007 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9780) covalent geometry : angle 0.49413 (13066) SS BOND : bond 0.00164 ( 6) SS BOND : angle 0.60809 ( 12) hydrogen bonds : bond 0.04624 ( 476) hydrogen bonds : angle 3.77125 ( 1353) link_BETA1-4 : bond 0.00425 ( 4) link_BETA1-4 : angle 1.22403 ( 12) link_NAG-ASN : bond 0.00217 ( 6) link_NAG-ASN : angle 1.69616 ( 18) *********************** 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 95 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.411 Fit side-chains REVERT: B 471 ASP cc_start: 0.8228 (m-30) cc_final: 0.7961 (m-30) REVERT: B 556 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6681 (mm-30) outliers start: 10 outliers final: 4 residues processed: 91 average time/residue: 0.4774 time to fit residues: 47.2929 Evaluate side-chains 87 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 618 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 93 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.140589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108077 restraints weight = 10416.863| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.61 r_work: 0.3155 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9796 Z= 0.167 Angle : 0.531 6.827 13108 Z= 0.265 Chirality : 0.042 0.126 1466 Planarity : 0.004 0.034 1468 Dihedral : 11.817 74.214 2312 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.08 % Allowed : 13.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.25), residues: 1054 helix: 2.68 (0.22), residues: 498 sheet: 1.32 (0.43), residues: 126 loop : -0.20 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 412 TYR 0.015 0.002 TYR B 570 PHE 0.017 0.001 PHE A 315 TRP 0.014 0.001 TRP A 647 HIS 0.008 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9780) covalent geometry : angle 0.52576 (13066) SS BOND : bond 0.00173 ( 6) SS BOND : angle 0.87846 ( 12) hydrogen bonds : bond 0.05008 ( 476) hydrogen bonds : angle 3.81493 ( 1353) link_BETA1-4 : bond 0.00441 ( 4) link_BETA1-4 : angle 1.28149 ( 12) link_NAG-ASN : bond 0.00220 ( 6) link_NAG-ASN : angle 1.75027 ( 18) *********************** 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 92 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.238 Fit side-chains REVERT: B 471 ASP cc_start: 0.8229 (m-30) cc_final: 0.7955 (m-30) REVERT: B 556 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6771 (mm-30) outliers start: 10 outliers final: 5 residues processed: 91 average time/residue: 0.4399 time to fit residues: 43.4907 Evaluate side-chains 87 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain A residue 488 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.140375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107910 restraints weight = 10433.027| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.60 r_work: 0.3151 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1323 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= 0.174 Angle : 0.540 7.009 13108 Z= 0.269 Chirality : 0.042 0.126 1466 Planarity : 0.004 0.033 1468 Dihedral : 11.839 73.926 2312 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.30 % Allowed : 13.42 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.25), residues: 1054 helix: 2.65 (0.22), residues: 498 sheet: 1.31 (0.42), residues: 126 loop : -0.23 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 412 TYR 0.015 0.002 TYR B 570 PHE 0.017 0.001 PHE A 315 TRP 0.014 0.001 TRP B 647 HIS 0.009 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 9780) covalent geometry : angle 0.53478 (13066) SS BOND : bond 0.00185 ( 6) SS BOND : angle 0.98320 ( 12) hydrogen bonds : bond 0.05105 ( 476) hydrogen bonds : angle 3.83326 ( 1353) link_BETA1-4 : bond 0.00456 ( 4) link_BETA1-4 : angle 1.28549 ( 12) link_NAG-ASN : bond 0.00206 ( 6) link_NAG-ASN : angle 1.79925 ( 18) *********************** 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 92 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.361 Fit side-chains REVERT: B 471 ASP cc_start: 0.8230 (m-30) cc_final: 0.7955 (m-30) REVERT: B 556 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6805 (mm-30) REVERT: A 471 ASP cc_start: 0.8175 (m-30) cc_final: 0.7926 (OUTLIER) REVERT: A 618 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8188 (pt0) outliers start: 12 outliers final: 8 residues processed: 89 average time/residue: 0.4197 time to fit residues: 40.3226 Evaluate side-chains 89 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 186 ASP 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 B residue 618 GLU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 618 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 84 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.141274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108953 restraints weight = 10380.053| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.60 r_work: 0.3165 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9796 Z= 0.143 Angle : 0.507 7.235 13108 Z= 0.254 Chirality : 0.041 0.126 1466 Planarity : 0.004 0.033 1468 Dihedral : 11.537 74.279 2312 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.97 % Allowed : 14.07 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.25), residues: 1054 helix: 2.77 (0.22), residues: 498 sheet: 1.25 (0.42), residues: 128 loop : -0.17 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 412 TYR 0.014 0.001 TYR B 570 PHE 0.016 0.001 PHE A 315 TRP 0.013 0.001 TRP B 647 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9780) covalent geometry : angle 0.50166 (13066) SS BOND : bond 0.00154 ( 6) SS BOND : angle 0.79825 ( 12) hydrogen bonds : bond 0.04695 ( 476) hydrogen bonds : angle 3.74600 ( 1353) link_BETA1-4 : bond 0.00436 ( 4) link_BETA1-4 : angle 1.21178 ( 12) link_NAG-ASN : bond 0.00204 ( 6) link_NAG-ASN : angle 1.70551 ( 18) *********************** 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 91 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.251 Fit side-chains REVERT: B 471 ASP cc_start: 0.8220 (m-30) cc_final: 0.7950 (m-30) REVERT: B 556 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6690 (mm-30) REVERT: A 618 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8199 (pt0) outliers start: 9 outliers final: 6 residues processed: 90 average time/residue: 0.4664 time to fit residues: 45.5452 Evaluate side-chains 89 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 180 ASP 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 4 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 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 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 = 0.140995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108572 restraints weight = 10445.472| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.61 r_work: 0.3163 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9796 Z= 0.143 Angle : 0.509 7.424 13108 Z= 0.255 Chirality : 0.041 0.126 1466 Planarity : 0.004 0.033 1468 Dihedral : 11.470 74.344 2312 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.08 % Allowed : 14.07 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.25), residues: 1054 helix: 2.77 (0.22), residues: 498 sheet: 1.24 (0.42), residues: 128 loop : -0.15 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 412 TYR 0.014 0.001 TYR B 570 PHE 0.016 0.001 PHE A 315 TRP 0.013 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9780) covalent geometry : angle 0.50318 (13066) SS BOND : bond 0.00216 ( 6) SS BOND : angle 1.15384 ( 12) hydrogen bonds : bond 0.04694 ( 476) hydrogen bonds : angle 3.74563 ( 1353) link_BETA1-4 : bond 0.00452 ( 4) link_BETA1-4 : angle 1.21731 ( 12) link_NAG-ASN : bond 0.00216 ( 6) link_NAG-ASN : angle 1.69906 ( 18) ********************** 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 92 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.327 Fit side-chains REVERT: B 471 ASP cc_start: 0.8225 (m-30) cc_final: 0.7955 (m-30) REVERT: B 556 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6734 (mm-30) REVERT: A 618 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8203 (pt0) outliers start: 10 outliers final: 6 residues processed: 90 average time/residue: 0.5029 time to fit residues: 48.9400 Evaluate side-chains 89 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 MET 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 B residue 618 GLU Chi-restraints excluded: chain A residue 131 VAL 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 20 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.138990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106576 restraints weight = 10449.953| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.61 r_work: 0.3127 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9796 Z= 0.250 Angle : 0.619 7.267 13108 Z= 0.304 Chirality : 0.045 0.151 1466 Planarity : 0.004 0.035 1468 Dihedral : 12.190 73.791 2312 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.19 % Allowed : 14.07 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.25), residues: 1054 helix: 2.34 (0.22), residues: 500 sheet: 1.18 (0.42), residues: 126 loop : -0.23 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 412 TYR 0.017 0.002 TYR B 570 PHE 0.018 0.002 PHE A 322 TRP 0.017 0.002 TRP A 647 HIS 0.008 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00622 ( 9780) covalent geometry : angle 0.61244 (13066) SS BOND : bond 0.00204 ( 6) SS BOND : angle 1.37116 ( 12) hydrogen bonds : bond 0.05906 ( 476) hydrogen bonds : angle 3.98026 ( 1353) link_BETA1-4 : bond 0.00468 ( 4) link_BETA1-4 : angle 1.39688 ( 12) link_NAG-ASN : bond 0.00180 ( 6) link_NAG-ASN : angle 2.02746 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3060.93 seconds wall clock time: 52 minutes 58.83 seconds (3178.83 seconds total)