Starting phenix.real_space_refine on Fri Nov 15 20:59:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4a_37264/11_2024/8w4a_37264.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4a_37264/11_2024/8w4a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4a_37264/11_2024/8w4a_37264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4a_37264/11_2024/8w4a_37264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4a_37264/11_2024/8w4a_37264.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4a_37264/11_2024/8w4a_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-5513/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: 7.31, per 1000 atoms: 0.76 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: 2.94 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: 0.92 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: 2.97 Time building geometry restraints manager: 3.16 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: 0.00 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: 4.330 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.720 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.010 ------------------------------------------------------------------------------- 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 9780 Z= 0.367 Angle : 0.570 8.020 13066 Z= 0.263 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 *********************** 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 : 0.895 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: 1.2524 time to fit residues: 144.5925 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 : 1.067 ------------------------------------------------------------------------------- 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: 0.0270 chunk 96 optimal weight: 0.9980 overall best weight: 0.9840 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9780 Z= 0.255 Angle : 0.538 6.527 13066 Z= 0.274 Chirality : 0.042 0.146 1466 Planarity : 0.004 0.054 1468 Dihedral : 12.748 72.628 2312 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.52 % Allowed : 7.03 % Favored : 91.45 % 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: 1.96 (0.25), residues: 1054 helix: 2.47 (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 0.001 ARG A 267 *********************** 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 102 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.988 Fit side-chains REVERT: B 471 ASP cc_start: 0.8192 (m-30) cc_final: 0.7856 (m-30) REVERT: B 556 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6731 (mm-30) REVERT: B 628 LYS cc_start: 0.8073 (tttp) cc_final: 0.7868 (tttp) REVERT: A 546 SER cc_start: 0.8291 (m) cc_final: 0.8025 (m) outliers start: 14 outliers final: 4 residues processed: 98 average time/residue: 1.1192 time to fit residues: 118.9739 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 : 1.000 ------------------------------------------------------------------------------- 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 53 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9780 Z= 0.243 Angle : 0.515 6.331 13066 Z= 0.261 Chirality : 0.041 0.127 1466 Planarity : 0.004 0.047 1468 Dihedral : 12.126 73.296 2312 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.30 % Allowed : 9.63 % Favored : 89.07 % 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: 2.11 (0.25), residues: 1054 helix: 2.69 (0.22), residues: 496 sheet: 1.47 (0.42), residues: 126 loop : -0.17 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.006 0.001 HIS B 614 PHE 0.016 0.001 PHE A 315 TYR 0.017 0.001 TYR B 481 ARG 0.004 0.001 ARG A 267 *********************** 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: 12 poor density : 85 time to evaluate : 1.076 Fit side-chains REVERT: B 471 ASP cc_start: 0.8266 (m-30) cc_final: 0.7919 (m-30) REVERT: B 556 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6710 (mm-30) REVERT: B 628 LYS cc_start: 0.8060 (tttp) cc_final: 0.7798 (tttp) REVERT: A 546 SER cc_start: 0.8282 (m) cc_final: 0.8043 (m) outliers start: 12 outliers final: 5 residues processed: 94 average time/residue: 1.0493 time to fit residues: 107.8348 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 : 1.027 ------------------------------------------------------------------------------- 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: 0.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9780 Z= 0.257 Angle : 0.523 6.597 13066 Z= 0.263 Chirality : 0.041 0.126 1466 Planarity : 0.004 0.041 1468 Dihedral : 11.935 73.861 2312 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.41 % Allowed : 11.15 % Favored : 87.45 % 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: 2.69 (0.22), residues: 498 sheet: 1.44 (0.43), residues: 126 loop : -0.20 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 647 HIS 0.008 0.001 HIS B 614 PHE 0.016 0.001 PHE A 315 TYR 0.016 0.002 TYR B 481 ARG 0.004 0.001 ARG B 412 *********************** 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 96 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.771 Fit side-chains REVERT: B 471 ASP cc_start: 0.8247 (m-30) cc_final: 0.7900 (m-30) REVERT: B 556 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6747 (mm-30) REVERT: B 628 LYS cc_start: 0.8064 (tttp) cc_final: 0.7800 (tttp) REVERT: A 546 SER cc_start: 0.8273 (m) cc_final: 0.8051 (m) outliers start: 13 outliers final: 6 residues processed: 90 average time/residue: 1.0845 time to fit residues: 106.0325 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 : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 330 GLN 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 552 VAL Chi-restraints excluded: chain A residue 614 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9780 Z= 0.309 Angle : 0.559 6.366 13066 Z= 0.279 Chirality : 0.043 0.132 1466 Planarity : 0.004 0.040 1468 Dihedral : 12.103 73.620 2312 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.19 % Allowed : 12.23 % Favored : 86.58 % 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: 1.98 (0.25), residues: 1054 helix: 2.58 (0.22), residues: 498 sheet: 1.37 (0.43), residues: 126 loop : -0.22 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 647 HIS 0.010 0.001 HIS B 614 PHE 0.017 0.002 PHE A 315 TYR 0.016 0.002 TYR B 570 ARG 0.004 0.001 ARG A 412 *********************** 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: 11 poor density : 82 time to evaluate : 1.046 Fit side-chains REVERT: B 471 ASP cc_start: 0.8219 (m-30) cc_final: 0.7900 (m-30) REVERT: B 556 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6780 (mm-30) REVERT: B 628 LYS cc_start: 0.8072 (tttp) cc_final: 0.7802 (tttp) REVERT: A 605 MET cc_start: 0.8982 (mtp) cc_final: 0.8718 (mtt) outliers start: 11 outliers final: 5 residues processed: 89 average time/residue: 1.0301 time to fit residues: 100.1704 Evaluate side-chains 88 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 556 GLU Chi-restraints excluded: chain B residue 618 GLU 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 92 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9780 Z= 0.312 Angle : 0.557 6.566 13066 Z= 0.278 Chirality : 0.043 0.131 1466 Planarity : 0.004 0.039 1468 Dihedral : 12.100 73.666 2312 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.41 % Allowed : 13.20 % 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: 1.94 (0.25), residues: 1054 helix: 2.55 (0.22), residues: 498 sheet: 1.29 (0.43), residues: 126 loop : -0.24 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 647 HIS 0.009 0.001 HIS B 614 PHE 0.017 0.001 PHE A 315 TYR 0.016 0.002 TYR B 570 ARG 0.004 0.001 ARG A 412 *********************** 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 97 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.952 Fit side-chains REVERT: B 471 ASP cc_start: 0.8218 (m-30) cc_final: 0.7898 (m-30) REVERT: B 556 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6794 (mm-30) REVERT: B 628 LYS cc_start: 0.8074 (tttp) cc_final: 0.7801 (tttp) REVERT: A 471 ASP cc_start: 0.8183 (m-30) cc_final: 0.7868 (OUTLIER) REVERT: A 618 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8147 (pt0) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 1.0738 time to fit residues: 107.9122 Evaluate side-chains 93 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 180 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 618 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9780 Z= 0.300 Angle : 0.552 6.946 13066 Z= 0.275 Chirality : 0.043 0.129 1466 Planarity : 0.004 0.037 1468 Dihedral : 12.071 73.609 2312 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.41 % Allowed : 13.10 % Favored : 85.50 % 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: 1.95 (0.25), residues: 1054 helix: 2.57 (0.22), residues: 498 sheet: 1.30 (0.43), residues: 126 loop : -0.24 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 647 HIS 0.009 0.001 HIS B 614 PHE 0.017 0.001 PHE A 315 TYR 0.016 0.002 TYR B 570 ARG 0.005 0.000 ARG A 412 *********************** 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 96 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.056 Fit side-chains REVERT: B 471 ASP cc_start: 0.8215 (m-30) cc_final: 0.7897 (m-30) REVERT: B 556 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6796 (mm-30) REVERT: B 628 LYS cc_start: 0.8076 (tttp) cc_final: 0.7801 (tttp) REVERT: A 471 ASP cc_start: 0.8205 (m-30) cc_final: 0.7862 (OUTLIER) REVERT: A 618 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8146 (pt0) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 1.0766 time to fit residues: 108.1451 Evaluate side-chains 94 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 180 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 618 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 0.0470 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.1882 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9780 Z= 0.291 Angle : 0.550 7.020 13066 Z= 0.274 Chirality : 0.042 0.127 1466 Planarity : 0.004 0.036 1468 Dihedral : 12.021 73.549 2312 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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 (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: 1.96 (0.25), residues: 1054 helix: 2.58 (0.22), residues: 498 sheet: 1.26 (0.43), residues: 126 loop : -0.24 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 647 HIS 0.009 0.001 HIS B 614 PHE 0.017 0.001 PHE A 315 TYR 0.016 0.002 TYR B 570 ARG 0.004 0.000 ARG A 412 *********************** 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 95 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 1.030 Fit side-chains REVERT: B 471 ASP cc_start: 0.8210 (m-30) cc_final: 0.7887 (m-30) REVERT: B 556 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6795 (mm-30) REVERT: B 628 LYS cc_start: 0.8115 (tttp) cc_final: 0.7801 (tttp) REVERT: A 471 ASP cc_start: 0.8181 (m-30) cc_final: 0.7833 (OUTLIER) REVERT: A 618 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8138 (pt0) outliers start: 12 outliers final: 9 residues processed: 91 average time/residue: 1.0865 time to fit residues: 107.6916 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 : 0.978 ------------------------------------------------------------------------------- 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 488 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 614 HIS 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 95 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 62 optimal weight: 0.0670 chunk 100 optimal weight: 1.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9780 Z= 0.223 Angle : 0.507 7.226 13066 Z= 0.256 Chirality : 0.041 0.135 1466 Planarity : 0.004 0.035 1468 Dihedral : 11.611 74.104 2312 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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 (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: 2.12 (0.25), residues: 1054 helix: 2.76 (0.22), residues: 498 sheet: 1.24 (0.43), residues: 128 loop : -0.17 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 647 HIS 0.008 0.001 HIS B 614 PHE 0.017 0.001 PHE A 315 TYR 0.014 0.001 TYR B 570 ARG 0.005 0.000 ARG A 412 *********************** 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 96 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.045 Fit side-chains REVERT: B 471 ASP cc_start: 0.8204 (m-30) cc_final: 0.7888 (m-30) REVERT: B 556 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6726 (mm-30) REVERT: B 628 LYS cc_start: 0.8112 (tttp) cc_final: 0.7799 (tttp) REVERT: A 605 MET cc_start: 0.8966 (mtp) cc_final: 0.8744 (mtt) outliers start: 12 outliers final: 7 residues processed: 93 average time/residue: 1.0408 time to fit residues: 105.8750 Evaluate side-chains 91 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 488 VAL Chi-restraints excluded: chain A residue 614 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9780 Z= 0.324 Angle : 0.568 7.249 13066 Z= 0.283 Chirality : 0.043 0.135 1466 Planarity : 0.004 0.035 1468 Dihedral : 11.962 73.843 2312 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.97 % Allowed : 13.64 % 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: 2.52 (0.22), residues: 500 sheet: 1.27 (0.42), residues: 126 loop : -0.22 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 647 HIS 0.008 0.001 HIS B 614 PHE 0.017 0.002 PHE A 315 TYR 0.016 0.002 TYR B 570 ARG 0.005 0.001 ARG A 412 ********************** 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 88 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 1.009 Fit side-chains REVERT: B 471 ASP cc_start: 0.8217 (m-30) cc_final: 0.7894 (m-30) REVERT: B 556 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6859 (mm-30) REVERT: B 628 LYS cc_start: 0.8125 (tttp) cc_final: 0.7810 (tttp) REVERT: A 471 ASP cc_start: 0.8204 (m-30) cc_final: 0.7864 (OUTLIER) outliers start: 9 outliers final: 8 residues processed: 86 average time/residue: 1.1048 time to fit residues: 104.1576 Evaluate side-chains 87 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 488 VAL Chi-restraints excluded: chain A residue 614 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 86 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.141622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109386 restraints weight = 10293.037| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.60 r_work: 0.3172 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9780 Z= 0.195 Angle : 0.492 7.337 13066 Z= 0.249 Chirality : 0.040 0.135 1466 Planarity : 0.004 0.035 1468 Dihedral : 11.397 74.177 2312 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.87 % Allowed : 14.07 % Favored : 85.06 % 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: 2.20 (0.25), residues: 1054 helix: 2.82 (0.22), residues: 498 sheet: 1.32 (0.43), residues: 128 loop : -0.15 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 647 HIS 0.005 0.001 HIS B 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2941.83 seconds wall clock time: 53 minutes 59.50 seconds (3239.50 seconds total)