Starting phenix.real_space_refine on Tue May 13 02:32:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jl4_36388/05_2025/8jl4_36388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jl4_36388/05_2025/8jl4_36388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jl4_36388/05_2025/8jl4_36388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jl4_36388/05_2025/8jl4_36388.map" model { file = "/net/cci-nas-00/data/ceres_data/8jl4_36388/05_2025/8jl4_36388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jl4_36388/05_2025/8jl4_36388.cif" } resolution = 2.68 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= 0.000 sd= 0.039 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 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9588 Number of models: 1 Model: "" Number of chains: 8 Chain: "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: "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: "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: "A" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 508 Unusual residues: {'C14': 12, 'CLR': 2, 'COA': 1, '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: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 508 Unusual residues: {'C14': 12, 'CLR': 2, 'COA': 1, '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: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.71, per 1000 atoms: 0.80 Number of scatterers: 9588 At special positions: 0 Unit cell: (108.73, 86.32, 106.24, 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 A 104 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 462 " distance=2.04 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=2.04 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 803 " - " ASN A 94 " " NAG B 804 " - " ASN B 94 " " NAG C 1 " - " ASN A 142 " " NAG D 1 " - " ASN A 162 " " NAG E 1 " - " ASN B 142 " " NAG F 1 " - " ASN B 162 " Time building additional restraints: 2.95 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: 40 helices and 4 sheets defined 56.1% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 191 through 214 Processing helix chain 'A' and resid 268 through 287 removed outlier: 3.500A pdb=" N ASP A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.599A pdb=" N TYR A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TRP A 293 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.590A 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 331 removed outlier: 3.548A pdb=" N TRP A 312 " --> pdb=" O LEU A 308 " (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 removed outlier: 3.557A pdb=" N PHE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 438 removed outlier: 3.651A pdb=" N LEU A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.690A pdb=" N PHE A 456 " --> pdb=" O ILE A 453 " (cutoff:3.500A) 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: 4.045A 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 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 helix chain 'B' and resid 191 through 214 Processing helix chain 'B' and resid 268 through 287 Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.599A pdb=" N TYR B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TRP B 293 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 308 through 331 removed outlier: 3.549A pdb=" N TRP B 312 " --> pdb=" O LEU B 308 " (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 removed outlier: 3.556A pdb=" N PHE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 438 removed outlier: 3.651A pdb=" N LEU B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.689A pdb=" N PHE B 456 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'B' and resid 484 through 488 removed outlier: 4.045A 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 sheet with id=AA1, first strand: chain 'A' and resid 125 through 132 removed outlier: 8.929A pdb=" N TYR A 163 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU A 83 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU A 165 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A 85 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL A 167 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N HIS A 87 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ASN A 169 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 162 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 168 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115 removed outlier: 6.946A pdb=" N VAL A 97 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN A 114 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU A 95 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS A 151 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASP A 143 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLU A 149 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 132 removed outlier: 8.929A pdb=" N TYR B 163 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 83 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU B 165 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU B 85 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B 167 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N HIS B 87 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ASN B 169 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 162 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 168 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 115 removed outlier: 6.947A pdb=" N VAL B 97 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN B 114 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU B 95 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 151 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ASP B 143 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLU B 149 " --> pdb=" O ASP B 143 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1365 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: 2.67 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1300 1.30 - 1.43: 2566 1.43 - 1.56: 5852 1.56 - 1.69: 10 1.69 - 1.82: 52 Bond restraints: 9780 Sorted by residual: bond pdb=" C13 UV6 A 801 " pdb=" O7 UV6 A 801 " ideal model delta sigma weight residual 1.351 1.497 -0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" C13 UV6 B 802 " pdb=" O7 UV6 B 802 " ideal model delta sigma weight residual 1.351 1.497 -0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" C8 UV6 A 801 " pdb=" N9 UV6 A 801 " ideal model delta sigma weight residual 1.351 1.476 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C8 UV6 B 802 " pdb=" N9 UV6 B 802 " ideal model delta sigma weight residual 1.351 1.476 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C4' UV6 B 802 " pdb=" O5 UV6 B 802 " ideal model delta sigma weight residual 1.419 1.541 -0.122 2.00e-02 2.50e+03 3.74e+01 ... (remaining 9775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 12826 2.48 - 4.95: 204 4.95 - 7.43: 26 7.43 - 9.90: 6 9.90 - 12.38: 4 Bond angle restraints: 13066 Sorted by residual: angle pdb=" P1A COA A 802 " pdb=" O3A COA A 802 " pdb=" P2A COA A 802 " ideal model delta sigma weight residual 135.11 122.73 12.38 3.00e+00 1.11e-01 1.70e+01 angle pdb=" P1A COA B 803 " pdb=" O3A COA B 803 " pdb=" P2A COA B 803 " ideal model delta sigma weight residual 135.11 122.87 12.24 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C18 UV6 A 801 " pdb=" C17 UV6 A 801 " pdb=" C5 UV6 A 801 " ideal model delta sigma weight residual 110.11 120.89 -10.78 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C18 UV6 B 802 " pdb=" C17 UV6 B 802 " pdb=" C5 UV6 B 802 " ideal model delta sigma weight residual 110.11 120.88 -10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C2' UV6 B 802 " pdb=" C1' UV6 B 802 " pdb=" N9 UV6 B 802 " ideal model delta sigma weight residual 112.50 102.86 9.64 3.00e+00 1.11e-01 1.03e+01 ... (remaining 13061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.97: 5605 18.97 - 37.95: 451 37.95 - 56.92: 128 56.92 - 75.90: 32 75.90 - 94.87: 8 Dihedral angle restraints: 6224 sinusoidal: 3152 harmonic: 3072 Sorted by residual: 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 93.00 165.67 -72.67 1 1.00e+01 1.00e-02 6.74e+01 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 93.00 165.63 -72.63 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS B 151 " pdb=" SG CYS B 151 " pdb=" SG CYS B 179 " pdb=" CB CYS B 179 " ideal model delta sinusoidal sigma weight residual 93.00 136.62 -43.62 1 1.00e+01 1.00e-02 2.65e+01 ... (remaining 6221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.366: 1464 0.366 - 0.733: 0 0.733 - 1.099: 0 1.099 - 1.466: 0 1.466 - 1.832: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C17 UV6 B 802 " pdb=" C12 UV6 B 802 " pdb=" C18 UV6 B 802 " pdb=" C5 UV6 B 802 " both_signs ideal model delta sigma weight residual False 2.54 0.71 1.83 2.00e-01 2.50e+01 8.39e+01 chirality pdb=" C17 UV6 A 801 " pdb=" C12 UV6 A 801 " pdb=" C18 UV6 A 801 " pdb=" C5 UV6 A 801 " both_signs ideal model delta sigma weight residual False 2.54 0.71 1.83 2.00e-01 2.50e+01 8.36e+01 chirality pdb=" C4' UV6 B 802 " pdb=" C3' UV6 B 802 " pdb=" C5' UV6 B 802 " pdb=" O5 UV6 B 802 " both_signs ideal model delta sigma weight residual False -2.25 -2.56 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 1463 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P COA B 803 " -0.270 2.00e-02 2.50e+03 2.22e-01 6.17e+02 pdb=" C9P COA B 803 " 0.078 2.00e-02 2.50e+03 pdb=" CAP COA B 803 " -0.185 2.00e-02 2.50e+03 pdb=" N8P COA B 803 " 0.366 2.00e-02 2.50e+03 pdb=" O9P COA B 803 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P COA A 802 " 0.246 2.00e-02 2.50e+03 2.02e-01 5.11e+02 pdb=" C9P COA A 802 " -0.071 2.00e-02 2.50e+03 pdb=" CAP COA A 802 " 0.174 2.00e-02 2.50e+03 pdb=" N8P COA A 802 " -0.329 2.00e-02 2.50e+03 pdb=" O9P COA A 802 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 373 " -0.031 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO A 374 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 374 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 374 " -0.025 5.00e-02 4.00e+02 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2563 2.82 - 3.34: 8120 3.34 - 3.86: 15385 3.86 - 4.38: 19408 4.38 - 4.90: 32858 Nonbonded interactions: 78334 Sorted by model distance: nonbonded pdb=" ND2 ASN B 506 " pdb=" O TRP B 566 " model vdw 2.302 3.120 nonbonded pdb=" ND2 ASN A 506 " pdb=" O TRP A 566 " model vdw 2.302 3.120 nonbonded pdb=" O LYS B 296 " pdb=" OG1 THR B 304 " model vdw 2.308 3.040 nonbonded pdb=" O LYS A 296 " pdb=" OG1 THR A 304 " model vdw 2.308 3.040 nonbonded pdb=" ND2 ASN A 286 " pdb=" O1 UV6 A 801 " model vdw 2.334 3.120 ... (remaining 78329 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 663 or resid 805 through 807 or resid 814 or re \ sid 819 through 820 or resid 824 or resid 829 through 830 or resid 832 or resid \ 835 through 838)) selection = (chain 'B' and (resid 75 through 663 or resid 805 through 807 or resid 814 or re \ sid 819 through 820 or resid 824 or resid 829 through 830 or resid 832 or resid \ 835 through 838)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.210 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 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 : 0.008 0.146 9796 Z= 0.377 Angle : 0.784 12.378 13108 Z= 0.345 Chirality : 0.083 1.832 1466 Planarity : 0.009 0.222 1468 Dihedral : 14.992 94.870 4242 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 1.43 (0.26), residues: 1054 helix: 1.80 (0.22), residues: 516 sheet: 1.63 (0.48), residues: 128 loop : -0.35 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 647 HIS 0.007 0.001 HIS A 633 PHE 0.015 0.002 PHE B 315 TYR 0.010 0.002 TYR B 481 ARG 0.004 0.001 ARG A 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 6) link_NAG-ASN : angle 2.84542 ( 18) link_BETA1-4 : bond 0.00316 ( 4) link_BETA1-4 : angle 0.92453 ( 12) hydrogen bonds : bond 0.15813 ( 483) hydrogen bonds : angle 5.58046 ( 1365) SS BOND : bond 0.00410 ( 6) SS BOND : angle 2.31395 ( 12) covalent geometry : bond 0.00830 ( 9780) covalent geometry : angle 0.77420 (13066) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 478 ASP cc_start: 0.8236 (m-30) cc_final: 0.8029 (m-30) REVERT: B 185 GLU cc_start: 0.7850 (tt0) cc_final: 0.7599 (tt0) REVERT: B 412 ARG cc_start: 0.7583 (ptt-90) cc_final: 0.6596 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 1.4330 time to fit residues: 157.2877 Evaluate side-chains 78 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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: 0.8980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 286 ASN A 358 ASN A 491 HIS A 624 GLN B 87 HIS B 286 ASN B 358 ASN B 491 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111071 restraints weight = 8896.395| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.36 r_work: 0.2983 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9796 Z= 0.144 Angle : 0.576 6.502 13108 Z= 0.282 Chirality : 0.042 0.131 1466 Planarity : 0.004 0.044 1468 Dihedral : 12.954 80.780 2332 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.30 % Allowed : 6.82 % Favored : 91.88 % 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 (0.26), residues: 1054 helix: 2.54 (0.23), residues: 502 sheet: 1.62 (0.47), residues: 128 loop : -0.37 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.005 0.001 HIS A 633 PHE 0.016 0.002 PHE B 315 TYR 0.014 0.001 TYR A 570 ARG 0.006 0.000 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 6) link_NAG-ASN : angle 2.06959 ( 18) link_BETA1-4 : bond 0.00259 ( 4) link_BETA1-4 : angle 1.25109 ( 12) hydrogen bonds : bond 0.05376 ( 483) hydrogen bonds : angle 4.14724 ( 1365) SS BOND : bond 0.00251 ( 6) SS BOND : angle 0.99808 ( 12) covalent geometry : bond 0.00333 ( 9780) covalent geometry : angle 0.56935 (13066) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7027 (tmtt) REVERT: A 180 ASP cc_start: 0.8241 (p0) cc_final: 0.8016 (p0) REVERT: A 478 ASP cc_start: 0.8191 (m-30) cc_final: 0.7990 (m-30) REVERT: A 628 LYS cc_start: 0.7835 (mttt) cc_final: 0.6870 (mmtt) REVERT: B 185 GLU cc_start: 0.8116 (tt0) cc_final: 0.7751 (tt0) REVERT: B 410 SER cc_start: 0.9005 (t) cc_final: 0.8641 (t) outliers start: 12 outliers final: 2 residues processed: 96 average time/residue: 1.1497 time to fit residues: 119.0559 Evaluate side-chains 83 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 422 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105864 restraints weight = 9134.774| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.38 r_work: 0.2904 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 9796 Z= 0.345 Angle : 0.797 11.568 13108 Z= 0.380 Chirality : 0.053 0.198 1466 Planarity : 0.006 0.052 1468 Dihedral : 14.162 82.844 2332 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.16 % Allowed : 8.23 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.25), residues: 1054 helix: 1.88 (0.22), residues: 504 sheet: 1.44 (0.46), residues: 128 loop : -0.45 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 647 HIS 0.007 0.002 HIS A 633 PHE 0.018 0.002 PHE B 315 TYR 0.017 0.003 TYR A 570 ARG 0.008 0.001 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 6) link_NAG-ASN : angle 2.75499 ( 18) link_BETA1-4 : bond 0.00372 ( 4) link_BETA1-4 : angle 1.52931 ( 12) hydrogen bonds : bond 0.07502 ( 483) hydrogen bonds : angle 4.51465 ( 1365) SS BOND : bond 0.00336 ( 6) SS BOND : angle 1.46238 ( 12) covalent geometry : bond 0.00866 ( 9780) covalent geometry : angle 0.78948 (13066) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.6987 (tmtt) REVERT: A 152 ARG cc_start: 0.8054 (ttt-90) cc_final: 0.7778 (ttt-90) REVERT: A 180 ASP cc_start: 0.8304 (p0) cc_final: 0.8024 (p0) REVERT: A 478 ASP cc_start: 0.8244 (m-30) cc_final: 0.8032 (m-30) REVERT: A 628 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.6920 (mmtt) REVERT: B 185 GLU cc_start: 0.8164 (tt0) cc_final: 0.7878 (tt0) REVERT: B 410 SER cc_start: 0.9057 (t) cc_final: 0.8685 (t) outliers start: 20 outliers final: 8 residues processed: 92 average time/residue: 1.1875 time to fit residues: 117.6655 Evaluate side-chains 91 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 663 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 117 GLN B 184 ASN 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 = 0.143580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.109238 restraints weight = 9020.311| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.37 r_work: 0.3029 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9796 Z= 0.148 Angle : 0.558 6.984 13108 Z= 0.275 Chirality : 0.042 0.127 1466 Planarity : 0.004 0.047 1468 Dihedral : 13.177 79.723 2332 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.27 % Allowed : 9.09 % Favored : 88.64 % 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: 1.84 (0.25), residues: 1054 helix: 2.47 (0.22), residues: 502 sheet: 1.43 (0.44), residues: 128 loop : -0.40 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.006 0.001 HIS B 614 PHE 0.016 0.001 PHE A 315 TYR 0.013 0.002 TYR A 570 ARG 0.005 0.000 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 6) link_NAG-ASN : angle 2.25125 ( 18) link_BETA1-4 : bond 0.00413 ( 4) link_BETA1-4 : angle 1.45814 ( 12) hydrogen bonds : bond 0.05280 ( 483) hydrogen bonds : angle 4.06041 ( 1365) SS BOND : bond 0.00607 ( 6) SS BOND : angle 0.86759 ( 12) covalent geometry : bond 0.00348 ( 9780) covalent geometry : angle 0.55023 (13066) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7022 (tmtt) REVERT: A 152 ARG cc_start: 0.8090 (ttt-90) cc_final: 0.7815 (ttt-90) REVERT: A 478 ASP cc_start: 0.8225 (m-30) cc_final: 0.8014 (m-30) REVERT: A 493 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: B 185 GLU cc_start: 0.8193 (tt0) cc_final: 0.7958 (tt0) REVERT: B 410 SER cc_start: 0.9041 (t) cc_final: 0.8769 (t) REVERT: B 663 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7780 (pt) outliers start: 21 outliers final: 4 residues processed: 83 average time/residue: 1.3237 time to fit residues: 117.7384 Evaluate side-chains 79 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 663 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108406 restraints weight = 9067.548| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.38 r_work: 0.2956 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9796 Z= 0.187 Angle : 0.597 7.808 13108 Z= 0.291 Chirality : 0.044 0.140 1466 Planarity : 0.004 0.041 1468 Dihedral : 13.046 80.348 2332 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.06 % Allowed : 10.28 % 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 (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: 1.79 (0.25), residues: 1054 helix: 2.41 (0.22), residues: 502 sheet: 1.46 (0.44), residues: 128 loop : -0.42 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 647 HIS 0.007 0.001 HIS B 614 PHE 0.016 0.002 PHE B 315 TYR 0.013 0.002 TYR A 570 ARG 0.004 0.000 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 6) link_NAG-ASN : angle 2.27943 ( 18) link_BETA1-4 : bond 0.00322 ( 4) link_BETA1-4 : angle 1.45432 ( 12) hydrogen bonds : bond 0.05652 ( 483) hydrogen bonds : angle 4.08346 ( 1365) SS BOND : bond 0.00213 ( 6) SS BOND : angle 0.95239 ( 12) covalent geometry : bond 0.00458 ( 9780) covalent geometry : angle 0.58940 (13066) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.6943 (tmtt) REVERT: A 152 ARG cc_start: 0.8090 (ttt-90) cc_final: 0.7768 (ttt180) REVERT: A 478 ASP cc_start: 0.8234 (m-30) cc_final: 0.8028 (m-30) REVERT: A 493 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: B 170 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6296 (tt) REVERT: B 185 GLU cc_start: 0.8196 (tt0) cc_final: 0.7970 (tt0) REVERT: B 410 SER cc_start: 0.9093 (t) cc_final: 0.8687 (t) REVERT: B 412 ARG cc_start: 0.7833 (ptt90) cc_final: 0.7472 (mtm180) REVERT: B 663 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7771 (pt) outliers start: 19 outliers final: 6 residues processed: 83 average time/residue: 1.2273 time to fit residues: 109.6699 Evaluate side-chains 85 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 663 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 3 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110263 restraints weight = 9058.440| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.36 r_work: 0.3042 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9796 Z= 0.134 Angle : 0.523 6.476 13108 Z= 0.259 Chirality : 0.041 0.128 1466 Planarity : 0.004 0.039 1468 Dihedral : 12.481 79.133 2332 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.73 % Allowed : 11.36 % Favored : 86.90 % 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: 2.02 (0.25), residues: 1054 helix: 2.68 (0.23), residues: 502 sheet: 1.44 (0.44), residues: 128 loop : -0.37 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 PHE 0.016 0.001 PHE A 315 TYR 0.012 0.001 TYR A 570 ARG 0.003 0.000 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 6) link_NAG-ASN : angle 2.04054 ( 18) link_BETA1-4 : bond 0.00314 ( 4) link_BETA1-4 : angle 1.36810 ( 12) hydrogen bonds : bond 0.04834 ( 483) hydrogen bonds : angle 3.89690 ( 1365) SS BOND : bond 0.00288 ( 6) SS BOND : angle 0.78309 ( 12) covalent geometry : bond 0.00316 ( 9780) covalent geometry : angle 0.51576 (13066) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.6939 (tmtt) REVERT: A 152 ARG cc_start: 0.8065 (ttt-90) cc_final: 0.7856 (ttt-90) REVERT: A 493 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: B 170 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6581 (mm) REVERT: B 185 GLU cc_start: 0.8221 (tt0) cc_final: 0.7992 (tt0) REVERT: B 410 SER cc_start: 0.9038 (t) cc_final: 0.8687 (t) REVERT: B 412 ARG cc_start: 0.7821 (ptt90) cc_final: 0.7441 (mtm180) REVERT: B 663 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7736 (pt) outliers start: 16 outliers final: 5 residues processed: 81 average time/residue: 1.2919 time to fit residues: 112.4476 Evaluate side-chains 80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 663 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 76 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 77 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN A 491 HIS B 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.145348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.113348 restraints weight = 9115.879| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.42 r_work: 0.3005 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1719 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= 0.118 Angle : 0.496 6.486 13108 Z= 0.247 Chirality : 0.040 0.127 1466 Planarity : 0.004 0.038 1468 Dihedral : 11.879 79.898 2332 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.62 % Allowed : 12.34 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.26), residues: 1054 helix: 2.81 (0.23), residues: 502 sheet: 1.47 (0.43), residues: 128 loop : -0.33 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.006 0.001 HIS A 614 PHE 0.015 0.001 PHE A 315 TYR 0.012 0.001 TYR A 570 ARG 0.004 0.000 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 6) link_NAG-ASN : angle 1.83613 ( 18) link_BETA1-4 : bond 0.00337 ( 4) link_BETA1-4 : angle 1.31088 ( 12) hydrogen bonds : bond 0.04464 ( 483) hydrogen bonds : angle 3.79426 ( 1365) SS BOND : bond 0.00211 ( 6) SS BOND : angle 0.70705 ( 12) covalent geometry : bond 0.00272 ( 9780) covalent geometry : angle 0.49021 (13066) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 152 ARG cc_start: 0.8081 (ttt-90) cc_final: 0.7860 (ttt-90) REVERT: A 184 ASN cc_start: 0.8652 (m110) cc_final: 0.8438 (m-40) REVERT: A 493 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: B 170 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6611 (mm) REVERT: B 185 GLU cc_start: 0.8237 (tt0) cc_final: 0.7978 (tt0) REVERT: B 410 SER cc_start: 0.9035 (t) cc_final: 0.8689 (t) REVERT: B 412 ARG cc_start: 0.7769 (ptt90) cc_final: 0.7392 (mpp-170) outliers start: 15 outliers final: 2 residues processed: 77 average time/residue: 1.2067 time to fit residues: 100.6466 Evaluate side-chains 72 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 170 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.109570 restraints weight = 9213.337| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.36 r_work: 0.3046 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9796 Z= 0.152 Angle : 0.539 6.669 13108 Z= 0.266 Chirality : 0.042 0.128 1466 Planarity : 0.004 0.040 1468 Dihedral : 11.999 81.252 2332 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.19 % Allowed : 12.66 % Favored : 86.15 % 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: 2.06 (0.25), residues: 1054 helix: 2.67 (0.22), residues: 502 sheet: 1.53 (0.44), residues: 128 loop : -0.33 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.008 0.001 HIS A 614 PHE 0.015 0.001 PHE A 322 TYR 0.013 0.002 TYR A 570 ARG 0.003 0.000 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 6) link_NAG-ASN : angle 2.00605 ( 18) link_BETA1-4 : bond 0.00327 ( 4) link_BETA1-4 : angle 1.32294 ( 12) hydrogen bonds : bond 0.05086 ( 483) hydrogen bonds : angle 3.90273 ( 1365) SS BOND : bond 0.00204 ( 6) SS BOND : angle 0.79657 ( 12) covalent geometry : bond 0.00364 ( 9780) covalent geometry : angle 0.53295 (13066) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 152 ARG cc_start: 0.8096 (ttt-90) cc_final: 0.7880 (ttt-90) REVERT: A 493 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: B 170 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6601 (mm) REVERT: B 185 GLU cc_start: 0.8228 (tt0) cc_final: 0.7981 (tt0) REVERT: B 410 SER cc_start: 0.9028 (t) cc_final: 0.8670 (t) REVERT: B 412 ARG cc_start: 0.7804 (ptt90) cc_final: 0.7408 (mpp-170) REVERT: B 663 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7709 (pt) outliers start: 11 outliers final: 3 residues processed: 77 average time/residue: 1.2503 time to fit residues: 103.7697 Evaluate side-chains 77 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 663 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.144098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.109904 restraints weight = 9032.664| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.36 r_work: 0.3013 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9796 Z= 0.147 Angle : 0.529 6.520 13108 Z= 0.262 Chirality : 0.041 0.127 1466 Planarity : 0.004 0.040 1468 Dihedral : 11.898 81.705 2332 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.97 % Allowed : 13.10 % Favored : 85.93 % 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: 2.07 (0.25), residues: 1054 helix: 2.69 (0.22), residues: 502 sheet: 1.52 (0.43), residues: 128 loop : -0.32 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.008 0.001 HIS A 614 PHE 0.015 0.001 PHE A 315 TYR 0.012 0.002 TYR A 570 ARG 0.003 0.000 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 6) link_NAG-ASN : angle 1.97496 ( 18) link_BETA1-4 : bond 0.00336 ( 4) link_BETA1-4 : angle 1.31402 ( 12) hydrogen bonds : bond 0.04977 ( 483) hydrogen bonds : angle 3.88142 ( 1365) SS BOND : bond 0.00217 ( 6) SS BOND : angle 0.76934 ( 12) covalent geometry : bond 0.00351 ( 9780) covalent geometry : angle 0.52316 (13066) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 152 ARG cc_start: 0.8081 (ttt-90) cc_final: 0.7869 (ttt-90) REVERT: B 170 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6637 (mm) REVERT: B 185 GLU cc_start: 0.8249 (tt0) cc_final: 0.7976 (tt0) REVERT: B 410 SER cc_start: 0.9039 (t) cc_final: 0.8687 (t) REVERT: B 412 ARG cc_start: 0.7833 (ptt90) cc_final: 0.7455 (mpp-170) REVERT: B 663 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7715 (pt) outliers start: 9 outliers final: 5 residues processed: 76 average time/residue: 1.2835 time to fit residues: 105.0440 Evaluate side-chains 76 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 663 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 94 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 0.0470 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.141508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.107315 restraints weight = 9177.868| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.37 r_work: 0.3011 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 9796 Z= 0.248 Angle : 0.662 9.135 13108 Z= 0.320 Chirality : 0.047 0.163 1466 Planarity : 0.005 0.044 1468 Dihedral : 12.833 85.700 2332 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.30 % Allowed : 12.55 % Favored : 86.15 % 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: 1.72 (0.25), residues: 1054 helix: 2.27 (0.22), residues: 504 sheet: 1.46 (0.44), residues: 128 loop : -0.36 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 647 HIS 0.012 0.002 HIS A 614 PHE 0.017 0.002 PHE A 322 TYR 0.015 0.002 TYR A 570 ARG 0.003 0.001 ARG B 372 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 6) link_NAG-ASN : angle 2.44557 ( 18) link_BETA1-4 : bond 0.00310 ( 4) link_BETA1-4 : angle 1.40273 ( 12) hydrogen bonds : bond 0.06319 ( 483) hydrogen bonds : angle 4.16495 ( 1365) SS BOND : bond 0.00197 ( 6) SS BOND : angle 1.14759 ( 12) covalent geometry : bond 0.00615 ( 9780) covalent geometry : angle 0.65481 (13066) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 152 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.7905 (ttt-90) REVERT: B 170 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6684 (mm) REVERT: B 185 GLU cc_start: 0.8218 (tt0) cc_final: 0.7998 (tt0) REVERT: B 410 SER cc_start: 0.9056 (t) cc_final: 0.8695 (t) REVERT: B 412 ARG cc_start: 0.7905 (ptt90) cc_final: 0.7517 (mpp-170) REVERT: B 663 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7730 (pt) outliers start: 12 outliers final: 2 residues processed: 84 average time/residue: 1.2581 time to fit residues: 113.6612 Evaluate side-chains 80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 663 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 76 optimal weight: 0.9990 chunk 98 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.144508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.110290 restraints weight = 9092.626| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.36 r_work: 0.3055 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1760 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= 0.126 Angle : 0.512 6.518 13108 Z= 0.255 Chirality : 0.040 0.130 1466 Planarity : 0.004 0.040 1468 Dihedral : 12.025 82.236 2332 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.43 % Allowed : 13.53 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.25), residues: 1054 helix: 2.69 (0.22), residues: 502 sheet: 1.53 (0.44), residues: 128 loop : -0.31 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 647 HIS 0.006 0.001 HIS A 614 PHE 0.014 0.001 PHE A 315 TYR 0.013 0.001 TYR A 570 ARG 0.003 0.000 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 6) link_NAG-ASN : angle 2.00875 ( 18) link_BETA1-4 : bond 0.00278 ( 4) link_BETA1-4 : angle 1.30409 ( 12) hydrogen bonds : bond 0.04777 ( 483) hydrogen bonds : angle 3.87226 ( 1365) SS BOND : bond 0.00232 ( 6) SS BOND : angle 0.73559 ( 12) covalent geometry : bond 0.00289 ( 9780) covalent geometry : angle 0.50547 (13066) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6384.25 seconds wall clock time: 111 minutes 18.37 seconds (6678.37 seconds total)