Starting phenix.real_space_refine on Sun Jul 27 19:09:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jl4_36388/07_2025/8jl4_36388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jl4_36388/07_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_36388/07_2025/8jl4_36388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jl4_36388/07_2025/8jl4_36388.map" model { file = "/net/cci-nas-00/data/ceres_data/8jl4_36388/07_2025/8jl4_36388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jl4_36388/07_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-5711/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: 8.42, per 1000 atoms: 0.88 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: 2.98 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: 0.92 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: 2.91 Time building geometry restraints manager: 3.41 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: 4.390 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.100 Find NCS groups from input model: 0.530 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:14.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.460 ------------------------------------------------------------------------------- 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 : 1.017 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: 1.5267 time to fit residues: 167.3705 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 : 1.004 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.111072 restraints weight = 8896.395| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.36 r_work: 0.2984 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 : 1.062 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.6995 (tmtt) REVERT: A 180 ASP cc_start: 0.8224 (p0) cc_final: 0.7998 (p0) REVERT: A 478 ASP cc_start: 0.8190 (m-30) cc_final: 0.7989 (m-30) REVERT: A 628 LYS cc_start: 0.7834 (mttt) cc_final: 0.6868 (mmtt) REVERT: B 185 GLU cc_start: 0.8110 (tt0) cc_final: 0.7741 (tt0) REVERT: B 410 SER cc_start: 0.9001 (t) cc_final: 0.8633 (t) outliers start: 12 outliers final: 2 residues processed: 96 average time/residue: 1.2013 time to fit residues: 124.4100 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 : 0.953 ------------------------------------------------------------------------------- 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: 2.9990 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: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 358 ASN B 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.105387 restraints weight = 9133.566| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.39 r_work: 0.2898 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.100 9796 Z= 0.366 Angle : 0.825 11.935 13108 Z= 0.392 Chirality : 0.054 0.206 1466 Planarity : 0.006 0.055 1468 Dihedral : 14.301 83.573 2332 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.16 % Allowed : 8.44 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1054 helix: 1.80 (0.22), residues: 504 sheet: 1.43 (0.46), residues: 128 loop : -0.46 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 647 HIS 0.007 0.002 HIS A 633 PHE 0.017 0.003 PHE B 315 TYR 0.018 0.003 TYR B 496 ARG 0.008 0.001 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 6) link_NAG-ASN : angle 2.81259 ( 18) link_BETA1-4 : bond 0.00325 ( 4) link_BETA1-4 : angle 1.56876 ( 12) hydrogen bonds : bond 0.07711 ( 483) hydrogen bonds : angle 4.55600 ( 1365) SS BOND : bond 0.00464 ( 6) SS BOND : angle 1.50792 ( 12) covalent geometry : bond 0.00915 ( 9780) covalent geometry : angle 0.81736 (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 : 0.980 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7021 (tmtt) REVERT: A 152 ARG cc_start: 0.8069 (ttt-90) cc_final: 0.7792 (ttt-90) REVERT: A 180 ASP cc_start: 0.8336 (p0) cc_final: 0.8055 (p0) REVERT: A 478 ASP cc_start: 0.8245 (m-30) cc_final: 0.8034 (m-30) REVERT: A 628 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.6930 (mmtt) REVERT: B 185 GLU cc_start: 0.8184 (tt0) cc_final: 0.7893 (tt0) REVERT: B 410 SER cc_start: 0.9078 (t) cc_final: 0.8658 (t) outliers start: 20 outliers final: 7 residues processed: 92 average time/residue: 1.2384 time to fit residues: 122.6539 Evaluate side-chains 91 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 358 ASN B 117 GLN B 184 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.143345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.108958 restraints weight = 9013.334| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.37 r_work: 0.3026 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9796 Z= 0.147 Angle : 0.564 7.395 13108 Z= 0.277 Chirality : 0.042 0.131 1466 Planarity : 0.004 0.047 1468 Dihedral : 13.335 80.176 2332 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.38 % Allowed : 9.20 % Favored : 88.42 % 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: 1.81 (0.25), residues: 1054 helix: 2.44 (0.22), residues: 502 sheet: 1.41 (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 0.005 0.001 HIS B 614 PHE 0.016 0.001 PHE A 315 TYR 0.013 0.001 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 2.32368 ( 18) link_BETA1-4 : bond 0.00325 ( 4) link_BETA1-4 : angle 1.44939 ( 12) hydrogen bonds : bond 0.05334 ( 483) hydrogen bonds : angle 4.09353 ( 1365) SS BOND : bond 0.00162 ( 6) SS BOND : angle 0.84940 ( 12) covalent geometry : bond 0.00348 ( 9780) covalent geometry : angle 0.55566 (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 97 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7002 (tmtt) REVERT: A 152 ARG cc_start: 0.8088 (ttt-90) cc_final: 0.7813 (ttt-90) REVERT: A 478 ASP cc_start: 0.8233 (m-30) cc_final: 0.8023 (m-30) REVERT: A 493 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: B 170 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6392 (tt) REVERT: B 185 GLU cc_start: 0.8203 (tt0) cc_final: 0.7942 (tt0) REVERT: B 410 SER cc_start: 0.9050 (t) cc_final: 0.8751 (t) REVERT: B 663 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7805 (pt) outliers start: 22 outliers final: 4 residues processed: 84 average time/residue: 1.3301 time to fit residues: 119.8614 Evaluate side-chains 82 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 170 ILE 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: 0.0970 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: 0.9980 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 0.0170 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.109921 restraints weight = 9056.451| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.37 r_work: 0.2982 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9796 Z= 0.140 Angle : 0.532 6.477 13108 Z= 0.264 Chirality : 0.041 0.128 1466 Planarity : 0.004 0.040 1468 Dihedral : 12.619 79.033 2332 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.95 % Allowed : 10.50 % Favored : 87.55 % 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: 2.00 (0.25), residues: 1054 helix: 2.65 (0.22), residues: 502 sheet: 1.43 (0.44), residues: 128 loop : -0.36 (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 B 614 PHE 0.015 0.001 PHE B 315 TYR 0.013 0.001 TYR A 570 ARG 0.004 0.000 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 6) link_NAG-ASN : angle 2.04697 ( 18) link_BETA1-4 : bond 0.00313 ( 4) link_BETA1-4 : angle 1.40876 ( 12) hydrogen bonds : bond 0.04919 ( 483) hydrogen bonds : angle 3.92423 ( 1365) SS BOND : bond 0.00205 ( 6) SS BOND : angle 0.78750 ( 12) covalent geometry : bond 0.00332 ( 9780) covalent geometry : angle 0.52535 (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 92 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.6922 (tmtt) REVERT: A 152 ARG cc_start: 0.8073 (ttt-90) cc_final: 0.7829 (ttt-90) REVERT: A 478 ASP cc_start: 0.8237 (m-30) cc_final: 0.8031 (m-30) REVERT: A 493 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: B 185 GLU cc_start: 0.8202 (tt0) cc_final: 0.7977 (tt0) REVERT: B 410 SER cc_start: 0.9040 (t) cc_final: 0.8673 (t) REVERT: B 412 ARG cc_start: 0.7795 (ptt90) cc_final: 0.7397 (mtm180) REVERT: B 663 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7758 (pt) outliers start: 18 outliers final: 4 residues processed: 82 average time/residue: 1.2834 time to fit residues: 113.4598 Evaluate side-chains 78 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 330 GLN 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: 2.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.142328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.108113 restraints weight = 9072.154| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.37 r_work: 0.3021 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9796 Z= 0.211 Angle : 0.619 8.184 13108 Z= 0.301 Chirality : 0.045 0.146 1466 Planarity : 0.004 0.042 1468 Dihedral : 12.979 80.930 2332 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.06 % Allowed : 11.58 % Favored : 86.36 % 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: 1.76 (0.25), residues: 1054 helix: 2.37 (0.22), residues: 502 sheet: 1.44 (0.44), residues: 128 loop : -0.42 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 647 HIS 0.009 0.001 HIS A 614 PHE 0.016 0.002 PHE B 315 TYR 0.014 0.002 TYR A 570 ARG 0.003 0.000 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 6) link_NAG-ASN : angle 2.30329 ( 18) link_BETA1-4 : bond 0.00301 ( 4) link_BETA1-4 : angle 1.42188 ( 12) hydrogen bonds : bond 0.05878 ( 483) hydrogen bonds : angle 4.10028 ( 1365) SS BOND : bond 0.00214 ( 6) SS BOND : angle 1.02947 ( 12) covalent geometry : bond 0.00521 ( 9780) covalent geometry : angle 0.61189 (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 95 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.6933 (tmtt) REVERT: A 152 ARG cc_start: 0.8094 (ttt-90) cc_final: 0.7865 (ttt-90) REVERT: A 478 ASP cc_start: 0.8222 (m-30) cc_final: 0.8014 (m-30) REVERT: B 170 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6574 (mm) REVERT: B 185 GLU cc_start: 0.8226 (tt0) cc_final: 0.8003 (tt0) REVERT: B 410 SER cc_start: 0.9080 (t) cc_final: 0.8681 (t) REVERT: B 412 ARG cc_start: 0.7855 (ptt90) cc_final: 0.7482 (mtm180) REVERT: B 663 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7744 (pt) outliers start: 19 outliers final: 7 residues processed: 86 average time/residue: 1.2497 time to fit residues: 115.7586 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 : 0.997 ------------------------------------------------------------------------------- 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 614 HIS 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 183 VAL 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: 0.0370 chunk 76 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 0.0970 chunk 77 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 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 = 0.3619 r_free = 0.3619 target = 0.145548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111556 restraints weight = 9131.888| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.35 r_work: 0.3014 rms_B_bonded: 1.99 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: 0.8466 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9796 Z= 0.113 Angle : 0.491 6.458 13108 Z= 0.245 Chirality : 0.040 0.128 1466 Planarity : 0.004 0.038 1468 Dihedral : 12.121 78.399 2332 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.62 % Allowed : 12.12 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.13 (0.26), residues: 1054 helix: 2.80 (0.23), residues: 502 sheet: 1.44 (0.43), residues: 128 loop : -0.34 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.005 0.001 HIS A 614 PHE 0.014 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 0.00226 ( 6) link_NAG-ASN : angle 1.89165 ( 18) link_BETA1-4 : bond 0.00347 ( 4) link_BETA1-4 : angle 1.33673 ( 12) hydrogen bonds : bond 0.04434 ( 483) hydrogen bonds : angle 3.80758 ( 1365) SS BOND : bond 0.00424 ( 6) SS BOND : angle 0.66045 ( 12) covalent geometry : bond 0.00253 ( 9780) covalent geometry : angle 0.48489 (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 87 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.6934 (tmtt) REVERT: A 478 ASP cc_start: 0.8165 (m-30) cc_final: 0.7951 (m-30) REVERT: A 493 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: A 630 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8455 (m-40) REVERT: B 170 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6620 (mm) REVERT: B 185 GLU cc_start: 0.8243 (tt0) cc_final: 0.8015 (tt0) REVERT: B 410 SER cc_start: 0.9014 (t) cc_final: 0.8675 (t) REVERT: B 412 ARG cc_start: 0.7772 (ptt90) cc_final: 0.7395 (mpp-170) outliers start: 15 outliers final: 2 residues processed: 78 average time/residue: 1.2492 time to fit residues: 105.1311 Evaluate side-chains 75 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 493 GLU Chi-restraints excluded: chain A residue 630 ASN 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: 0.7980 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.143351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.109185 restraints weight = 9215.379| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.35 r_work: 0.3039 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9796 Z= 0.169 Angle : 0.562 7.149 13108 Z= 0.276 Chirality : 0.043 0.136 1466 Planarity : 0.004 0.040 1468 Dihedral : 12.342 81.262 2332 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.08 % Allowed : 12.99 % 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: 1.98 (0.25), residues: 1054 helix: 2.60 (0.22), residues: 502 sheet: 1.46 (0.43), residues: 128 loop : -0.34 (0.28), 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 B 315 TYR 0.013 0.002 TYR A 570 ARG 0.002 0.000 ARG B 372 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 6) link_NAG-ASN : angle 2.09922 ( 18) link_BETA1-4 : bond 0.00329 ( 4) link_BETA1-4 : angle 1.37144 ( 12) hydrogen bonds : bond 0.05340 ( 483) hydrogen bonds : angle 3.95766 ( 1365) SS BOND : bond 0.00214 ( 6) SS BOND : angle 0.84845 ( 12) covalent geometry : bond 0.00411 ( 9780) covalent geometry : angle 0.55545 (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 81 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 152 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7720 (ttt-90) REVERT: A 478 ASP cc_start: 0.8236 (m-30) cc_final: 0.8029 (m-30) REVERT: B 170 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6628 (mm) REVERT: B 185 GLU cc_start: 0.8225 (tt0) cc_final: 0.8013 (tt0) REVERT: B 410 SER cc_start: 0.9037 (t) cc_final: 0.8660 (t) REVERT: B 412 ARG cc_start: 0.7867 (ptt90) cc_final: 0.7481 (mpp-170) outliers start: 10 outliers final: 4 residues processed: 77 average time/residue: 1.3175 time to fit residues: 109.2616 Evaluate side-chains 76 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 170 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 80 optimal weight: 0.0270 chunk 2 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.145338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111224 restraints weight = 9001.597| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.35 r_work: 0.3057 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9796 Z= 0.117 Angle : 0.494 6.469 13108 Z= 0.247 Chirality : 0.040 0.128 1466 Planarity : 0.004 0.039 1468 Dihedral : 11.735 79.933 2332 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.87 % Allowed : 13.20 % 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: 2.18 (0.26), residues: 1054 helix: 2.82 (0.23), residues: 502 sheet: 1.50 (0.43), residues: 128 loop : -0.29 (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 0.012 0.001 TYR A 570 ARG 0.001 0.000 ARG B 372 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 6) link_NAG-ASN : angle 1.84762 ( 18) link_BETA1-4 : bond 0.00358 ( 4) link_BETA1-4 : angle 1.29508 ( 12) hydrogen bonds : bond 0.04491 ( 483) hydrogen bonds : angle 3.79309 ( 1365) SS BOND : bond 0.00221 ( 6) SS BOND : angle 0.67587 ( 12) covalent geometry : bond 0.00267 ( 9780) covalent geometry : angle 0.48765 (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 76 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 478 ASP cc_start: 0.8176 (m-30) cc_final: 0.7964 (m-30) REVERT: B 170 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6636 (mm) REVERT: B 185 GLU cc_start: 0.8247 (tt0) cc_final: 0.7989 (tt0) REVERT: B 410 SER cc_start: 0.9027 (t) cc_final: 0.8683 (t) REVERT: B 412 ARG cc_start: 0.7801 (ptt90) cc_final: 0.7416 (mpp-170) outliers start: 8 outliers final: 3 residues processed: 72 average time/residue: 1.2215 time to fit residues: 95.0659 Evaluate side-chains 71 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 170 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: 4.9990 chunk 77 optimal weight: 2.9990 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: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.140341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.106183 restraints weight = 9212.134| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.36 r_work: 0.2996 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 9796 Z= 0.338 Angle : 0.759 10.698 13108 Z= 0.363 Chirality : 0.052 0.199 1466 Planarity : 0.005 0.055 1468 Dihedral : 13.475 89.603 2332 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.08 % Allowed : 13.20 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1054 helix: 1.99 (0.22), residues: 504 sheet: 1.31 (0.43), residues: 128 loop : -0.39 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 647 HIS 0.009 0.002 HIS A 614 PHE 0.017 0.002 PHE A 322 TYR 0.018 0.003 TYR B 496 ARG 0.005 0.001 ARG B 372 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 6) link_NAG-ASN : angle 2.69063 ( 18) link_BETA1-4 : bond 0.00333 ( 4) link_BETA1-4 : angle 1.47071 ( 12) hydrogen bonds : bond 0.07155 ( 483) hydrogen bonds : angle 4.32022 ( 1365) SS BOND : bond 0.00239 ( 6) SS BOND : angle 1.34890 ( 12) covalent geometry : bond 0.00845 ( 9780) covalent geometry : angle 0.75167 (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 91 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 478 ASP cc_start: 0.8248 (m-30) cc_final: 0.8034 (m-30) REVERT: B 170 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6608 (mm) REVERT: B 185 GLU cc_start: 0.8135 (tt0) cc_final: 0.7900 (tt0) REVERT: B 412 ARG cc_start: 0.7909 (ptt90) cc_final: 0.7596 (mtm180) REVERT: B 663 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7712 (pt) outliers start: 10 outliers final: 4 residues processed: 87 average time/residue: 1.3114 time to fit residues: 122.4017 Evaluate side-chains 85 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 628 LYS 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: 0.9980 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.143734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.109562 restraints weight = 9109.750| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.37 r_work: 0.3045 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1739 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= 0.141 Angle : 0.537 6.696 13108 Z= 0.266 Chirality : 0.041 0.143 1466 Planarity : 0.004 0.041 1468 Dihedral : 12.565 84.867 2332 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.76 % Allowed : 13.42 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.25), residues: 1054 helix: 2.55 (0.22), residues: 502 sheet: 1.41 (0.43), residues: 128 loop : -0.34 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.007 0.001 HIS A 614 PHE 0.015 0.001 PHE A 315 TYR 0.013 0.002 TYR A 570 ARG 0.002 0.000 ARG B 267 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 6) link_NAG-ASN : angle 2.16396 ( 18) link_BETA1-4 : bond 0.00338 ( 4) link_BETA1-4 : angle 1.35477 ( 12) hydrogen bonds : bond 0.05056 ( 483) hydrogen bonds : angle 3.94054 ( 1365) SS BOND : bond 0.00259 ( 6) SS BOND : angle 0.80070 ( 12) covalent geometry : bond 0.00335 ( 9780) covalent geometry : angle 0.52992 (13066) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6641.37 seconds wall clock time: 114 minutes 23.33 seconds (6863.33 seconds total)