Starting phenix.real_space_refine on Tue May 13 17:56:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fq5_29378/05_2025/8fq5_29378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fq5_29378/05_2025/8fq5_29378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fq5_29378/05_2025/8fq5_29378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fq5_29378/05_2025/8fq5_29378.map" model { file = "/net/cci-nas-00/data/ceres_data/8fq5_29378/05_2025/8fq5_29378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fq5_29378/05_2025/8fq5_29378.cif" } resolution = 2.34 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= 0.004 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 S 77 5.16 5 Cl 4 4.86 5 C 7005 2.51 5 N 1709 2.21 5 O 2091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 10886 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Chain: "B" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 bond proxies already assigned to first conformer: 1253 Chain: "C" Number of atoms: 1183 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Conformer: "C" Number of residues, atoms: 148, 1159 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Chain: "D" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 bond proxies already assigned to first conformer: 1253 Chain: "E" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1467 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1467 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS A 589 " occ=0.58 ... (10 atoms not shown) pdb=" SG BCYS A 589 " occ=0.42 residue: pdb=" N ASER A 615 " occ=0.71 ... (10 atoms not shown) pdb=" OG BSER A 615 " occ=0.29 residue: pdb=" N ACYS B 589 " occ=0.89 ... (10 atoms not shown) pdb=" SG BCYS B 589 " occ=0.11 residue: pdb=" N ACYS C 589 " occ=0.21 ... (16 atoms not shown) pdb=" SG CCYS C 589 " occ=0.56 residue: pdb=" N ASER C 615 " occ=0.66 ... (10 atoms not shown) pdb=" OG BSER C 615 " occ=0.34 residue: pdb=" N ACYS D 589 " occ=0.83 ... (10 atoms not shown) pdb=" SG BCYS D 589 " occ=0.17 Time building chain proxies: 10.09, per 1000 atoms: 0.93 Number of scatterers: 10886 At special positions: 0 Unit cell: (114.73, 113.091, 91.784, 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) Cl 4 17.00 S 77 16.00 O 2091 8.00 N 1709 7.00 C 7005 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.9 seconds 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2522 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 73.4% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 826 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 618 Processing helix chain 'B' and resid 619 through 625 removed outlier: 3.604A pdb=" N THR B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 826 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 549 No H-bonds generated for 'chain 'C' and resid 547 through 549' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 625 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 826 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 618 Processing helix chain 'D' and resid 619 through 625 removed outlier: 3.621A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 826 Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 127 Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.893A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.587A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 29 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 127 removed outlier: 3.627A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.977A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY G 162 " --> pdb=" O SER G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.533A pdb=" N TYR G 181 " --> pdb=" O GLY G 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.790A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 129 Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.612A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 216 removed outlier: 3.593A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.844A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 129 Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.659A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 216 removed outlier: 3.617A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 551 through 552 Processing sheet with id=AA2, first strand: chain 'B' and resid 509 through 510 Processing sheet with id=AA3, first strand: chain 'C' and resid 551 through 552 Processing sheet with id=AA4, first strand: chain 'D' and resid 509 through 510 Processing sheet with id=AA5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AA6, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA7, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA8, first strand: chain 'H' and resid 77 through 79 859 hydrogen bonds defined for protein. 2483 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: 3.29 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3224 1.34 - 1.46: 2224 1.46 - 1.58: 5366 1.58 - 1.70: 0 1.70 - 1.81: 117 Bond restraints: 10931 Sorted by residual: bond pdb=" C VAL D 792 " pdb=" O VAL D 792 " ideal model delta sigma weight residual 1.236 1.249 -0.012 1.19e-02 7.06e+03 1.08e+00 bond pdb=" C VAL B 792 " pdb=" O VAL B 792 " ideal model delta sigma weight residual 1.236 1.248 -0.012 1.19e-02 7.06e+03 1.02e+00 bond pdb=" C PHE F 83 " pdb=" N PRO F 84 " ideal model delta sigma weight residual 1.326 1.339 -0.013 1.44e-02 4.82e+03 8.26e-01 bond pdb=" N LYS F 129 " pdb=" CA LYS F 129 " ideal model delta sigma weight residual 1.460 1.470 -0.010 1.39e-02 5.18e+03 5.32e-01 bond pdb=" C ALA F 87 " pdb=" N ASP F 88 " ideal model delta sigma weight residual 1.328 1.337 -0.009 1.30e-02 5.92e+03 4.90e-01 ... (remaining 10926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 14674 1.75 - 3.50: 116 3.50 - 5.25: 16 5.25 - 7.00: 1 7.00 - 8.75: 2 Bond angle restraints: 14809 Sorted by residual: angle pdb=" CB PRO D 512 " pdb=" CG PRO D 512 " pdb=" CD PRO D 512 " ideal model delta sigma weight residual 106.10 97.35 8.75 3.20e+00 9.77e-02 7.47e+00 angle pdb=" N ASP G 88 " pdb=" CA ASP G 88 " pdb=" C ASP G 88 " ideal model delta sigma weight residual 114.31 111.05 3.26 1.29e+00 6.01e-01 6.41e+00 angle pdb=" CA PRO D 512 " pdb=" N PRO D 512 " pdb=" CD PRO D 512 " ideal model delta sigma weight residual 112.00 108.61 3.39 1.40e+00 5.10e-01 5.85e+00 angle pdb=" CA PRO D 512 " pdb=" CB PRO D 512 " pdb=" CG PRO D 512 " ideal model delta sigma weight residual 104.50 99.99 4.51 1.90e+00 2.77e-01 5.63e+00 angle pdb=" C ASP H 86 " pdb=" N ALA H 87 " pdb=" CA ALA H 87 " ideal model delta sigma weight residual 121.54 125.66 -4.12 1.91e+00 2.74e-01 4.65e+00 ... (remaining 14804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5419 17.94 - 35.89: 616 35.89 - 53.83: 167 53.83 - 71.77: 22 71.77 - 89.72: 13 Dihedral angle restraints: 6237 sinusoidal: 2299 harmonic: 3938 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual -86.00 -128.03 42.03 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual -86.00 -122.67 36.67 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual -86.00 -121.18 35.18 1 1.00e+01 1.00e-02 1.75e+01 ... (remaining 6234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1065 0.027 - 0.054: 380 0.054 - 0.080: 171 0.080 - 0.107: 52 0.107 - 0.134: 7 Chirality restraints: 1675 Sorted by residual: chirality pdb=" CA PHE E 127 " pdb=" N PHE E 127 " pdb=" C PHE E 127 " pdb=" CB PHE E 127 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA PHE H 107 " pdb=" N PHE H 107 " pdb=" C PHE H 107 " pdb=" CB PHE H 107 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA VAL F 57 " pdb=" N VAL F 57 " pdb=" C VAL F 57 " pdb=" CB VAL F 57 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.24e-01 ... (remaining 1672 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 511 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.50e+00 pdb=" N PRO B 512 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 512 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 512 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 107 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.61e+00 pdb=" N PRO G 108 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO G 108 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 108 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 107 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.53e+00 pdb=" N PRO E 108 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " 0.018 5.00e-02 4.00e+02 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1042 2.74 - 3.28: 10912 3.28 - 3.82: 20498 3.82 - 4.36: 21678 4.36 - 4.90: 38001 Nonbonded interactions: 92131 Sorted by model distance: nonbonded pdb=" O THR G 30 " pdb=" O HOH G 501 " model vdw 2.202 3.040 nonbonded pdb=" O THR E 30 " pdb=" O HOH E 501 " model vdw 2.210 3.040 nonbonded pdb=" O VAL A 514 " pdb=" O HOH A 901 " model vdw 2.231 3.040 nonbonded pdb=" O HOH A 926 " pdb=" O HOH A 927 " model vdw 2.237 3.040 nonbonded pdb=" O HOH C 925 " pdb=" O HOH C 927 " model vdw 2.238 3.040 ... (remaining 92126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 511 through 552 or resid 564 through 588 or resid 590 thro \ ugh 614 or resid 616 through 826)) selection = (chain 'B' and (resid 511 through 588 or resid 590 through 614 or resid 616 thro \ ugh 626 or resid 784 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826)) selection = (chain 'C' and (resid 511 through 552 or resid 564 through 588 or resid 590 thro \ ugh 614 or resid 616 through 826)) selection = (chain 'D' and (resid 511 through 588 or resid 590 through 614 or resid 616 thro \ ugh 626 or resid 784 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826)) } ncs_group { reference = (chain 'E' and (resid 5 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 214 or resid 401)) selection = (chain 'F' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 214 or resid 401)) selection = (chain 'G' and (resid 5 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 214 or resid 401)) selection = (chain 'H' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 214 or resid 401)) } 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=0.11 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.470 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 : 0.002 0.033 10939 Z= 0.118 Angle : 0.441 8.747 14825 Z= 0.247 Chirality : 0.035 0.134 1675 Planarity : 0.003 0.047 1810 Dihedral : 16.557 89.716 3691 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.34 % Allowed : 22.25 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.07 (0.23), residues: 1339 helix: 3.81 (0.16), residues: 946 sheet: -1.75 (1.63), residues: 10 loop : -0.27 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 606 HIS 0.004 0.001 HIS E 205 PHE 0.018 0.001 PHE F 107 TYR 0.016 0.001 TYR A 523 ARG 0.005 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.10079 ( 859) hydrogen bonds : angle 3.82656 ( 2483) SS BOND : bond 0.00223 ( 8) SS BOND : angle 0.77237 ( 16) covalent geometry : bond 0.00226 (10931) covalent geometry : angle 0.44088 (14809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7661 (mm-40) REVERT: C 586 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7611 (mm-40) REVERT: F 99 ARG cc_start: 0.7289 (tpp-160) cc_final: 0.6785 (tpp-160) outliers start: 15 outliers final: 11 residues processed: 174 average time/residue: 1.2586 time to fit residues: 235.9957 Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 GLN Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain C residue 586 GLN Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 818 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 104 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 ASN F 149 ASN H 72 ASN H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.184570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.135641 restraints weight = 37000.340| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.27 r_work: 0.3054 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10939 Z= 0.125 Angle : 0.448 6.713 14825 Z= 0.250 Chirality : 0.036 0.133 1675 Planarity : 0.003 0.039 1810 Dihedral : 5.113 81.424 1489 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.14 % Allowed : 19.12 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.20 (0.23), residues: 1339 helix: 3.91 (0.16), residues: 946 sheet: -2.30 (1.35), residues: 10 loop : -0.21 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 178 HIS 0.004 0.001 HIS E 205 PHE 0.021 0.001 PHE E 97 TYR 0.014 0.001 TYR G 181 ARG 0.003 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.05049 ( 859) hydrogen bonds : angle 3.30061 ( 2483) SS BOND : bond 0.00206 ( 8) SS BOND : angle 0.81676 ( 16) covalent geometry : bond 0.00243 (10931) covalent geometry : angle 0.44727 (14809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.8029 (m-80) cc_final: 0.7804 (m-80) REVERT: C 514 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7264 (p) REVERT: G 97 PHE cc_start: 0.6486 (t80) cc_final: 0.6254 (t80) REVERT: F 65 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6948 (mtp85) REVERT: F 99 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6771 (tpp-160) REVERT: F 174 TYR cc_start: 0.8045 (p90) cc_final: 0.7820 (p90) REVERT: H 99 ARG cc_start: 0.7266 (mmt180) cc_final: 0.6741 (mmm160) outliers start: 24 outliers final: 14 residues processed: 182 average time/residue: 1.1887 time to fit residues: 233.5171 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 205 HIS F 149 ASN H 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.184439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.133457 restraints weight = 33345.612| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.39 r_work: 0.3045 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10939 Z= 0.121 Angle : 0.437 8.268 14825 Z= 0.244 Chirality : 0.036 0.131 1675 Planarity : 0.003 0.035 1810 Dihedral : 3.914 42.511 1478 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.59 % Allowed : 19.75 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.26 (0.23), residues: 1339 helix: 3.93 (0.16), residues: 946 sheet: 1.84 (1.50), residues: 10 loop : -0.24 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 178 HIS 0.005 0.001 HIS E 205 PHE 0.023 0.001 PHE E 97 TYR 0.014 0.001 TYR A 523 ARG 0.003 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.04903 ( 859) hydrogen bonds : angle 3.23069 ( 2483) SS BOND : bond 0.00213 ( 8) SS BOND : angle 0.60423 ( 16) covalent geometry : bond 0.00234 (10931) covalent geometry : angle 0.43704 (14809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.8002 (m-80) cc_final: 0.7774 (m-80) REVERT: D 549 TYR cc_start: 0.8035 (m-80) cc_final: 0.7832 (m-80) REVERT: G 97 PHE cc_start: 0.6302 (t80) cc_final: 0.6075 (t80) REVERT: F 65 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6920 (mtp85) REVERT: F 90 GLU cc_start: 0.1700 (OUTLIER) cc_final: 0.1407 (tt0) REVERT: F 99 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6784 (tpp-160) REVERT: F 174 TYR cc_start: 0.8019 (p90) cc_final: 0.7813 (p90) REVERT: F 204 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7193 (mtp180) REVERT: H 99 ARG cc_start: 0.7239 (mmt180) cc_final: 0.6658 (mmm160) REVERT: H 204 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7347 (mtp180) outliers start: 29 outliers final: 16 residues processed: 181 average time/residue: 1.2130 time to fit residues: 236.7922 Evaluate side-chains 179 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 204 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 ASN G 205 HIS F 149 ASN H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.185103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.134098 restraints weight = 39342.893| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.59 r_work: 0.3017 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10939 Z= 0.113 Angle : 0.417 5.880 14825 Z= 0.234 Chirality : 0.035 0.128 1675 Planarity : 0.003 0.035 1810 Dihedral : 3.762 41.529 1475 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.86 % Allowed : 19.39 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.32 (0.23), residues: 1339 helix: 3.98 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.21 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 178 HIS 0.004 0.001 HIS G 205 PHE 0.023 0.001 PHE E 97 TYR 0.015 0.001 TYR H 174 ARG 0.004 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 859) hydrogen bonds : angle 3.15131 ( 2483) SS BOND : bond 0.00187 ( 8) SS BOND : angle 0.48258 ( 16) covalent geometry : bond 0.00213 (10931) covalent geometry : angle 0.41682 (14809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.7917 (m-80) cc_final: 0.7697 (m-80) REVERT: D 549 TYR cc_start: 0.7982 (m-80) cc_final: 0.7704 (m-80) REVERT: E 208 LEU cc_start: 0.7093 (tp) cc_final: 0.6781 (tp) REVERT: F 65 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6908 (mtp85) REVERT: F 90 GLU cc_start: 0.1668 (OUTLIER) cc_final: 0.1373 (tt0) REVERT: F 99 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6673 (tpp-160) REVERT: H 99 ARG cc_start: 0.7207 (mmt180) cc_final: 0.6612 (tpp-160) outliers start: 32 outliers final: 21 residues processed: 193 average time/residue: 1.1280 time to fit residues: 235.3218 Evaluate side-chains 190 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 85 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 205 HIS F 72 ASN F 149 ASN H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.184471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.134176 restraints weight = 44263.775| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.59 r_work: 0.2999 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10939 Z= 0.118 Angle : 0.426 7.095 14825 Z= 0.239 Chirality : 0.035 0.128 1675 Planarity : 0.003 0.035 1810 Dihedral : 3.787 40.803 1475 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.59 % Allowed : 19.75 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.29 (0.23), residues: 1339 helix: 3.95 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.18 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 178 HIS 0.004 0.001 HIS G 205 PHE 0.025 0.001 PHE E 97 TYR 0.016 0.001 TYR C 523 ARG 0.006 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.04824 ( 859) hydrogen bonds : angle 3.17462 ( 2483) SS BOND : bond 0.00191 ( 8) SS BOND : angle 0.42309 ( 16) covalent geometry : bond 0.00227 (10931) covalent geometry : angle 0.42622 (14809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.7973 (m-80) cc_final: 0.7748 (m-80) REVERT: D 549 TYR cc_start: 0.7979 (m-80) cc_final: 0.7750 (m-80) REVERT: E 208 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6866 (tp) REVERT: G 208 LEU cc_start: 0.7063 (tp) cc_final: 0.6773 (tp) REVERT: F 65 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6931 (mtp85) REVERT: F 90 GLU cc_start: 0.1794 (OUTLIER) cc_final: 0.1481 (tt0) REVERT: F 99 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6683 (tpp-160) REVERT: F 174 TYR cc_start: 0.8047 (p90) cc_final: 0.7810 (p90) REVERT: H 99 ARG cc_start: 0.7219 (mmt180) cc_final: 0.6581 (mmm160) REVERT: H 174 TYR cc_start: 0.7969 (p90) cc_final: 0.7721 (p90) outliers start: 29 outliers final: 20 residues processed: 191 average time/residue: 1.2004 time to fit residues: 247.5338 Evaluate side-chains 186 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 28 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 125 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 22 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 ASN G 205 HIS F 149 ASN H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.184068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.135018 restraints weight = 43020.077| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.39 r_work: 0.3013 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10939 Z= 0.123 Angle : 0.433 6.572 14825 Z= 0.243 Chirality : 0.036 0.130 1675 Planarity : 0.003 0.035 1810 Dihedral : 3.799 39.873 1474 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.68 % Allowed : 19.39 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.29 (0.23), residues: 1339 helix: 3.94 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.18 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 178 HIS 0.005 0.001 HIS G 205 PHE 0.026 0.001 PHE E 97 TYR 0.016 0.001 TYR C 523 ARG 0.007 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.04943 ( 859) hydrogen bonds : angle 3.18533 ( 2483) SS BOND : bond 0.00202 ( 8) SS BOND : angle 0.40737 ( 16) covalent geometry : bond 0.00238 (10931) covalent geometry : angle 0.43277 (14809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.8010 (m-80) cc_final: 0.7783 (m-80) REVERT: E 208 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6925 (tp) REVERT: G 208 LEU cc_start: 0.7153 (tp) cc_final: 0.6873 (tp) REVERT: F 65 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6952 (mtp85) REVERT: F 90 GLU cc_start: 0.1672 (OUTLIER) cc_final: 0.1328 (tt0) REVERT: F 99 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6726 (tpp-160) REVERT: F 174 TYR cc_start: 0.8054 (p90) cc_final: 0.7779 (p90) REVERT: H 99 ARG cc_start: 0.7270 (mmt180) cc_final: 0.6646 (mmm160) REVERT: H 174 TYR cc_start: 0.7988 (p90) cc_final: 0.7743 (p90) outliers start: 30 outliers final: 20 residues processed: 184 average time/residue: 1.2419 time to fit residues: 246.5716 Evaluate side-chains 183 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 205 HIS F 149 ASN H 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.184094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135234 restraints weight = 38725.082| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.30 r_work: 0.3042 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10939 Z= 0.121 Angle : 0.433 7.140 14825 Z= 0.242 Chirality : 0.036 0.129 1675 Planarity : 0.003 0.036 1810 Dihedral : 3.781 38.831 1474 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.32 % Allowed : 19.93 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.30 (0.23), residues: 1339 helix: 3.95 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.19 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 178 HIS 0.004 0.001 HIS G 205 PHE 0.026 0.001 PHE E 97 TYR 0.016 0.001 TYR C 523 ARG 0.007 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.04881 ( 859) hydrogen bonds : angle 3.17757 ( 2483) SS BOND : bond 0.00194 ( 8) SS BOND : angle 0.38999 ( 16) covalent geometry : bond 0.00233 (10931) covalent geometry : angle 0.43306 (14809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.8001 (m-80) cc_final: 0.7777 (m-80) REVERT: E 208 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6898 (tp) REVERT: G 208 LEU cc_start: 0.7181 (tp) cc_final: 0.6893 (tp) REVERT: F 65 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6952 (mtp85) REVERT: F 90 GLU cc_start: 0.1719 (OUTLIER) cc_final: 0.1351 (tt0) REVERT: F 99 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6740 (tpp-160) REVERT: F 174 TYR cc_start: 0.8035 (p90) cc_final: 0.7761 (p90) REVERT: H 99 ARG cc_start: 0.7276 (mmt180) cc_final: 0.6653 (mmm160) REVERT: H 174 TYR cc_start: 0.7980 (p90) cc_final: 0.7727 (p90) outliers start: 26 outliers final: 21 residues processed: 186 average time/residue: 1.1930 time to fit residues: 239.5734 Evaluate side-chains 184 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 128 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 0.0070 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 ASN G 205 HIS F 149 ASN H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.184145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134955 restraints weight = 41807.993| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.40 r_work: 0.3016 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10939 Z= 0.120 Angle : 0.436 7.917 14825 Z= 0.243 Chirality : 0.035 0.129 1675 Planarity : 0.003 0.036 1810 Dihedral : 3.760 36.950 1474 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.59 % Allowed : 19.93 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.32 (0.23), residues: 1339 helix: 3.97 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.20 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 178 HIS 0.004 0.001 HIS G 205 PHE 0.026 0.001 PHE E 97 TYR 0.016 0.001 TYR A 523 ARG 0.007 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.04855 ( 859) hydrogen bonds : angle 3.16569 ( 2483) SS BOND : bond 0.00191 ( 8) SS BOND : angle 0.38765 ( 16) covalent geometry : bond 0.00233 (10931) covalent geometry : angle 0.43652 (14809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.7988 (m-80) cc_final: 0.7764 (m-80) REVERT: B 825 MET cc_start: 0.5127 (OUTLIER) cc_final: 0.4040 (mpp) REVERT: E 208 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6875 (tp) REVERT: G 76 LEU cc_start: 0.6069 (mt) cc_final: 0.5827 (pt) REVERT: G 208 LEU cc_start: 0.7169 (tp) cc_final: 0.6881 (tp) REVERT: F 65 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6970 (mtp85) REVERT: F 90 GLU cc_start: 0.1507 (OUTLIER) cc_final: 0.0770 (tm-30) REVERT: F 99 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6694 (tpp-160) REVERT: H 99 ARG cc_start: 0.7245 (mmt180) cc_final: 0.6621 (mmm160) REVERT: H 174 TYR cc_start: 0.7985 (p90) cc_final: 0.7731 (p90) outliers start: 29 outliers final: 23 residues processed: 187 average time/residue: 1.2027 time to fit residues: 242.8406 Evaluate side-chains 191 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 ASN G 205 HIS F 149 ASN H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.182249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.129812 restraints weight = 43633.484| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.80 r_work: 0.2967 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10939 Z= 0.154 Angle : 0.484 6.987 14825 Z= 0.272 Chirality : 0.038 0.132 1675 Planarity : 0.003 0.037 1810 Dihedral : 3.960 35.339 1474 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.32 % Allowed : 19.84 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.05 (0.23), residues: 1339 helix: 3.76 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.23 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 178 HIS 0.006 0.001 HIS G 205 PHE 0.027 0.002 PHE E 97 TYR 0.018 0.002 TYR A 523 ARG 0.004 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.05662 ( 859) hydrogen bonds : angle 3.32115 ( 2483) SS BOND : bond 0.00248 ( 8) SS BOND : angle 0.47024 ( 16) covalent geometry : bond 0.00320 (10931) covalent geometry : angle 0.48419 (14809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.8013 (m-80) cc_final: 0.7797 (m-80) REVERT: B 825 MET cc_start: 0.5074 (OUTLIER) cc_final: 0.3986 (mpp) REVERT: E 208 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.7018 (tp) REVERT: G 207 GLN cc_start: 0.6834 (mt0) cc_final: 0.6267 (mm-40) REVERT: G 208 LEU cc_start: 0.7125 (tp) cc_final: 0.6870 (tp) REVERT: F 65 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6928 (mtp85) REVERT: F 90 GLU cc_start: 0.1526 (OUTLIER) cc_final: 0.1256 (tt0) REVERT: F 99 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6659 (tpp-160) REVERT: F 174 TYR cc_start: 0.7996 (p90) cc_final: 0.7752 (p90) REVERT: H 99 ARG cc_start: 0.7203 (mmt180) cc_final: 0.6538 (mmm160) outliers start: 26 outliers final: 16 residues processed: 175 average time/residue: 1.2085 time to fit residues: 228.1217 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 122 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 0.0470 chunk 72 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 chunk 14 optimal weight: 6.9990 chunk 108 optimal weight: 0.0470 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 ASN G 205 HIS F 149 ASN H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.187105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138939 restraints weight = 43734.584| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.47 r_work: 0.3065 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10939 Z= 0.103 Angle : 0.407 6.358 14825 Z= 0.228 Chirality : 0.035 0.125 1675 Planarity : 0.003 0.037 1810 Dihedral : 3.641 36.597 1474 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.43 % Allowed : 20.82 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.46 (0.23), residues: 1339 helix: 4.11 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.22 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 178 HIS 0.004 0.001 HIS E 205 PHE 0.017 0.001 PHE E 127 TYR 0.013 0.001 TYR F 156 ARG 0.008 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 859) hydrogen bonds : angle 3.09647 ( 2483) SS BOND : bond 0.00163 ( 8) SS BOND : angle 0.40163 ( 16) covalent geometry : bond 0.00185 (10931) covalent geometry : angle 0.40695 (14809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.7866 (m-80) cc_final: 0.7646 (m-80) REVERT: B 825 MET cc_start: 0.5044 (OUTLIER) cc_final: 0.3958 (mpp) REVERT: E 131 ARG cc_start: 0.5912 (mmm160) cc_final: 0.5554 (mmm160) REVERT: E 208 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6751 (tp) REVERT: G 58 MET cc_start: 0.6730 (tpt) cc_final: 0.6434 (tmm) REVERT: G 208 LEU cc_start: 0.7138 (tp) cc_final: 0.6834 (tp) REVERT: F 65 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6931 (mtp85) REVERT: F 90 GLU cc_start: 0.1684 (OUTLIER) cc_final: 0.1123 (tm-30) REVERT: F 99 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6682 (tpp-160) REVERT: F 174 TYR cc_start: 0.7933 (p90) cc_final: 0.7712 (p90) REVERT: H 99 ARG cc_start: 0.7201 (mmt180) cc_final: 0.6586 (mmm160) REVERT: H 174 TYR cc_start: 0.7911 (p90) cc_final: 0.7684 (p90) outliers start: 16 outliers final: 9 residues processed: 181 average time/residue: 1.2113 time to fit residues: 236.5456 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 99 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 109 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 ASN G 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.184235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132289 restraints weight = 40295.797| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.66 r_work: 0.2995 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10939 Z= 0.128 Angle : 0.447 6.592 14825 Z= 0.251 Chirality : 0.036 0.271 1675 Planarity : 0.003 0.036 1810 Dihedral : 3.738 37.072 1473 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.61 % Allowed : 21.00 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.34 (0.23), residues: 1339 helix: 4.01 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.25 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 178 HIS 0.005 0.001 HIS G 205 PHE 0.025 0.002 PHE E 97 TYR 0.019 0.002 TYR C 523 ARG 0.004 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.04888 ( 859) hydrogen bonds : angle 3.17625 ( 2483) SS BOND : bond 0.00241 ( 8) SS BOND : angle 0.55248 ( 16) covalent geometry : bond 0.00254 (10931) covalent geometry : angle 0.44692 (14809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9755.66 seconds wall clock time: 168 minutes 18.34 seconds (10098.34 seconds total)