Starting phenix.real_space_refine on Mon Jul 28 23:53:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fq5_29378/07_2025/8fq5_29378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fq5_29378/07_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_29378/07_2025/8fq5_29378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fq5_29378/07_2025/8fq5_29378.map" model { file = "/net/cci-nas-00/data/ceres_data/8fq5_29378/07_2025/8fq5_29378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fq5_29378/07_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 10.55, per 1000 atoms: 0.97 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: 2.62 Conformation dependent library (CDL) restraints added in 2.1 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: 1.00 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: 3.20 Time building geometry restraints manager: 3.11 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: 13.250 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.220 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.310 ------------------------------------------------------------------------------- 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 : 1.094 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: 1.4556 time to fit residues: 273.0188 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 : 1.568 ------------------------------------------------------------------------------- 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: 3.88 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 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 = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- 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 : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.8032 (m-80) cc_final: 0.7807 (m-80) REVERT: C 514 VAL cc_start: 0.7503 (OUTLIER) cc_final: 0.7266 (p) REVERT: G 97 PHE cc_start: 0.6490 (t80) cc_final: 0.6258 (t80) REVERT: F 65 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6953 (mtp85) REVERT: F 99 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6774 (tpp-160) REVERT: F 174 TYR cc_start: 0.8047 (p90) cc_final: 0.7822 (p90) REVERT: H 99 ARG cc_start: 0.7278 (mmt180) cc_final: 0.6747 (mmm160) outliers start: 24 outliers final: 14 residues processed: 182 average time/residue: 1.3514 time to fit residues: 265.1263 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 : 1.291 ------------------------------------------------------------------------------- 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: 4.9990 chunk 22 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4053 r_free = 0.4053 target = 0.184246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133233 restraints weight = 33290.630| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.39 r_work: 0.3037 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 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 = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0736 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= 0.123 Angle : 0.440 8.233 14825 Z= 0.246 Chirality : 0.036 0.132 1675 Planarity : 0.003 0.035 1810 Dihedral : 3.931 42.588 1478 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.50 % Allowed : 19.75 % 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: 4.24 (0.23), residues: 1339 helix: 3.92 (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 0.004 0.001 HIS E 205 PHE 0.022 0.001 PHE E 97 TYR 0.014 0.001 TYR A 523 ARG 0.004 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 859) hydrogen bonds : angle 3.24291 ( 2483) SS BOND : bond 0.00215 ( 8) SS BOND : angle 0.60627 ( 16) covalent geometry : bond 0.00239 (10931) covalent geometry : angle 0.44008 (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: 28 poor density : 163 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.8003 (m-80) cc_final: 0.7773 (m-80) REVERT: D 549 TYR cc_start: 0.8035 (m-80) cc_final: 0.7829 (m-80) REVERT: G 97 PHE cc_start: 0.6323 (t80) cc_final: 0.6096 (t80) REVERT: F 65 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6921 (mtp85) REVERT: F 90 GLU cc_start: 0.1637 (OUTLIER) cc_final: 0.1350 (tt0) REVERT: F 99 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6758 (tpp-160) REVERT: F 174 TYR cc_start: 0.8017 (p90) cc_final: 0.7810 (p90) REVERT: F 204 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7174 (mtp180) REVERT: H 99 ARG cc_start: 0.7220 (mmt180) cc_final: 0.6653 (mmm160) REVERT: H 204 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7191 (mtp180) outliers start: 28 outliers final: 16 residues processed: 181 average time/residue: 1.2876 time to fit residues: 250.4502 Evaluate side-chains 180 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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: 0.7980 chunk 80 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 126 optimal weight: 0.0270 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.0770 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 ASN H 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.186406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137970 restraints weight = 39751.303| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.39 r_work: 0.3056 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10939 Z= 0.104 Angle : 0.405 8.136 14825 Z= 0.225 Chirality : 0.034 0.126 1675 Planarity : 0.003 0.035 1810 Dihedral : 3.685 41.263 1475 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.68 % Allowed : 19.66 % 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: 4.41 (0.23), residues: 1339 helix: 4.06 (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 0.012 0.001 TRP G 178 HIS 0.004 0.001 HIS G 205 PHE 0.022 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 0.04310 ( 859) hydrogen bonds : angle 3.09561 ( 2483) SS BOND : bond 0.00172 ( 8) SS BOND : angle 0.47679 ( 16) covalent geometry : bond 0.00189 (10931) covalent geometry : angle 0.40490 (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: 30 poor density : 171 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.7894 (m-80) cc_final: 0.7676 (m-80) REVERT: E 208 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6727 (tp) REVERT: F 90 GLU cc_start: 0.1757 (OUTLIER) cc_final: 0.1458 (tt0) REVERT: F 99 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6744 (tpp-160) REVERT: H 99 ARG cc_start: 0.7268 (mmt180) cc_final: 0.6645 (mmm160) outliers start: 30 outliers final: 16 residues processed: 195 average time/residue: 1.6110 time to fit residues: 340.0099 Evaluate side-chains 184 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 F residue 89 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 85 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 122 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.184139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134841 restraints weight = 44101.941| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.43 r_work: 0.3018 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- 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 = 0.19 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: 0.8380 moved from start: 0.0878 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= 0.123 Angle : 0.433 6.940 14825 Z= 0.243 Chirality : 0.036 0.129 1675 Planarity : 0.003 0.035 1810 Dihedral : 3.804 40.633 1475 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.32 % Allowed : 19.75 % 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: 4.30 (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 0.009 0.001 TRP G 178 HIS 0.005 0.001 HIS G 205 PHE 0.024 0.001 PHE E 97 TYR 0.017 0.001 TYR C 523 ARG 0.006 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.04947 ( 859) hydrogen bonds : angle 3.18656 ( 2483) SS BOND : bond 0.00197 ( 8) SS BOND : angle 0.43116 ( 16) covalent geometry : bond 0.00239 (10931) covalent geometry : angle 0.43293 (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 190 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.8008 (m-80) cc_final: 0.7782 (m-80) REVERT: D 549 TYR cc_start: 0.8015 (m-80) cc_final: 0.7789 (m-80) REVERT: E 208 LEU cc_start: 0.7135 (tp) cc_final: 0.6922 (tp) REVERT: F 90 GLU cc_start: 0.1877 (OUTLIER) cc_final: 0.1559 (tt0) REVERT: F 99 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6738 (tpp-160) REVERT: F 174 TYR cc_start: 0.8067 (p90) cc_final: 0.7838 (p90) REVERT: H 99 ARG cc_start: 0.7274 (mmt180) cc_final: 0.6657 (mmm160) REVERT: H 174 TYR cc_start: 0.8030 (p90) cc_final: 0.7780 (p90) outliers start: 26 outliers final: 16 residues processed: 185 average time/residue: 1.4924 time to fit residues: 297.9372 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 817 LYS Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 130 THR 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 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 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: 0.3980 chunk 26 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.182644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130396 restraints weight = 42029.285| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.78 r_work: 0.2958 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10939 Z= 0.145 Angle : 0.470 6.859 14825 Z= 0.263 Chirality : 0.037 0.134 1675 Planarity : 0.003 0.035 1810 Dihedral : 3.955 40.416 1474 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.14 % Allowed : 20.02 % 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: 4.12 (0.23), residues: 1339 helix: 3.82 (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 0.010 0.001 TRP G 178 HIS 0.006 0.001 HIS G 205 PHE 0.026 0.002 PHE E 97 TYR 0.017 0.002 TYR C 523 ARG 0.007 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.05505 ( 859) hydrogen bonds : angle 3.29286 ( 2483) SS BOND : bond 0.00245 ( 8) SS BOND : angle 0.44009 ( 16) covalent geometry : bond 0.00297 (10931) covalent geometry : angle 0.46963 (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 184 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.8014 (m-80) cc_final: 0.7798 (m-80) REVERT: E 208 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.7041 (tp) REVERT: G 207 GLN cc_start: 0.6888 (mt0) cc_final: 0.6308 (mm-40) REVERT: G 208 LEU cc_start: 0.7158 (tp) cc_final: 0.6913 (tp) REVERT: F 90 GLU cc_start: 0.1629 (OUTLIER) cc_final: 0.1282 (tt0) REVERT: F 99 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6666 (tpp-160) REVERT: H 99 ARG cc_start: 0.7188 (mmt180) cc_final: 0.6563 (mmm160) REVERT: H 174 TYR cc_start: 0.7975 (p90) cc_final: 0.7713 (p90) outliers start: 24 outliers final: 13 residues processed: 177 average time/residue: 1.6150 time to fit residues: 309.4689 Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 795 VAL 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 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 172 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 47 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.183493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131940 restraints weight = 38219.412| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.48 r_work: 0.3004 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 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 = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10939 Z= 0.132 Angle : 0.448 7.152 14825 Z= 0.252 Chirality : 0.036 0.132 1675 Planarity : 0.003 0.036 1810 Dihedral : 3.884 38.818 1474 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.79 % Allowed : 20.55 % 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: 4.20 (0.23), residues: 1339 helix: 3.89 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.24 (0.31), residues: 391 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 0.001 PHE E 97 TYR 0.012 0.002 TYR C 523 ARG 0.007 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.05151 ( 859) hydrogen bonds : angle 3.23725 ( 2483) SS BOND : bond 0.00218 ( 8) SS BOND : angle 0.41500 ( 16) covalent geometry : bond 0.00262 (10931) covalent geometry : angle 0.44784 (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 180 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.8003 (m-80) cc_final: 0.7788 (m-80) REVERT: B 585 MET cc_start: 0.8996 (mmt) cc_final: 0.8788 (mmp) REVERT: B 825 MET cc_start: 0.5055 (OUTLIER) cc_final: 0.3982 (mpp) REVERT: E 208 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6962 (tp) REVERT: G 208 LEU cc_start: 0.7168 (tp) cc_final: 0.6841 (tp) REVERT: F 90 GLU cc_start: 0.1466 (OUTLIER) cc_final: 0.0746 (tm-30) REVERT: F 99 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6709 (tpp-160) REVERT: F 174 TYR cc_start: 0.7937 (p90) cc_final: 0.7693 (p90) REVERT: H 99 ARG cc_start: 0.7214 (mmt180) cc_final: 0.6574 (mmm160) REVERT: H 174 TYR cc_start: 0.7985 (p90) cc_final: 0.7725 (p90) outliers start: 20 outliers final: 13 residues processed: 174 average time/residue: 1.8470 time to fit residues: 346.3114 Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 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 172 ASN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 128 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 0.0470 chunk 14 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 0.0170 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.186425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137955 restraints weight = 42095.711| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.43 r_work: 0.3051 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10939 Z= 0.103 Angle : 0.399 6.619 14825 Z= 0.223 Chirality : 0.035 0.127 1675 Planarity : 0.003 0.036 1810 Dihedral : 3.638 36.363 1474 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.43 % Allowed : 20.91 % 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: 4.48 (0.23), residues: 1339 helix: 4.12 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.22 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 178 HIS 0.004 0.001 HIS G 205 PHE 0.025 0.001 PHE E 97 TYR 0.014 0.001 TYR C 523 ARG 0.006 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 859) hydrogen bonds : angle 3.08335 ( 2483) SS BOND : bond 0.00149 ( 8) SS BOND : angle 0.35608 ( 16) covalent geometry : bond 0.00186 (10931) covalent geometry : angle 0.39927 (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 190 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.7885 (m-80) cc_final: 0.7586 (m-80) REVERT: B 585 MET cc_start: 0.8893 (mmt) cc_final: 0.8679 (mmp) REVERT: E 208 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6779 (tp) REVERT: G 76 LEU cc_start: 0.6048 (mt) cc_final: 0.5817 (pt) REVERT: G 208 LEU cc_start: 0.7128 (tp) cc_final: 0.6810 (tp) REVERT: F 90 GLU cc_start: 0.1538 (OUTLIER) cc_final: 0.0785 (tm-30) REVERT: F 99 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6699 (tpp-160) REVERT: F 174 TYR cc_start: 0.7948 (p90) cc_final: 0.7710 (p90) REVERT: H 99 ARG cc_start: 0.7240 (mmt180) cc_final: 0.6592 (mmm160) REVERT: H 174 TYR cc_start: 0.7950 (p90) cc_final: 0.7731 (p90) outliers start: 16 outliers final: 11 residues processed: 187 average time/residue: 1.1918 time to fit residues: 240.8266 Evaluate side-chains 184 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 795 VAL 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 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 F residue 89 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN G 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.180348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128413 restraints weight = 41549.779| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.56 r_work: 0.2924 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10939 Z= 0.236 Angle : 0.592 7.242 14825 Z= 0.332 Chirality : 0.043 0.144 1675 Planarity : 0.004 0.054 1810 Dihedral : 4.281 35.359 1474 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.66 % Favored : 97.27 % Rotamer: Outliers : 2.06 % Allowed : 20.38 % Favored : 77.57 % 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: 3.59 (0.23), residues: 1339 helix: 3.38 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.32 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 606 HIS 0.007 0.002 HIS G 205 PHE 0.028 0.003 PHE E 97 TYR 0.025 0.003 TYR C 523 ARG 0.006 0.001 ARG C 599 Details of bonding type rmsd hydrogen bonds : bond 0.06806 ( 859) hydrogen bonds : angle 3.55338 ( 2483) SS BOND : bond 0.00377 ( 8) SS BOND : angle 0.59410 ( 16) covalent geometry : bond 0.00528 (10931) covalent geometry : angle 0.59206 (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 179 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 MET cc_start: 0.9062 (mmt) cc_final: 0.8842 (mmp) REVERT: B 825 MET cc_start: 0.5196 (OUTLIER) cc_final: 0.4099 (mpp) REVERT: G 97 PHE cc_start: 0.6454 (t80) cc_final: 0.6143 (t80) REVERT: G 207 GLN cc_start: 0.6964 (mt0) cc_final: 0.6380 (mm-40) REVERT: F 90 GLU cc_start: 0.1641 (OUTLIER) cc_final: 0.0968 (tm-30) REVERT: F 204 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7446 (mtp180) REVERT: H 99 ARG cc_start: 0.7137 (mmt180) cc_final: 0.6534 (mmm160) REVERT: H 204 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7482 (mtp180) outliers start: 23 outliers final: 11 residues processed: 172 average time/residue: 1.4269 time to fit residues: 264.4736 Evaluate side-chains 167 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS 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 204 ARG Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 204 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 0.0020 chunk 72 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.0010 chunk 105 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN C 586 GLN G 149 ASN G 205 HIS 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 = 0.185167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136486 restraints weight = 43777.538| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.40 r_work: 0.3044 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1225 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= 0.111 Angle : 0.428 6.652 14825 Z= 0.240 Chirality : 0.035 0.129 1675 Planarity : 0.003 0.035 1810 Dihedral : 3.809 35.963 1474 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.34 % Allowed : 21.27 % 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: 4.25 (0.23), residues: 1339 helix: 3.94 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.24 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 178 HIS 0.004 0.001 HIS G 205 PHE 0.018 0.001 PHE E 127 TYR 0.015 0.001 TYR B 549 ARG 0.008 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 859) hydrogen bonds : angle 3.18837 ( 2483) SS BOND : bond 0.00206 ( 8) SS BOND : angle 0.43068 ( 16) covalent geometry : bond 0.00203 (10931) covalent geometry : angle 0.42790 (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 179 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.7946 (m-80) cc_final: 0.7733 (m-80) REVERT: B 585 MET cc_start: 0.8886 (mmt) cc_final: 0.8666 (mmp) REVERT: C 515 PHE cc_start: 0.8222 (m-80) cc_final: 0.8018 (m-80) REVERT: D 585 MET cc_start: 0.8872 (mmt) cc_final: 0.8648 (mmp) REVERT: G 76 LEU cc_start: 0.6104 (mt) cc_final: 0.5868 (pt) REVERT: G 207 GLN cc_start: 0.6915 (mt0) cc_final: 0.6318 (mm-40) REVERT: G 208 LEU cc_start: 0.7203 (tp) cc_final: 0.6868 (tp) REVERT: F 90 GLU cc_start: 0.1625 (OUTLIER) cc_final: 0.1036 (tm-30) REVERT: F 99 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6682 (tpp-160) REVERT: F 174 TYR cc_start: 0.7983 (p90) cc_final: 0.7700 (p90) REVERT: H 99 ARG cc_start: 0.7246 (mmt180) cc_final: 0.6634 (mmm160) REVERT: H 174 TYR cc_start: 0.7989 (p90) cc_final: 0.7724 (p90) outliers start: 15 outliers final: 10 residues processed: 176 average time/residue: 1.2976 time to fit residues: 247.8010 Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 790 SER 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 G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS 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: 3.9990 chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 chunk 83 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 120 optimal weight: 0.0070 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 586 GLN G 149 ASN G 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.183027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130802 restraints weight = 39514.037| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.79 r_work: 0.2960 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10939 Z= 0.138 Angle : 0.461 6.650 14825 Z= 0.259 Chirality : 0.036 0.131 1675 Planarity : 0.003 0.036 1810 Dihedral : 3.885 33.839 1474 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.52 % Allowed : 20.82 % 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: 4.10 (0.23), residues: 1339 helix: 3.80 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.21 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 178 HIS 0.006 0.001 HIS G 205 PHE 0.018 0.002 PHE E 127 TYR 0.017 0.002 TYR A 523 ARG 0.007 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.05270 ( 859) hydrogen bonds : angle 3.27277 ( 2483) SS BOND : bond 0.00226 ( 8) SS BOND : angle 0.41593 ( 16) covalent geometry : bond 0.00279 (10931) covalent geometry : angle 0.46070 (14809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11582.21 seconds wall clock time: 210 minutes 41.73 seconds (12641.73 seconds total)