Starting phenix.real_space_refine on Thu Jul 2 23:08:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fq5_29378/07_2026/8fq5_29378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fq5_29378/07_2026/8fq5_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_2026/8fq5_29378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fq5_29378/07_2026/8fq5_29378.map" model { file = "/net/cci-nas-00/data/ceres_data/8fq5_29378/07_2026/8fq5_29378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fq5_29378/07_2026/8fq5_29378.cif" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 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: 3.06, per 1000 atoms: 0.28 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: 0.89 Conformation dependent library (CDL) restraints added in 793.1 milliseconds 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: 0.35 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: 1.59 Time building geometry restraints manager: 1.25 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 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 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: 4.300 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.510 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:7.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG E 65 TYR 0.016 0.001 TYR A 523 PHE 0.018 0.001 PHE F 107 TRP 0.010 0.001 TRP C 606 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.12 (10931) covalent geometry : angle 0.44088 / 0.25 (14809) SS BOND : bond 0.00223 / 0.11 ( 8) SS BOND : angle 0.77237 / 0.44 ( 16) hydrogen bonds : bond 0.10079 / 7.00 ( 859) hydrogen bonds : angle 3.82656 / 2.74 ( 2483) *********************** 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 : 0.323 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: 0.5998 time to fit residues: 112.0986 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 : 0.322 ------------------------------------------------------------------------------- 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 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4077 r_free = 0.4077 target = 0.186635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.138089 restraints weight = 43981.951| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.47 r_work: 0.3079 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10939 Z= 0.108 Angle : 0.419 6.739 14825 Z= 0.233 Chirality : 0.035 0.132 1675 Planarity : 0.003 0.038 1810 Dihedral : 5.007 83.029 1489 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.14 % Allowed : 19.39 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.32 (0.23), residues: 1339 helix: 4.02 (0.16), residues: 948 sheet: -2.34 (1.35), residues: 10 loop : -0.24 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 65 TYR 0.011 0.001 TYR C 523 PHE 0.021 0.001 PHE E 97 TRP 0.011 0.001 TRP G 178 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.11 (10931) covalent geometry : angle 0.41840 / 0.23 (14809) SS BOND : bond 0.00186 / 0.10 ( 8) SS BOND : angle 0.81073 / 0.39 ( 16) hydrogen bonds : bond 0.04486 / 2.96 ( 859) hydrogen bonds : angle 3.20361 / 2.28 ( 2483) *********************** 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 198 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 97 PHE cc_start: 0.6448 (t80) cc_final: 0.6226 (t80) REVERT: F 99 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6749 (tpp-160) REVERT: F 174 TYR cc_start: 0.8036 (p90) cc_final: 0.7741 (p90) REVERT: F 191 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8507 (mm-30) REVERT: H 99 ARG cc_start: 0.7263 (mmt180) cc_final: 0.6735 (mmm160) outliers start: 24 outliers final: 14 residues processed: 190 average time/residue: 0.5156 time to fit residues: 105.9914 Evaluate side-chains 180 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain D residue 817 LYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 200 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 47 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 108 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.185659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.136602 restraints weight = 43933.934| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.47 r_work: 0.3050 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0723 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= 0.112 Angle : 0.422 7.969 14825 Z= 0.235 Chirality : 0.035 0.129 1675 Planarity : 0.003 0.034 1810 Dihedral : 3.808 41.554 1477 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.32 % Allowed : 20.38 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.35 (0.23), residues: 1339 helix: 4.02 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.22 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 65 TYR 0.016 0.001 TYR C 523 PHE 0.023 0.001 PHE E 97 TRP 0.010 0.001 TRP G 178 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (10931) covalent geometry : angle 0.42152 / 0.24 (14809) SS BOND : bond 0.00181 / 0.10 ( 8) SS BOND : angle 0.60038 / 0.30 ( 16) hydrogen bonds : bond 0.04629 / 3.04 ( 859) hydrogen bonds : angle 3.17459 / 2.25 ( 2483) *********************** 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 193 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.7959 (m-80) cc_final: 0.7637 (m-80) REVERT: C 514 VAL cc_start: 0.7507 (OUTLIER) cc_final: 0.7249 (p) REVERT: F 90 GLU cc_start: 0.1705 (OUTLIER) cc_final: 0.1433 (tt0) REVERT: F 99 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6777 (tpp-160) REVERT: F 174 TYR cc_start: 0.8029 (p90) cc_final: 0.7825 (p90) REVERT: H 99 ARG cc_start: 0.7305 (mmt180) cc_final: 0.6756 (mmm160) outliers start: 26 outliers final: 14 residues processed: 187 average time/residue: 0.5347 time to fit residues: 107.9683 Evaluate side-chains 182 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 11 LEU 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 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 200 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 125 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 33 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.185376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136336 restraints weight = 43807.294| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.46 r_work: 0.3046 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.0812 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= 0.112 Angle : 0.421 8.774 14825 Z= 0.234 Chirality : 0.035 0.127 1675 Planarity : 0.003 0.034 1810 Dihedral : 3.788 40.706 1477 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.41 % Allowed : 19.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.39 (0.23), residues: 1339 helix: 4.02 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.17 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 65 TYR 0.014 0.001 TYR H 174 PHE 0.023 0.001 PHE E 97 TRP 0.010 0.001 TRP G 178 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (10931) covalent geometry : angle 0.42058 / 0.23 (14809) SS BOND : bond 0.00183 / 0.10 ( 8) SS BOND : angle 0.49172 / 0.25 ( 16) hydrogen bonds : bond 0.04618 / 3.03 ( 859) hydrogen bonds : angle 3.13784 / 2.22 ( 2483) *********************** 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 194 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.7941 (m-80) cc_final: 0.7636 (m-80) REVERT: E 208 LEU cc_start: 0.7039 (tp) cc_final: 0.6729 (tp) REVERT: F 90 GLU cc_start: 0.1830 (OUTLIER) cc_final: 0.1541 (tt0) REVERT: F 99 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6751 (tpp-160) REVERT: H 99 ARG cc_start: 0.7274 (mmt180) cc_final: 0.6698 (tpp-160) outliers start: 27 outliers final: 18 residues processed: 188 average time/residue: 0.4633 time to fit residues: 94.3564 Evaluate side-chains 181 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 31 ASP Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 149 ASN G 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.133618 restraints weight = 42479.557| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.39 r_work: 0.3010 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10939 Z= 0.144 Angle : 0.472 8.123 14825 Z= 0.263 Chirality : 0.037 0.131 1675 Planarity : 0.003 0.035 1810 Dihedral : 3.965 40.759 1476 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.68 % Allowed : 19.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.19 (0.23), residues: 1339 helix: 3.86 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.18 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 65 TYR 0.015 0.002 TYR C 523 PHE 0.024 0.002 PHE E 97 TRP 0.008 0.001 TRP G 178 HIS 0.005 0.001 HIS F 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (10931) covalent geometry : angle 0.47236 / 0.26 (14809) SS BOND : bond 0.00244 / 0.13 ( 8) SS BOND : angle 0.45121 / 0.25 ( 16) hydrogen bonds : bond 0.05448 / 3.57 ( 859) hydrogen bonds : angle 3.28036 / 2.32 ( 2483) *********************** 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: 30 poor density : 160 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.8070 (m-80) cc_final: 0.7846 (m-80) REVERT: E 208 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6998 (tp) REVERT: G 207 GLN cc_start: 0.6905 (mt0) cc_final: 0.6337 (mm-40) REVERT: F 90 GLU cc_start: 0.1800 (OUTLIER) cc_final: 0.1538 (tt0) REVERT: F 99 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6734 (tpp-160) REVERT: F 174 TYR cc_start: 0.8056 (p90) cc_final: 0.7804 (p90) REVERT: H 99 ARG cc_start: 0.7241 (mmt180) cc_final: 0.6644 (mmm160) REVERT: H 174 TYR cc_start: 0.8003 (p90) cc_final: 0.7776 (p90) outliers start: 30 outliers final: 17 residues processed: 180 average time/residue: 0.5048 time to fit residues: 98.2358 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 130 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 149 ASN 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 F residue 200 MET Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 120 optimal weight: 6.9990 chunk 33 optimal weight: 0.0070 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 97 optimal weight: 10.0000 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 205 HIS F 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.184437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.135475 restraints weight = 42703.652| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.43 r_work: 0.3021 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 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 = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10939 Z= 0.118 Angle : 0.436 8.674 14825 Z= 0.242 Chirality : 0.035 0.130 1675 Planarity : 0.003 0.036 1810 Dihedral : 3.839 39.635 1476 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.97 % Allowed : 20.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.31 (0.23), residues: 1339 helix: 3.96 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.19 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 65 TYR 0.014 0.001 TYR A 523 PHE 0.025 0.001 PHE E 97 TRP 0.012 0.001 TRP G 178 HIS 0.005 0.001 HIS G 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 (10931) covalent geometry : angle 0.43645 / 0.24 (14809) SS BOND : bond 0.00193 / 0.10 ( 8) SS BOND : angle 0.39758 / 0.21 ( 16) hydrogen bonds : bond 0.04793 / 3.14 ( 859) hydrogen bonds : angle 3.17187 / 2.24 ( 2483) *********************** 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 190 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TYR cc_start: 0.7993 (m-80) cc_final: 0.7775 (m-80) REVERT: E 208 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6915 (tp) REVERT: G 208 LEU cc_start: 0.7124 (tp) cc_final: 0.6815 (tp) REVERT: F 90 GLU cc_start: 0.1637 (OUTLIER) cc_final: 0.1314 (tt0) REVERT: F 99 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6732 (tpp-160) REVERT: F 174 TYR cc_start: 0.8052 (p90) cc_final: 0.7754 (p90) REVERT: H 99 ARG cc_start: 0.7270 (mmt180) cc_final: 0.6638 (mmm160) REVERT: H 174 TYR cc_start: 0.7983 (p90) cc_final: 0.7744 (p90) outliers start: 22 outliers final: 16 residues processed: 186 average time/residue: 0.5413 time to fit residues: 108.8500 Evaluate side-chains 182 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 130 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 149 ASN 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 200 MET 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 131 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 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 = 0.4001 r_free = 0.4001 target = 0.179401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.127557 restraints weight = 35746.927| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.56 r_work: 0.2919 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 10939 Z= 0.282 Angle : 0.660 8.106 14825 Z= 0.368 Chirality : 0.046 0.152 1675 Planarity : 0.005 0.061 1810 Dihedral : 4.538 41.121 1476 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.58 % Favored : 97.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.23), residues: 1339 helix: 3.11 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.43 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 599 TYR 0.025 0.003 TYR F 96 PHE 0.028 0.003 PHE E 97 TRP 0.010 0.002 TRP B 606 HIS 0.008 0.002 HIS G 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.28 (10931) covalent geometry : angle 0.66031 / 0.37 (14809) SS BOND : bond 0.00439 / 0.23 ( 8) SS BOND : angle 0.66142 / 0.38 ( 16) hydrogen bonds : bond 0.07349 / 4.80 ( 859) hydrogen bonds : angle 3.69983 / 2.62 ( 2483) *********************** 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 184 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 825 MET cc_start: 0.5103 (OUTLIER) cc_final: 0.4055 (mpp) REVERT: G 97 PHE cc_start: 0.6509 (t80) cc_final: 0.6213 (t80) REVERT: G 207 GLN cc_start: 0.6982 (mt0) cc_final: 0.6406 (mm-40) REVERT: F 90 GLU cc_start: 0.1424 (OUTLIER) cc_final: 0.0733 (tm-30) REVERT: F 204 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7408 (mtp180) REVERT: H 99 ARG cc_start: 0.7121 (mmt180) cc_final: 0.6546 (mmm160) REVERT: H 204 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7415 (mtp180) outliers start: 28 outliers final: 15 residues processed: 176 average time/residue: 0.5902 time to fit residues: 112.0724 Evaluate side-chains 174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 149 ASN 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 F residue 204 ARG Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 89 TYR Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 204 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 149 ASN G 205 HIS F 149 ASN H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.183764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134991 restraints weight = 44390.070| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.35 r_work: 0.3018 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10939 Z= 0.122 Angle : 0.439 6.865 14825 Z= 0.248 Chirality : 0.036 0.130 1675 Planarity : 0.003 0.037 1810 Dihedral : 3.935 38.448 1474 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.43 % Allowed : 20.55 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.02 (0.23), residues: 1339 helix: 3.74 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.27 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 65 TYR 0.012 0.001 TYR D 549 PHE 0.017 0.001 PHE E 127 TRP 0.014 0.001 TRP G 178 HIS 0.005 0.001 HIS G 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (10931) covalent geometry : angle 0.43889 / 0.25 (14809) SS BOND : bond 0.00158 / 0.08 ( 8) SS BOND : angle 0.52044 / 0.26 ( 16) hydrogen bonds : bond 0.04932 / 3.23 ( 859) hydrogen bonds : angle 3.25962 / 2.30 ( 2483) *********************** 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 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 825 MET cc_start: 0.4903 (OUTLIER) cc_final: 0.3848 (mpp) REVERT: C 817 LYS cc_start: 0.7802 (mptm) cc_final: 0.7597 (mmtp) REVERT: E 208 LEU cc_start: 0.7208 (tp) cc_final: 0.6891 (tp) REVERT: G 207 GLN cc_start: 0.6945 (mt0) cc_final: 0.6344 (mm-40) REVERT: G 208 LEU cc_start: 0.7162 (tp) cc_final: 0.6828 (tp) REVERT: F 90 GLU cc_start: 0.1549 (OUTLIER) cc_final: 0.0880 (tm-30) REVERT: F 99 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6757 (tpp-160) REVERT: F 174 TYR cc_start: 0.8009 (p90) cc_final: 0.7731 (p90) REVERT: H 99 ARG cc_start: 0.7242 (mmt180) cc_final: 0.6630 (mmm160) REVERT: H 174 TYR cc_start: 0.7932 (p90) cc_final: 0.7692 (p90) outliers start: 16 outliers final: 11 residues processed: 176 average time/residue: 0.5854 time to fit residues: 111.3428 Evaluate side-chains 174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 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 G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 149 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 H residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 0.0070 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 149 ASN G 205 HIS F 149 ASN H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.182718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131481 restraints weight = 35799.322| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.41 r_work: 0.2983 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1246 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 : 0.462 6.784 14825 Z= 0.261 Chirality : 0.037 0.134 1675 Planarity : 0.003 0.038 1810 Dihedral : 3.968 36.838 1474 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.52 % Allowed : 20.11 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.00 (0.23), residues: 1339 helix: 3.74 (0.16), residues: 946 sheet: None (None), residues: 0 loop : -0.28 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 65 TYR 0.018 0.002 TYR C 523 PHE 0.018 0.002 PHE E 127 TRP 0.013 0.001 TRP G 178 HIS 0.006 0.001 HIS G 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (10931) covalent geometry : angle 0.46207 / 0.26 (14809) SS BOND : bond 0.00161 / 0.08 ( 8) SS BOND : angle 0.55426 / 0.27 ( 16) hydrogen bonds : bond 0.05341 / 3.49 ( 859) hydrogen bonds : angle 3.29800 / 2.33 ( 2483) *********************** 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 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 825 MET cc_start: 0.5066 (OUTLIER) cc_final: 0.4000 (mpp) REVERT: E 208 LEU cc_start: 0.7183 (tp) cc_final: 0.6939 (tp) REVERT: G 58 MET cc_start: 0.6657 (tpt) cc_final: 0.6369 (tmm) REVERT: G 207 GLN cc_start: 0.6868 (mt0) cc_final: 0.6270 (mm-40) REVERT: G 208 LEU cc_start: 0.7179 (tp) cc_final: 0.6844 (tp) REVERT: F 90 GLU cc_start: 0.1637 (OUTLIER) cc_final: 0.0977 (tm-30) REVERT: F 99 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6674 (tpp-160) REVERT: F 174 TYR cc_start: 0.8022 (p90) cc_final: 0.7792 (p90) REVERT: H 99 ARG cc_start: 0.7202 (mmt180) cc_final: 0.6563 (mmm160) REVERT: H 174 TYR cc_start: 0.7959 (p90) cc_final: 0.7729 (p90) outliers start: 17 outliers final: 12 residues processed: 172 average time/residue: 0.6238 time to fit residues: 115.5970 Evaluate side-chains 174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 149 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 200 MET Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 117 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 149 ASN G 205 HIS F 149 ASN H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.182083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130201 restraints weight = 39339.688| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.54 r_work: 0.2968 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10939 Z= 0.158 Angle : 0.492 6.740 14825 Z= 0.277 Chirality : 0.038 0.136 1675 Planarity : 0.004 0.039 1810 Dihedral : 4.034 36.116 1474 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.43 % Allowed : 20.20 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.87 (0.23), residues: 1339 helix: 3.62 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.29 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 65 TYR 0.018 0.002 TYR D 549 PHE 0.030 0.002 PHE E 97 TRP 0.013 0.001 TRP G 178 HIS 0.006 0.001 HIS G 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (10931) covalent geometry : angle 0.49197 / 0.28 (14809) SS BOND : bond 0.00179 / 0.09 ( 8) SS BOND : angle 0.56058 / 0.31 ( 16) hydrogen bonds : bond 0.05684 / 3.72 ( 859) hydrogen bonds : angle 3.36360 / 2.38 ( 2483) ********************** 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 175 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 825 MET cc_start: 0.5073 (OUTLIER) cc_final: 0.4007 (mpp) REVERT: E 208 LEU cc_start: 0.7208 (tp) cc_final: 0.6985 (tp) REVERT: G 207 GLN cc_start: 0.6843 (mt0) cc_final: 0.6259 (mm-40) REVERT: G 208 LEU cc_start: 0.7175 (tp) cc_final: 0.6880 (tp) REVERT: F 90 GLU cc_start: 0.1621 (OUTLIER) cc_final: 0.0962 (tm-30) REVERT: F 99 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6654 (tpp-160) REVERT: F 174 TYR cc_start: 0.8033 (p90) cc_final: 0.7797 (p90) REVERT: H 99 ARG cc_start: 0.7187 (mmt180) cc_final: 0.6551 (mmm160) REVERT: H 174 TYR cc_start: 0.7965 (p90) cc_final: 0.7717 (p90) outliers start: 16 outliers final: 12 residues processed: 171 average time/residue: 0.5983 time to fit residues: 110.4679 Evaluate side-chains 174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 149 ASN 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 H residue 66 THR Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 47 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 149 ASN G 205 HIS F 149 ASN H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.183047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.131311 restraints weight = 45812.351| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.84 r_work: 0.2948 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10939 Z= 0.133 Angle : 0.459 6.639 14825 Z= 0.258 Chirality : 0.036 0.133 1675 Planarity : 0.003 0.039 1810 Dihedral : 3.939 35.282 1474 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.34 % Allowed : 20.38 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.02 (0.23), residues: 1339 helix: 3.74 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.25 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 65 TYR 0.017 0.002 TYR D 549 PHE 0.018 0.001 PHE E 127 TRP 0.014 0.001 TRP G 178 HIS 0.006 0.001 HIS G 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (10931) covalent geometry : angle 0.45857 / 0.26 (14809) SS BOND : bond 0.00154 / 0.08 ( 8) SS BOND : angle 0.50552 / 0.29 ( 16) hydrogen bonds : bond 0.05249 / 3.44 ( 859) hydrogen bonds : angle 3.29321 / 2.33 ( 2483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4601.35 seconds wall clock time: 79 minutes 0.75 seconds (4740.75 seconds total)