Starting phenix.real_space_refine on Sat May 10 22:28:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eka_28196/05_2025/8eka_28196.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eka_28196/05_2025/8eka_28196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eka_28196/05_2025/8eka_28196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eka_28196/05_2025/8eka_28196.map" model { file = "/net/cci-nas-00/data/ceres_data/8eka_28196/05_2025/8eka_28196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eka_28196/05_2025/8eka_28196.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4435 2.51 5 N 1197 2.21 5 O 1363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7023 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 195 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 6, 'TRANS': 20} Chain: "H" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1608 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 197} Chain breaks: 1 Chain: "L" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1652 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "A" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 944 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 835 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "C" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 946 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 843 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Time building chain proxies: 4.69, per 1000 atoms: 0.67 Number of scatterers: 7023 At special positions: 0 Unit cell: (76.36, 125.12, 119.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1363 8.00 N 1197 7.00 C 4435 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " 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: 1.46 Conformation dependent library (CDL) restraints added in 911.1 milliseconds 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 24 sheets defined 2.1% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'L' and resid 122 through 128 Processing helix chain 'L' and resid 182 through 188 removed outlier: 3.596A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.838A pdb=" N VAL B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.809A pdb=" N VAL H 5 " --> pdb=" O GLU H 23 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET H 83 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.638A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 97 through 102 Processing sheet with id=AA4, first strand: chain 'H' and resid 129 through 131 removed outlier: 3.582A pdb=" N LEU H 131 " --> pdb=" O GLY H 146 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER H 187 " --> pdb=" O CYS H 147 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU H 185 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL H 188 " --> pdb=" O HIS H 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 129 through 131 removed outlier: 3.582A pdb=" N LEU H 131 " --> pdb=" O GLY H 146 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER H 187 " --> pdb=" O CYS H 147 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU H 185 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 158 through 161 removed outlier: 3.566A pdb=" N CYS H 203 " --> pdb=" O LYS H 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA8, first strand: chain 'L' and resid 48 through 49 removed outlier: 3.585A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 85 through 86 Processing sheet with id=AB1, first strand: chain 'L' and resid 130 through 135 removed outlier: 3.536A pdb=" N LEU L 181 " --> pdb=" O ALA L 130 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL L 132 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU L 179 " --> pdb=" O VAL L 132 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR L 178 " --> pdb=" O GLN L 160 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN L 160 " --> pdb=" O THR L 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 145 through 148 removed outlier: 3.938A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.781A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.621A pdb=" N GLY A 10 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR A 117 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 12 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 37 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A 36 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 100 through 101 removed outlier: 3.648A pdb=" N PHE A 100 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 107 " --> pdb=" O PHE A 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 10 through 13 removed outlier: 4.029A pdb=" N ALA B 13 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 19 through 22 removed outlier: 3.912A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 75 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 72 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.769A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.536A pdb=" N LYS C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER C 25 " --> pdb=" O LYS C 3 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL C 5 " --> pdb=" O GLU C 23 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 23 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU C 18 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET C 83 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 20 " --> pdb=" O MET C 81 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS C 22 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C 79 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.736A pdb=" N GLY C 10 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 34 through 39 removed outlier: 3.783A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 59 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 97 through 100 Processing sheet with id=AC4, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.518A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR D 74 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 13 removed outlier: 7.090A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.814A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 333 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: 1.62 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1256 1.33 - 1.45: 2070 1.45 - 1.58: 3832 1.58 - 1.70: 0 1.70 - 1.83: 40 Bond restraints: 7198 Sorted by residual: bond pdb=" N VAL C 64 " pdb=" CA VAL C 64 " ideal model delta sigma weight residual 1.460 1.494 -0.034 8.60e-03 1.35e+04 1.55e+01 bond pdb=" CA ALA D 84 " pdb=" CB ALA D 84 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.69e-02 3.50e+03 1.04e+01 bond pdb=" N GLN H 199 " pdb=" CA GLN H 199 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.29e-02 6.01e+03 8.15e+00 bond pdb=" C PRO D 80 " pdb=" O PRO D 80 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.30e-02 5.92e+03 7.54e+00 bond pdb=" N PRO D 80 " pdb=" CA PRO D 80 " ideal model delta sigma weight residual 1.469 1.437 0.032 1.28e-02 6.10e+03 6.30e+00 ... (remaining 7193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 9515 1.94 - 3.88: 217 3.88 - 5.82: 34 5.82 - 7.75: 6 7.75 - 9.69: 1 Bond angle restraints: 9773 Sorted by residual: angle pdb=" N VAL C 64 " pdb=" CA VAL C 64 " pdb=" C VAL C 64 " ideal model delta sigma weight residual 113.71 108.76 4.95 9.50e-01 1.11e+00 2.72e+01 angle pdb=" N PRO D 80 " pdb=" CA PRO D 80 " pdb=" CB PRO D 80 " ideal model delta sigma weight residual 103.25 98.21 5.04 1.05e+00 9.07e-01 2.30e+01 angle pdb=" N ASP D 82 " pdb=" CA ASP D 82 " pdb=" C ASP D 82 " ideal model delta sigma weight residual 113.72 108.21 5.51 1.30e+00 5.92e-01 1.79e+01 angle pdb=" CA VAL D 83 " pdb=" C VAL D 83 " pdb=" O VAL D 83 " ideal model delta sigma weight residual 121.36 117.05 4.31 1.10e+00 8.26e-01 1.54e+01 angle pdb=" CA ARG C 16 " pdb=" CB ARG C 16 " pdb=" CG ARG C 16 " ideal model delta sigma weight residual 114.10 120.86 -6.76 2.00e+00 2.50e-01 1.14e+01 ... (remaining 9768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 3582 18.01 - 36.01: 529 36.01 - 54.01: 104 54.01 - 72.02: 23 72.02 - 90.02: 11 Dihedral angle restraints: 4249 sinusoidal: 1648 harmonic: 2601 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual -86.00 -176.02 90.02 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual -86.00 -147.63 61.63 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual 93.00 147.82 -54.82 1 1.00e+01 1.00e-02 4.07e+01 ... (remaining 4246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 762 0.040 - 0.080: 181 0.080 - 0.120: 105 0.120 - 0.160: 8 0.160 - 0.200: 3 Chirality restraints: 1059 Sorted by residual: chirality pdb=" CA GLN D 79 " pdb=" N GLN D 79 " pdb=" C GLN D 79 " pdb=" CB GLN D 79 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CA VAL C 64 " pdb=" N VAL C 64 " pdb=" C VAL C 64 " pdb=" CB VAL C 64 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA GLU C 89 " pdb=" N GLU C 89 " pdb=" C GLU C 89 " pdb=" CB GLU C 89 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 1056 not shown) Planarity restraints: 1255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 39 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO D 40 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO D 40 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 40 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 13 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 14 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 7 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO D 8 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 8 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 8 " 0.023 5.00e-02 4.00e+02 ... (remaining 1252 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 753 2.75 - 3.29: 6422 3.29 - 3.82: 10022 3.82 - 4.36: 10946 4.36 - 4.90: 20619 Nonbonded interactions: 48762 Sorted by model distance: nonbonded pdb=" OD1 ASP L 17 " pdb=" N ARG L 18 " model vdw 2.209 3.120 nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 102 " model vdw 2.231 3.040 nonbonded pdb=" N GLU H 89 " pdb=" OE1 GLU H 89 " model vdw 2.272 3.120 nonbonded pdb=" O SER H 120 " pdb=" OG SER H 120 " model vdw 2.297 3.040 nonbonded pdb=" O LEU C 18 " pdb=" NE2 GLN C 82 " model vdw 2.306 3.120 ... (remaining 48757 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' selection = (chain 'C' and (resid 1 through 118 or (resid 119 through 120 and (name N or nam \ e CA or name C or name O or name CB )))) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 2 through 108) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.030 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.320 Find NCS groups from input model: 0.150 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.003 0.054 7206 Z= 0.175 Angle : 0.681 9.692 9789 Z= 0.370 Chirality : 0.045 0.200 1059 Planarity : 0.004 0.053 1255 Dihedral : 17.359 89.537 2567 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.26 % Favored : 87.40 % Rotamer: Outliers : 0.26 % Allowed : 34.15 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.29), residues: 889 helix: 0.11 (1.94), residues: 8 sheet: -0.42 (0.32), residues: 323 loop : -1.99 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.003 0.001 HIS H 97 PHE 0.013 0.001 PHE L 118 TYR 0.011 0.001 TYR B 91 ARG 0.007 0.000 ARG C 87 Details of bonding type rmsd hydrogen bonds : bond 0.32922 ( 134) hydrogen bonds : angle 10.22464 ( 333) SS BOND : bond 0.00253 ( 8) SS BOND : angle 1.07307 ( 16) covalent geometry : bond 0.00338 ( 7198) covalent geometry : angle 0.68063 ( 9773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.755 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 106 average time/residue: 0.1878 time to fit residues: 26.7520 Evaluate side-chains 104 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain A residue 108 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.0070 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN D 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.103249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.078836 restraints weight = 14762.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.078219 restraints weight = 14328.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.079035 restraints weight = 12712.753| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7206 Z= 0.154 Angle : 0.635 8.859 9789 Z= 0.330 Chirality : 0.045 0.147 1059 Planarity : 0.004 0.049 1255 Dihedral : 4.621 54.587 988 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.94 % Favored : 86.84 % Rotamer: Outliers : 3.74 % Allowed : 29.90 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.29), residues: 889 helix: 0.97 (1.39), residues: 14 sheet: -0.22 (0.31), residues: 340 loop : -2.10 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.004 0.001 HIS H 97 PHE 0.014 0.001 PHE H 80 TYR 0.012 0.001 TYR B 91 ARG 0.004 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 134) hydrogen bonds : angle 7.17221 ( 333) SS BOND : bond 0.00461 ( 8) SS BOND : angle 0.97424 ( 16) covalent geometry : bond 0.00357 ( 7198) covalent geometry : angle 0.63479 ( 9773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.783 Fit side-chains REVERT: H 196 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8044 (pt) REVERT: B 105 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: D 11 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7945 (tt) REVERT: D 81 ASP cc_start: 0.8581 (t0) cc_final: 0.8325 (t0) outliers start: 29 outliers final: 14 residues processed: 126 average time/residue: 0.1891 time to fit residues: 32.1522 Evaluate side-chains 119 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 36 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 178 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.099652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.075682 restraints weight = 14957.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.074838 restraints weight = 14514.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.075481 restraints weight = 12856.529| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7206 Z= 0.220 Angle : 0.692 9.036 9789 Z= 0.359 Chirality : 0.046 0.140 1059 Planarity : 0.005 0.045 1255 Dihedral : 5.064 59.767 986 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.34 % Allowed : 14.51 % Favored : 85.15 % Rotamer: Outliers : 4.38 % Allowed : 31.44 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.29), residues: 889 helix: 0.98 (1.40), residues: 14 sheet: -0.26 (0.31), residues: 328 loop : -2.24 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.006 0.001 HIS A 35 PHE 0.013 0.002 PHE H 80 TYR 0.014 0.002 TYR B 91 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.04587 ( 134) hydrogen bonds : angle 6.63872 ( 333) SS BOND : bond 0.00609 ( 8) SS BOND : angle 1.29003 ( 16) covalent geometry : bond 0.00527 ( 7198) covalent geometry : angle 0.69105 ( 9773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: H 196 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8158 (pt) REVERT: L 166 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: B 105 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: D 81 ASP cc_start: 0.8733 (t0) cc_final: 0.8354 (t0) outliers start: 34 outliers final: 22 residues processed: 131 average time/residue: 0.1804 time to fit residues: 31.7536 Evaluate side-chains 125 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 57 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.0870 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 178 GLN H 199 GLN L 138 ASN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.104726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.077808 restraints weight = 14879.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.077955 restraints weight = 10144.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.078779 restraints weight = 9064.163| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7206 Z= 0.108 Angle : 0.614 8.367 9789 Z= 0.311 Chirality : 0.044 0.153 1059 Planarity : 0.004 0.049 1255 Dihedral : 4.193 20.227 984 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.02 % Favored : 88.75 % Rotamer: Outliers : 4.25 % Allowed : 31.70 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.29), residues: 889 helix: 1.19 (1.45), residues: 14 sheet: -0.24 (0.31), residues: 328 loop : -2.16 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.003 0.001 HIS A 35 PHE 0.012 0.001 PHE L 118 TYR 0.015 0.001 TYR H 152 ARG 0.002 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03077 ( 134) hydrogen bonds : angle 5.79925 ( 333) SS BOND : bond 0.00420 ( 8) SS BOND : angle 0.91117 ( 16) covalent geometry : bond 0.00246 ( 7198) covalent geometry : angle 0.61311 ( 9773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.759 Fit side-chains REVERT: H 152 TYR cc_start: 0.8458 (p90) cc_final: 0.8227 (p90) REVERT: H 199 GLN cc_start: 0.6403 (OUTLIER) cc_final: 0.6162 (mp10) REVERT: H 201 TYR cc_start: 0.7720 (m-80) cc_final: 0.7326 (m-80) REVERT: L 166 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: B 105 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: D 81 ASP cc_start: 0.8669 (t0) cc_final: 0.8452 (t0) outliers start: 33 outliers final: 14 residues processed: 133 average time/residue: 0.1796 time to fit residues: 32.0443 Evaluate side-chains 117 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 83 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 70 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 178 GLN H 199 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.102758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.078315 restraints weight = 14765.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.077657 restraints weight = 13595.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.078534 restraints weight = 12147.344| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7206 Z= 0.138 Angle : 0.652 8.499 9789 Z= 0.331 Chirality : 0.044 0.158 1059 Planarity : 0.004 0.049 1255 Dihedral : 4.254 18.645 984 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.60 % Favored : 87.18 % Rotamer: Outliers : 5.03 % Allowed : 30.28 % Favored : 64.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.29), residues: 889 helix: 1.23 (1.45), residues: 14 sheet: -0.18 (0.31), residues: 334 loop : -2.20 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.004 0.001 HIS A 35 PHE 0.021 0.001 PHE L 118 TYR 0.012 0.001 TYR H 152 ARG 0.006 0.000 ARG A 16 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 134) hydrogen bonds : angle 5.74666 ( 333) SS BOND : bond 0.00395 ( 8) SS BOND : angle 1.19871 ( 16) covalent geometry : bond 0.00326 ( 7198) covalent geometry : angle 0.65034 ( 9773) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.851 Fit side-chains REVERT: H 152 TYR cc_start: 0.8418 (p90) cc_final: 0.8192 (p90) REVERT: L 166 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: D 81 ASP cc_start: 0.8692 (t0) cc_final: 0.8479 (t0) outliers start: 39 outliers final: 28 residues processed: 133 average time/residue: 0.1762 time to fit residues: 31.9849 Evaluate side-chains 126 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 201 TYR Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 0.0970 chunk 17 optimal weight: 0.0570 chunk 23 optimal weight: 0.0030 overall best weight: 0.3906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 178 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.105122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.080881 restraints weight = 14798.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.080150 restraints weight = 14406.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.081088 restraints weight = 12584.300| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7206 Z= 0.106 Angle : 0.621 7.421 9789 Z= 0.314 Chirality : 0.044 0.156 1059 Planarity : 0.004 0.048 1255 Dihedral : 4.025 20.119 984 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.35 % Favored : 89.43 % Rotamer: Outliers : 3.48 % Allowed : 31.57 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.29), residues: 889 helix: 1.26 (1.46), residues: 14 sheet: -0.13 (0.31), residues: 326 loop : -2.13 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 32 HIS 0.002 0.001 HIS H 97 PHE 0.014 0.001 PHE L 118 TYR 0.012 0.001 TYR H 201 ARG 0.004 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.02769 ( 134) hydrogen bonds : angle 5.44026 ( 333) SS BOND : bond 0.00316 ( 8) SS BOND : angle 0.99039 ( 16) covalent geometry : bond 0.00246 ( 7198) covalent geometry : angle 0.61977 ( 9773) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: H 199 GLN cc_start: 0.8703 (mp10) cc_final: 0.7228 (tm-30) REVERT: L 166 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: A 83 MET cc_start: 0.8219 (mmp) cc_final: 0.7949 (mmp) outliers start: 27 outliers final: 18 residues processed: 125 average time/residue: 0.1837 time to fit residues: 30.8779 Evaluate side-chains 119 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 47 optimal weight: 0.0050 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.0770 chunk 77 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 0.0770 chunk 17 optimal weight: 9.9990 overall best weight: 1.0314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.103322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.078969 restraints weight = 14802.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.078262 restraints weight = 14781.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.079067 restraints weight = 12976.151| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7206 Z= 0.135 Angle : 0.649 7.854 9789 Z= 0.330 Chirality : 0.044 0.147 1059 Planarity : 0.004 0.048 1255 Dihedral : 4.112 18.325 984 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.49 % Favored : 87.29 % Rotamer: Outliers : 4.25 % Allowed : 32.09 % Favored : 63.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.29), residues: 889 helix: 1.28 (1.47), residues: 14 sheet: -0.06 (0.31), residues: 332 loop : -2.15 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 36 HIS 0.003 0.001 HIS A 35 PHE 0.011 0.001 PHE L 118 TYR 0.011 0.001 TYR B 91 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03123 ( 134) hydrogen bonds : angle 5.50049 ( 333) SS BOND : bond 0.00374 ( 8) SS BOND : angle 1.19447 ( 16) covalent geometry : bond 0.00322 ( 7198) covalent geometry : angle 0.64729 ( 9773) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.7919 (ttm170) REVERT: H 199 GLN cc_start: 0.8565 (mp10) cc_final: 0.7322 (tm-30) REVERT: L 166 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: B 105 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7443 (mt-10) outliers start: 33 outliers final: 25 residues processed: 129 average time/residue: 0.1870 time to fit residues: 32.5100 Evaluate side-chains 128 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 0.0470 chunk 26 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 61 optimal weight: 0.0060 chunk 82 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 3 optimal weight: 0.0010 overall best weight: 0.2300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 178 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.106280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.082122 restraints weight = 14754.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.080998 restraints weight = 14101.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081847 restraints weight = 15301.918| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7206 Z= 0.109 Angle : 0.626 8.691 9789 Z= 0.319 Chirality : 0.044 0.151 1059 Planarity : 0.004 0.049 1255 Dihedral : 3.906 20.471 984 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.90 % Favored : 89.88 % Rotamer: Outliers : 3.74 % Allowed : 32.73 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.29), residues: 889 helix: 1.29 (1.48), residues: 14 sheet: 0.10 (0.32), residues: 313 loop : -2.12 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 32 HIS 0.002 0.001 HIS H 207 PHE 0.009 0.001 PHE A 80 TYR 0.022 0.001 TYR H 152 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.02448 ( 134) hydrogen bonds : angle 5.15977 ( 333) SS BOND : bond 0.00265 ( 8) SS BOND : angle 0.95338 ( 16) covalent geometry : bond 0.00254 ( 7198) covalent geometry : angle 0.62498 ( 9773) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: H 199 GLN cc_start: 0.8455 (mp10) cc_final: 0.7320 (tm-30) REVERT: L 166 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8116 (tt0) outliers start: 29 outliers final: 23 residues processed: 126 average time/residue: 0.1873 time to fit residues: 32.2547 Evaluate side-chains 123 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 ASN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.099613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.074910 restraints weight = 14949.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.074234 restraints weight = 14970.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.074939 restraints weight = 12946.862| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 7206 Z= 0.292 Angle : 0.792 10.547 9789 Z= 0.411 Chirality : 0.048 0.170 1059 Planarity : 0.005 0.047 1255 Dihedral : 4.885 22.772 984 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 15.97 % Favored : 83.80 % Rotamer: Outliers : 3.87 % Allowed : 32.73 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.29), residues: 889 helix: 1.25 (1.51), residues: 14 sheet: -0.28 (0.31), residues: 336 loop : -2.28 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 148 HIS 0.008 0.002 HIS A 35 PHE 0.014 0.002 PHE D 71 TYR 0.025 0.002 TYR H 152 ARG 0.003 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 134) hydrogen bonds : angle 6.25981 ( 333) SS BOND : bond 0.00648 ( 8) SS BOND : angle 2.30889 ( 16) covalent geometry : bond 0.00697 ( 7198) covalent geometry : angle 0.78687 ( 9773) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8005 (ttm170) REVERT: H 199 GLN cc_start: 0.8317 (mp10) cc_final: 0.7243 (tm-30) REVERT: L 166 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: B 105 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: C 23 GLU cc_start: 0.8417 (pp20) cc_final: 0.8176 (pp20) outliers start: 30 outliers final: 23 residues processed: 123 average time/residue: 0.1834 time to fit residues: 30.6836 Evaluate side-chains 125 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.102551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.077995 restraints weight = 14944.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.077575 restraints weight = 14621.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.078344 restraints weight = 12854.204| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7206 Z= 0.150 Angle : 0.709 11.437 9789 Z= 0.363 Chirality : 0.045 0.203 1059 Planarity : 0.004 0.049 1255 Dihedral : 4.542 23.245 984 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.49 % Favored : 87.29 % Rotamer: Outliers : 3.35 % Allowed : 33.38 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.29), residues: 889 helix: 1.27 (1.49), residues: 14 sheet: -0.18 (0.31), residues: 334 loop : -2.29 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 148 HIS 0.004 0.001 HIS H 97 PHE 0.021 0.001 PHE L 118 TYR 0.024 0.001 TYR H 152 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 134) hydrogen bonds : angle 5.76635 ( 333) SS BOND : bond 0.00387 ( 8) SS BOND : angle 1.93822 ( 16) covalent geometry : bond 0.00357 ( 7198) covalent geometry : angle 0.70499 ( 9773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.900 Fit side-chains REVERT: H 199 GLN cc_start: 0.8240 (mp10) cc_final: 0.7199 (tm-30) REVERT: L 166 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: B 105 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: C 23 GLU cc_start: 0.8313 (pp20) cc_final: 0.8108 (pp20) outliers start: 26 outliers final: 22 residues processed: 118 average time/residue: 0.1890 time to fit residues: 31.0600 Evaluate side-chains 120 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.102589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.078170 restraints weight = 14669.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.077509 restraints weight = 14586.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.078228 restraints weight = 12762.299| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7206 Z= 0.145 Angle : 0.693 8.939 9789 Z= 0.354 Chirality : 0.045 0.200 1059 Planarity : 0.004 0.050 1255 Dihedral : 4.397 22.606 984 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.50 % Favored : 86.28 % Rotamer: Outliers : 3.35 % Allowed : 33.38 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.29), residues: 889 helix: 1.28 (1.49), residues: 14 sheet: -0.15 (0.31), residues: 334 loop : -2.28 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 148 HIS 0.004 0.001 HIS A 35 PHE 0.019 0.001 PHE L 118 TYR 0.026 0.001 TYR H 152 ARG 0.010 0.000 ARG A 16 Details of bonding type rmsd hydrogen bonds : bond 0.03204 ( 134) hydrogen bonds : angle 5.58216 ( 333) SS BOND : bond 0.00406 ( 8) SS BOND : angle 1.81536 ( 16) covalent geometry : bond 0.00348 ( 7198) covalent geometry : angle 0.69010 ( 9773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2269.37 seconds wall clock time: 40 minutes 45.42 seconds (2445.42 seconds total)