Starting phenix.real_space_refine on Tue Feb 3 16:24:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ru5_54262/02_2026/9ru5_54262.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ru5_54262/02_2026/9ru5_54262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ru5_54262/02_2026/9ru5_54262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ru5_54262/02_2026/9ru5_54262.map" model { file = "/net/cci-nas-00/data/ceres_data/9ru5_54262/02_2026/9ru5_54262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ru5_54262/02_2026/9ru5_54262.cif" } resolution = 3.26 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= 0.001 sd= 0.018 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 20 5.16 5 C 3039 2.51 5 N 838 2.21 5 O 928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4825 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1537 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1819 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 217} Chain breaks: 1 Chain: "M" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1383 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 86 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Time building chain proxies: 1.04, per 1000 atoms: 0.22 Number of scatterers: 4825 At special positions: 0 Unit cell: (68.475, 74.25, 103.95, 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 20 16.00 O 928 8.00 N 838 7.00 C 3039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 143 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS M 99 " - pdb=" SG CYS M 162 " 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: 0.29 Conformation dependent library (CDL) restraints added in 416.0 milliseconds 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 12 sheets defined 16.4% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.701A pdb=" N SER B 84 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.531A pdb=" N ASN B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 removed outlier: 3.655A pdb=" N ILE B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 51 removed outlier: 3.920A pdb=" N ILE M 50 " --> pdb=" O ALA M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 83 removed outlier: 3.720A pdb=" N ASP M 59 " --> pdb=" O PRO M 55 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLN M 60 " --> pdb=" O GLU M 56 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN M 70 " --> pdb=" O LYS M 66 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY M 81 " --> pdb=" O GLY M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 148 removed outlier: 3.700A pdb=" N THR M 141 " --> pdb=" O ALA M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 159 Processing helix chain 'M' and resid 160 through 173 removed outlier: 3.966A pdb=" N GLY M 173 " --> pdb=" O TYR M 169 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.648A pdb=" N LEU A 87 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A 32 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS A 48 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP A 34 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 127 removed outlier: 3.595A pdb=" N TYR A 125 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 139 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 127 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 137 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 165 through 166 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 12 removed outlier: 7.333A pdb=" N LEU B 9 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL B 112 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS B 11 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 29 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 45 " --> pdb=" O TRP B 32 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLN B 34 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N PHE B 43 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR B 36 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU B 41 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE B 48 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLN B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 122 through 126 Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 163 removed outlier: 3.602A pdb=" N GLN B 211 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 207 " --> pdb=" O TRP B 158 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 235 " --> pdb=" O CYS B 208 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 233 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 19 through 21 Processing sheet with id=AB2, first strand: chain 'M' and resid 19 through 21 removed outlier: 4.316A pdb=" N TYR M 97 " --> pdb=" O TYR M 5 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE M 95 " --> pdb=" O PHE M 7 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN M 113 " --> pdb=" O MET M 96 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG M 109 " --> pdb=" O ASP M 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 123 through 124 158 hydrogen bonds defined for protein. 396 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: 0.67 Time building geometry restraints manager: 0.46 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: 1599 1.34 - 1.46: 1118 1.46 - 1.58: 2197 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 4942 Sorted by residual: bond pdb=" CA MET M 96 " pdb=" CB MET M 96 " ideal model delta sigma weight residual 1.528 1.549 -0.021 1.47e-02 4.63e+03 2.08e+00 bond pdb=" CB MET M 43 " pdb=" CG MET M 43 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" C LYS A 153 " pdb=" O LYS A 153 " ideal model delta sigma weight residual 1.234 1.247 -0.013 1.17e-02 7.31e+03 1.20e+00 bond pdb=" CB PRO B 37 " pdb=" CG PRO B 37 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.10e+00 bond pdb=" CB MET M 96 " pdb=" CG MET M 96 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.02e+00 ... (remaining 4937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 6544 2.02 - 4.05: 127 4.05 - 6.07: 16 6.07 - 8.09: 1 8.09 - 10.12: 3 Bond angle restraints: 6691 Sorted by residual: angle pdb=" CA MET M 96 " pdb=" CB MET M 96 " pdb=" CG MET M 96 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CB MET M 43 " pdb=" CG MET M 43 " pdb=" SD MET M 43 " ideal model delta sigma weight residual 112.70 102.58 10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C ASN M 64 " pdb=" N MET M 65 " pdb=" CA MET M 65 " ideal model delta sigma weight residual 122.06 116.02 6.04 1.86e+00 2.89e-01 1.05e+01 angle pdb=" CB MET M 96 " pdb=" CG MET M 96 " pdb=" SD MET M 96 " ideal model delta sigma weight residual 112.70 121.92 -9.22 3.00e+00 1.11e-01 9.45e+00 angle pdb=" N ARG M 33 " pdb=" CA ARG M 33 " pdb=" C ARG M 33 " ideal model delta sigma weight residual 107.23 112.36 -5.13 1.67e+00 3.59e-01 9.44e+00 ... (remaining 6686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 2624 16.68 - 33.35: 263 33.35 - 50.02: 39 50.02 - 66.70: 10 66.70 - 83.37: 7 Dihedral angle restraints: 2943 sinusoidal: 1190 harmonic: 1753 Sorted by residual: dihedral pdb=" CA MET M 65 " pdb=" C MET M 65 " pdb=" N LYS M 66 " pdb=" CA LYS M 66 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA VAL M 156 " pdb=" C VAL M 156 " pdb=" N TYR M 157 " pdb=" CA TYR M 157 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LEU M 158 " pdb=" C LEU M 158 " pdb=" N GLU M 159 " pdb=" CA GLU M 159 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 2940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 528 0.042 - 0.083: 123 0.083 - 0.125: 42 0.125 - 0.167: 5 0.167 - 0.208: 2 Chirality restraints: 700 Sorted by residual: chirality pdb=" CA MET M 65 " pdb=" N MET M 65 " pdb=" C MET M 65 " pdb=" CB MET M 65 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CG LEU M 76 " pdb=" CB LEU M 76 " pdb=" CD1 LEU M 76 " pdb=" CD2 LEU M 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA VAL B 17 " pdb=" N VAL B 17 " pdb=" C VAL B 17 " pdb=" CB VAL B 17 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 697 not shown) Planarity restraints: 881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 36 " 0.064 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO B 37 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 37 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 37 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 16 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO A 17 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 17 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 17 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU M 17 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO M 18 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO M 18 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO M 18 " 0.024 5.00e-02 4.00e+02 ... (remaining 878 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 56 2.56 - 3.15: 3888 3.15 - 3.73: 7443 3.73 - 4.32: 10729 4.32 - 4.90: 17496 Nonbonded interactions: 39612 Sorted by model distance: nonbonded pdb=" OE1 GLU M 61 " pdb=" OG1 THR P 2 " model vdw 1.981 3.040 nonbonded pdb=" OG SER B 63 " pdb=" OD1 ASN B 75 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR B 47 " pdb=" O GLY B 64 " model vdw 2.247 3.040 nonbonded pdb=" OD1 ASP M 100 " pdb=" OH TYR M 111 " model vdw 2.249 3.040 nonbonded pdb=" O VAL B 118 " pdb=" NH2 ARG B 225 " model vdw 2.262 3.120 ... (remaining 39607 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.340 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 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 0.052 4948 Z= 0.156 Angle : 0.696 10.115 6703 Z= 0.390 Chirality : 0.042 0.208 700 Planarity : 0.006 0.097 881 Dihedral : 13.948 83.372 1799 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.98 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.48 (0.34), residues: 587 helix: -1.84 (0.50), residues: 80 sheet: -1.63 (0.46), residues: 129 loop : -1.64 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 80 TYR 0.015 0.001 TYR M 116 PHE 0.029 0.002 PHE A 73 TRP 0.012 0.001 TRP M 49 HIS 0.002 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4942) covalent geometry : angle 0.69676 ( 6691) SS BOND : bond 0.00177 ( 6) SS BOND : angle 0.44132 ( 12) hydrogen bonds : bond 0.27736 ( 149) hydrogen bonds : angle 10.97884 ( 396) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.186 Fit side-chains REVERT: B 8 TYR cc_start: 0.6270 (m-80) cc_final: 0.4792 (m-80) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0748 time to fit residues: 6.4745 Evaluate side-chains 64 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN B 160 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** 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 = 0.4296 r_free = 0.4296 target = 0.178567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.167857 restraints weight = 7375.990| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.30 r_work: 0.4081 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4948 Z= 0.216 Angle : 0.675 7.286 6703 Z= 0.355 Chirality : 0.045 0.181 700 Planarity : 0.006 0.072 881 Dihedral : 5.488 22.115 666 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.35 % Favored : 91.48 % Rotamer: Outliers : 0.96 % Allowed : 8.03 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.48 (0.33), residues: 587 helix: -1.95 (0.50), residues: 83 sheet: -1.37 (0.45), residues: 122 loop : -1.73 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 19 TYR 0.026 0.002 TYR M 97 PHE 0.017 0.002 PHE A 203 TRP 0.014 0.002 TRP B 221 HIS 0.006 0.002 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 4942) covalent geometry : angle 0.67451 ( 6691) SS BOND : bond 0.00293 ( 6) SS BOND : angle 0.79918 ( 12) hydrogen bonds : bond 0.05506 ( 149) hydrogen bonds : angle 8.05638 ( 396) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.109 Fit side-chains REVERT: A 142 ASP cc_start: 0.5575 (m-30) cc_final: 0.5337 (m-30) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 0.0552 time to fit residues: 4.7038 Evaluate side-chains 63 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 76 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** 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 = 0.4286 r_free = 0.4286 target = 0.177712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.166907 restraints weight = 7359.272| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 2.29 r_work: 0.4070 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4948 Z= 0.216 Angle : 0.658 10.050 6703 Z= 0.347 Chirality : 0.045 0.223 700 Planarity : 0.006 0.061 881 Dihedral : 5.580 20.752 666 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 2.49 % Allowed : 10.90 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.59 (0.33), residues: 587 helix: -2.27 (0.46), residues: 83 sheet: -1.32 (0.45), residues: 122 loop : -1.79 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 19 TYR 0.021 0.002 TYR M 97 PHE 0.018 0.002 PHE A 203 TRP 0.011 0.002 TRP B 221 HIS 0.005 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 4942) covalent geometry : angle 0.65801 ( 6691) SS BOND : bond 0.00263 ( 6) SS BOND : angle 0.66344 ( 12) hydrogen bonds : bond 0.05045 ( 149) hydrogen bonds : angle 7.82268 ( 396) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.181 Fit side-chains REVERT: A 142 ASP cc_start: 0.5515 (m-30) cc_final: 0.5281 (m-30) outliers start: 13 outliers final: 6 residues processed: 61 average time/residue: 0.0630 time to fit residues: 5.3152 Evaluate side-chains 60 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain M residue 156 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** 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 = 0.4307 r_free = 0.4307 target = 0.179232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.168629 restraints weight = 7327.980| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.24 r_work: 0.4091 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4948 Z= 0.169 Angle : 0.610 7.826 6703 Z= 0.319 Chirality : 0.043 0.192 700 Planarity : 0.005 0.055 881 Dihedral : 5.339 19.245 666 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.10 % Allowed : 14.34 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.52 (0.33), residues: 587 helix: -2.33 (0.46), residues: 82 sheet: -1.25 (0.45), residues: 122 loop : -1.72 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 19 TYR 0.018 0.002 TYR M 97 PHE 0.016 0.002 PHE A 203 TRP 0.009 0.001 TRP M 58 HIS 0.004 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 4942) covalent geometry : angle 0.60972 ( 6691) SS BOND : bond 0.00202 ( 6) SS BOND : angle 0.55156 ( 12) hydrogen bonds : bond 0.04304 ( 149) hydrogen bonds : angle 7.44176 ( 396) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.5412 (m-30) cc_final: 0.5207 (m-30) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.0589 time to fit residues: 5.0636 Evaluate side-chains 61 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain M residue 65 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 53 optimal weight: 0.0000 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 0.0370 chunk 19 optimal weight: 0.3980 overall best weight: 0.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN ** B 178 GLN ** 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 = 0.4329 r_free = 0.4329 target = 0.181259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.170103 restraints weight = 7525.437| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 2.36 r_work: 0.4106 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4948 Z= 0.137 Angle : 0.594 10.764 6703 Z= 0.307 Chirality : 0.042 0.196 700 Planarity : 0.005 0.053 881 Dihedral : 5.092 18.889 666 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.87 % Allowed : 13.96 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.43 (0.34), residues: 587 helix: -2.22 (0.47), residues: 83 sheet: -1.41 (0.44), residues: 137 loop : -1.57 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 19 TYR 0.014 0.002 TYR M 97 PHE 0.012 0.001 PHE A 203 TRP 0.012 0.001 TRP M 58 HIS 0.004 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4942) covalent geometry : angle 0.59404 ( 6691) SS BOND : bond 0.00120 ( 6) SS BOND : angle 0.47893 ( 12) hydrogen bonds : bond 0.03853 ( 149) hydrogen bonds : angle 7.07525 ( 396) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.5241 (m-30) cc_final: 0.5038 (m-30) REVERT: B 43 PHE cc_start: 0.7306 (t80) cc_final: 0.7069 (t80) REVERT: M 96 MET cc_start: 0.6138 (tmm) cc_final: 0.5860 (tmm) outliers start: 15 outliers final: 12 residues processed: 65 average time/residue: 0.0584 time to fit residues: 5.3693 Evaluate side-chains 66 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 35 ASP Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 136 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN ** B 178 GLN ** 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 = 0.4309 r_free = 0.4309 target = 0.179479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.168245 restraints weight = 7438.407| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.35 r_work: 0.4085 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4948 Z= 0.181 Angle : 0.611 7.724 6703 Z= 0.320 Chirality : 0.043 0.193 700 Planarity : 0.005 0.051 881 Dihedral : 5.283 19.563 666 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 2.10 % Allowed : 15.49 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.44 (0.34), residues: 587 helix: -2.20 (0.47), residues: 82 sheet: -1.38 (0.45), residues: 142 loop : -1.59 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 19 TYR 0.014 0.002 TYR M 97 PHE 0.016 0.002 PHE A 203 TRP 0.011 0.001 TRP M 58 HIS 0.004 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 4942) covalent geometry : angle 0.61122 ( 6691) SS BOND : bond 0.00215 ( 6) SS BOND : angle 0.65000 ( 12) hydrogen bonds : bond 0.04121 ( 149) hydrogen bonds : angle 7.10300 ( 396) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 PHE cc_start: 0.7290 (t80) cc_final: 0.6932 (t80) REVERT: M 114 ASP cc_start: 0.6680 (m-30) cc_final: 0.6473 (m-30) outliers start: 11 outliers final: 11 residues processed: 62 average time/residue: 0.0676 time to fit residues: 5.8475 Evaluate side-chains 66 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 35 ASP Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 122 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.0670 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.0370 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 32 optimal weight: 0.0770 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN ** B 178 GLN ** 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 = 0.4331 r_free = 0.4331 target = 0.181662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.170536 restraints weight = 7414.130| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.35 r_work: 0.4112 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4948 Z= 0.129 Angle : 0.566 6.709 6703 Z= 0.295 Chirality : 0.042 0.181 700 Planarity : 0.005 0.049 881 Dihedral : 4.987 18.722 666 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.87 % Allowed : 15.87 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.30 (0.34), residues: 587 helix: -2.01 (0.49), residues: 82 sheet: -1.23 (0.45), residues: 142 loop : -1.55 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 19 TYR 0.012 0.001 TYR M 97 PHE 0.012 0.001 PHE A 203 TRP 0.010 0.001 TRP M 131 HIS 0.003 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4942) covalent geometry : angle 0.56628 ( 6691) SS BOND : bond 0.00138 ( 6) SS BOND : angle 0.47415 ( 12) hydrogen bonds : bond 0.03701 ( 149) hydrogen bonds : angle 6.80484 ( 396) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 PHE cc_start: 0.7157 (t80) cc_final: 0.6922 (t80) outliers start: 15 outliers final: 13 residues processed: 64 average time/residue: 0.0643 time to fit residues: 5.7365 Evaluate side-chains 67 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 35 ASP Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 166 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** 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 = 0.4305 r_free = 0.4305 target = 0.179595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.168347 restraints weight = 7522.435| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.37 r_work: 0.4083 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4948 Z= 0.191 Angle : 0.626 7.792 6703 Z= 0.328 Chirality : 0.044 0.196 700 Planarity : 0.005 0.047 881 Dihedral : 5.294 19.855 666 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 2.87 % Allowed : 16.83 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.39 (0.34), residues: 587 helix: -2.14 (0.47), residues: 82 sheet: -1.29 (0.45), residues: 142 loop : -1.60 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 19 TYR 0.014 0.002 TYR M 97 PHE 0.018 0.002 PHE A 203 TRP 0.010 0.001 TRP B 221 HIS 0.005 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 4942) covalent geometry : angle 0.62641 ( 6691) SS BOND : bond 0.00186 ( 6) SS BOND : angle 0.58959 ( 12) hydrogen bonds : bond 0.04208 ( 149) hydrogen bonds : angle 6.98702 ( 396) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 TYR cc_start: 0.6835 (m-80) cc_final: 0.5316 (m-80) REVERT: B 43 PHE cc_start: 0.7188 (t80) cc_final: 0.6938 (t80) outliers start: 15 outliers final: 14 residues processed: 63 average time/residue: 0.0700 time to fit residues: 5.9511 Evaluate side-chains 68 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 35 ASP Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 122 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 50 optimal weight: 0.2980 chunk 5 optimal weight: 0.0270 chunk 54 optimal weight: 0.3980 chunk 56 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** 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 = 0.4323 r_free = 0.4323 target = 0.181377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.170035 restraints weight = 7411.461| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.36 r_work: 0.4101 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4948 Z= 0.143 Angle : 0.608 9.994 6703 Z= 0.313 Chirality : 0.043 0.193 700 Planarity : 0.005 0.048 881 Dihedral : 5.135 22.045 666 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.06 % Allowed : 16.63 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.31 (0.35), residues: 587 helix: -2.04 (0.49), residues: 82 sheet: -1.26 (0.46), residues: 142 loop : -1.54 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 19 TYR 0.014 0.002 TYR M 97 PHE 0.013 0.002 PHE A 203 TRP 0.010 0.001 TRP M 131 HIS 0.004 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4942) covalent geometry : angle 0.60801 ( 6691) SS BOND : bond 0.00160 ( 6) SS BOND : angle 0.44667 ( 12) hydrogen bonds : bond 0.03809 ( 149) hydrogen bonds : angle 6.80582 ( 396) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 66 average time/residue: 0.0621 time to fit residues: 5.5553 Evaluate side-chains 68 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 52 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 chunk 11 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.2254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 GLN ** 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 = 0.4342 r_free = 0.4342 target = 0.183324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.171989 restraints weight = 7440.415| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.36 r_work: 0.4112 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4948 Z= 0.111 Angle : 0.586 11.470 6703 Z= 0.299 Chirality : 0.042 0.179 700 Planarity : 0.005 0.047 881 Dihedral : 4.851 21.408 666 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.68 % Allowed : 16.83 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.22 (0.34), residues: 587 helix: -1.83 (0.51), residues: 82 sheet: -1.08 (0.47), residues: 137 loop : -1.58 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 19 TYR 0.017 0.001 TYR M 97 PHE 0.010 0.001 PHE A 203 TRP 0.012 0.001 TRP M 131 HIS 0.003 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 4942) covalent geometry : angle 0.58641 ( 6691) SS BOND : bond 0.00143 ( 6) SS BOND : angle 0.36739 ( 12) hydrogen bonds : bond 0.03421 ( 149) hydrogen bonds : angle 6.45942 ( 396) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.6354 (ttpt) cc_final: 0.6058 (ttpt) REVERT: M 42 LYS cc_start: 0.7806 (mtmm) cc_final: 0.7519 (mtmm) outliers start: 14 outliers final: 13 residues processed: 66 average time/residue: 0.0676 time to fit residues: 6.0191 Evaluate side-chains 69 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 49 optimal weight: 0.2980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** 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 = 0.4295 r_free = 0.4295 target = 0.178905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.167477 restraints weight = 7455.902| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.34 r_work: 0.4074 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4948 Z= 0.204 Angle : 0.660 11.049 6703 Z= 0.342 Chirality : 0.045 0.198 700 Planarity : 0.005 0.047 881 Dihedral : 5.370 20.726 666 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 2.29 % Allowed : 17.40 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.32 (0.34), residues: 587 helix: -2.11 (0.47), residues: 83 sheet: -1.28 (0.46), residues: 142 loop : -1.52 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 73 TYR 0.017 0.002 TYR M 97 PHE 0.019 0.002 PHE A 203 TRP 0.011 0.002 TRP B 221 HIS 0.004 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 4942) covalent geometry : angle 0.66000 ( 6691) SS BOND : bond 0.00211 ( 6) SS BOND : angle 0.60693 ( 12) hydrogen bonds : bond 0.04331 ( 149) hydrogen bonds : angle 6.83053 ( 396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1216.85 seconds wall clock time: 21 minutes 45.78 seconds (1305.78 seconds total)