Starting phenix.real_space_refine on Tue Aug 4 11:45:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kig_37259/08_2026/8kig_37259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kig_37259/08_2026/8kig_37259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kig_37259/08_2026/8kig_37259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kig_37259/08_2026/8kig_37259.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kig_37259/08_2026/8kig_37259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kig_37259/08_2026/8kig_37259.map" } resolution = 3.1 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= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 27 5.16 5 C 1405 2.51 5 N 327 2.21 5 O 344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2104 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2025 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 1, 'ASP:plan': 1, '4J2:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.01, per 1000 atoms: 0.48 Number of scatterers: 2104 At special positions: 0 Unit cell: (74.8, 64.6, 79.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 27 16.00 O 344 8.00 N 327 7.00 C 1405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 268 " - pdb=" SG CYS R 274 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 72.3 milliseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 4J2 L 4 " Number of C-beta restraints generated: 514 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 83.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'R' and resid 41 through 66 removed outlier: 4.125A pdb=" N PHE R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 103 removed outlier: 3.522A pdb=" N ALA R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 121 removed outlier: 3.752A pdb=" N ASN R 118 " --> pdb=" O GLN R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 148 removed outlier: 3.680A pdb=" N VAL R 129 " --> pdb=" O CYS R 125 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER R 131 " --> pdb=" O SER R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 156 Processing helix chain 'R' and resid 157 through 182 removed outlier: 3.794A pdb=" N ILE R 180 " --> pdb=" O GLY R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 211 removed outlier: 3.505A pdb=" N VAL R 190 " --> pdb=" O LYS R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 241 removed outlier: 4.053A pdb=" N ALA R 241 " --> pdb=" O CYS R 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 237 through 241' Processing helix chain 'R' and resid 242 through 265 removed outlier: 3.526A pdb=" N PHE R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE R 252 " --> pdb=" O LEU R 248 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE R 253 " --> pdb=" O GLY R 249 " (cutoff:3.500A) Proline residue: R 257 - end of helix removed outlier: 3.565A pdb=" N HIS R 261 " --> pdb=" O PRO R 257 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU R 262 " --> pdb=" O PHE R 258 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE R 265 " --> pdb=" O HIS R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 279 removed outlier: 3.845A pdb=" N CYS R 276 " --> pdb=" O PRO R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 Processing helix chain 'R' and resid 285 through 291 Processing helix chain 'R' and resid 294 through 301 Processing helix chain 'R' and resid 303 through 315 removed outlier: 3.627A pdb=" N ARG R 307 " --> pdb=" O SER R 303 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 432 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: 0.31 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 604 1.34 - 1.46: 406 1.46 - 1.58: 1101 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 2151 Sorted by residual: bond pdb=" CA 4J2 L 4 " pdb=" C 4J2 L 4 " ideal model delta sigma weight residual 1.525 1.561 -0.036 2.10e-02 2.27e+03 2.98e+00 bond pdb=" CG PRO R 72 " pdb=" CD PRO R 72 " ideal model delta sigma weight residual 1.503 1.556 -0.053 3.40e-02 8.65e+02 2.46e+00 bond pdb=" C TYR R 74 " pdb=" O TYR R 74 " ideal model delta sigma weight residual 1.235 1.215 0.021 1.33e-02 5.65e+03 2.39e+00 bond pdb=" N TYR R 74 " pdb=" CA TYR R 74 " ideal model delta sigma weight residual 1.456 1.475 -0.019 1.32e-02 5.74e+03 2.08e+00 bond pdb=" CB 4J2 L 4 " pdb=" CG 4J2 L 4 " ideal model delta sigma weight residual 1.501 1.472 0.029 2.00e-02 2.50e+03 2.06e+00 ... (remaining 2146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 2795 1.46 - 2.92: 101 2.92 - 4.37: 22 4.37 - 5.83: 5 5.83 - 7.29: 3 Bond angle restraints: 2926 Sorted by residual: angle pdb=" CA TYR R 105 " pdb=" C TYR R 105 " pdb=" N LEU R 106 " ideal model delta sigma weight residual 118.22 121.03 -2.81 1.03e+00 9.43e-01 7.46e+00 angle pdb=" CB MET R 289 " pdb=" CG MET R 289 " pdb=" SD MET R 289 " ideal model delta sigma weight residual 112.70 105.60 7.10 3.00e+00 1.11e-01 5.60e+00 angle pdb=" C THR R 107 " pdb=" N PHE R 108 " pdb=" CA PHE R 108 " ideal model delta sigma weight residual 122.50 118.53 3.97 1.82e+00 3.02e-01 4.76e+00 angle pdb=" N VAL R 263 " pdb=" CA VAL R 263 " pdb=" C VAL R 263 " ideal model delta sigma weight residual 113.16 109.94 3.22 1.49e+00 4.50e-01 4.66e+00 angle pdb=" CA LEU R 106 " pdb=" CB LEU R 106 " pdb=" CG LEU R 106 " ideal model delta sigma weight residual 116.30 123.59 -7.29 3.50e+00 8.16e-02 4.34e+00 ... (remaining 2921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 1047 16.43 - 32.86: 159 32.86 - 49.30: 38 49.30 - 65.73: 8 65.73 - 82.16: 2 Dihedral angle restraints: 1254 sinusoidal: 468 harmonic: 786 Sorted by residual: dihedral pdb=" CA GLU R 109 " pdb=" C GLU R 109 " pdb=" N ASP R 110 " pdb=" CA ASP R 110 " ideal model delta harmonic sigma weight residual -180.00 -154.24 -25.76 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA LEU R 262 " pdb=" C LEU R 262 " pdb=" N VAL R 263 " pdb=" CA VAL R 263 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CB CYS R 268 " pdb=" SG CYS R 268 " pdb=" SG CYS R 274 " pdb=" CB CYS R 274 " ideal model delta sinusoidal sigma weight residual -86.00 -122.89 36.89 1 1.00e+01 1.00e-02 1.92e+01 ... (remaining 1251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 196 0.033 - 0.065: 126 0.065 - 0.098: 28 0.098 - 0.131: 7 0.131 - 0.163: 7 Chirality restraints: 364 Sorted by residual: chirality pdb=" CG LEU R 106 " pdb=" CB LEU R 106 " pdb=" CD1 LEU R 106 " pdb=" CD2 LEU R 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CB THR R 194 " pdb=" CA THR R 194 " pdb=" OG1 THR R 194 " pdb=" CG2 THR R 194 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA PRO R 72 " pdb=" N PRO R 72 " pdb=" C PRO R 72 " pdb=" CB PRO R 72 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 361 not shown) Planarity restraints: 344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER R 71 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO R 72 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO R 72 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 72 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 302 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C ARG R 302 " 0.020 2.00e-02 2.50e+03 pdb=" O ARG R 302 " -0.007 2.00e-02 2.50e+03 pdb=" N SER R 303 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 197 " -0.009 2.00e-02 2.50e+03 6.30e-03 6.95e-01 pdb=" CG PHE R 197 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE R 197 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 197 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 197 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE R 197 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 197 " -0.001 2.00e-02 2.50e+03 ... (remaining 341 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 62 2.69 - 3.24: 2154 3.24 - 3.80: 3228 3.80 - 4.35: 4073 4.35 - 4.90: 6765 Nonbonded interactions: 16282 Sorted by model distance: nonbonded pdb=" O VAL R 263 " pdb=" OG1 THR R 267 " model vdw 2.138 3.040 nonbonded pdb=" OG SER R 52 " pdb=" OG SER R 88 " model vdw 2.146 3.040 nonbonded pdb=" OE2 GLU R 94 " pdb="CA CA R 401 " model vdw 2.173 2.510 nonbonded pdb=" O SER R 127 " pdb=" OG SER R 127 " model vdw 2.196 3.040 nonbonded pdb=" OD2 ASP R 121 " pdb="CA CA R 401 " model vdw 2.262 2.510 ... (remaining 16277 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: 3.330 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.860 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 : 0.007 0.102 2153 Z= 0.354 Angle : 0.719 7.289 2928 Z= 0.370 Chirality : 0.046 0.163 364 Planarity : 0.005 0.066 344 Dihedral : 16.913 82.158 737 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.85 % Allowed : 37.02 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.56), residues: 255 helix: 0.14 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -1.55 (1.06), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 302 TYR 0.011 0.002 TYR R 152 PHE 0.014 0.002 PHE R 259 TRP 0.010 0.002 TRP R 169 HIS 0.002 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.28 ( 2151) covalent geometry : angle 0.71890 / 0.37 ( 2926) SS BOND : bond 0.00209 / 0.11 ( 1) SS BOND : angle 1.04727 / 0.62 ( 2) hydrogen bonds : bond 0.20409 / 13.37 ( 146) hydrogen bonds : angle 7.09416 / 5.05 ( 432) Misc. bond : bond 0.10198 / 5.37 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.100 Fit side-chains REVERT: R 307 ARG cc_start: 0.8720 (mtp85) cc_final: 0.8370 (mtm-85) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.0841 time to fit residues: 5.1042 Evaluate side-chains 51 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 145 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.160906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.127427 restraints weight = 2809.658| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.68 r_work: 0.3502 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2153 Z= 0.147 Angle : 0.609 6.385 2928 Z= 0.316 Chirality : 0.041 0.153 364 Planarity : 0.003 0.019 344 Dihedral : 5.125 26.694 286 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.53 % Allowed : 29.79 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.56), residues: 255 helix: 0.79 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -0.65 (1.18), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 302 TYR 0.012 0.001 TYR R 277 PHE 0.018 0.001 PHE R 197 TRP 0.013 0.002 TRP R 169 HIS 0.001 0.000 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 2151) covalent geometry : angle 0.60882 / 0.32 ( 2926) SS BOND : bond 0.00285 / 0.15 ( 1) SS BOND : angle 0.78704 / 0.46 ( 2) hydrogen bonds : bond 0.04941 / 3.33 ( 146) hydrogen bonds : angle 4.81835 / 3.43 ( 432) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.086 Fit side-chains REVERT: R 184 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.5668 (pm20) REVERT: R 197 PHE cc_start: 0.8069 (t80) cc_final: 0.7868 (t80) REVERT: R 307 ARG cc_start: 0.8682 (mtp85) cc_final: 0.8175 (mtm-85) outliers start: 13 outliers final: 3 residues processed: 62 average time/residue: 0.0626 time to fit residues: 4.5561 Evaluate side-chains 57 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 102 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.166660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133387 restraints weight = 2763.699| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.64 r_work: 0.3539 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2153 Z= 0.124 Angle : 0.545 6.101 2928 Z= 0.286 Chirality : 0.039 0.127 364 Planarity : 0.003 0.019 344 Dihedral : 4.635 25.556 285 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.68 % Allowed : 30.64 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.56), residues: 255 helix: 1.25 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -0.27 (1.16), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 302 TYR 0.009 0.001 TYR R 152 PHE 0.021 0.001 PHE R 197 TRP 0.010 0.001 TRP R 169 HIS 0.001 0.000 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 2151) covalent geometry : angle 0.54471 / 0.29 ( 2926) SS BOND : bond 0.00192 / 0.10 ( 1) SS BOND : angle 0.64341 / 0.38 ( 2) hydrogen bonds : bond 0.04215 / 2.88 ( 146) hydrogen bonds : angle 4.25626 / 3.03 ( 432) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.049 Fit side-chains REVERT: R 184 GLU cc_start: 0.5697 (OUTLIER) cc_final: 0.5440 (pm20) REVERT: R 197 PHE cc_start: 0.8036 (t80) cc_final: 0.7796 (t80) REVERT: R 201 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8218 (mp) REVERT: R 307 ARG cc_start: 0.8670 (mtp85) cc_final: 0.8147 (mtm-85) outliers start: 11 outliers final: 4 residues processed: 61 average time/residue: 0.0623 time to fit residues: 4.4261 Evaluate side-chains 60 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.167134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133733 restraints weight = 2717.937| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.64 r_work: 0.3554 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2153 Z= 0.118 Angle : 0.560 7.309 2928 Z= 0.283 Chirality : 0.038 0.138 364 Planarity : 0.003 0.018 344 Dihedral : 4.416 24.622 285 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.96 % Allowed : 28.94 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.57), residues: 255 helix: 1.51 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.10 (1.17), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 302 TYR 0.012 0.001 TYR R 277 PHE 0.021 0.001 PHE R 197 TRP 0.008 0.001 TRP R 169 HIS 0.001 0.000 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 2151) covalent geometry : angle 0.56003 / 0.28 ( 2926) SS BOND : bond 0.00236 / 0.12 ( 1) SS BOND : angle 0.72364 / 0.43 ( 2) hydrogen bonds : bond 0.04003 / 2.75 ( 146) hydrogen bonds : angle 4.01400 / 2.86 ( 432) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.080 Fit side-chains REVERT: R 184 GLU cc_start: 0.5765 (OUTLIER) cc_final: 0.5512 (pm20) REVERT: R 201 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8195 (mp) outliers start: 14 outliers final: 7 residues processed: 62 average time/residue: 0.0620 time to fit residues: 4.5045 Evaluate side-chains 60 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 chunk 17 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.169129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135657 restraints weight = 2683.939| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.64 r_work: 0.3578 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2153 Z= 0.109 Angle : 0.543 7.488 2928 Z= 0.273 Chirality : 0.038 0.140 364 Planarity : 0.003 0.020 344 Dihedral : 4.254 24.055 285 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.11 % Allowed : 30.64 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.57), residues: 255 helix: 1.73 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.20 (1.14), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 302 TYR 0.014 0.001 TYR R 277 PHE 0.014 0.001 PHE R 197 TRP 0.008 0.001 TRP R 169 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 2151) covalent geometry : angle 0.54266 / 0.27 ( 2926) SS BOND : bond 0.00195 / 0.10 ( 1) SS BOND : angle 0.57332 / 0.33 ( 2) hydrogen bonds : bond 0.03745 / 2.58 ( 146) hydrogen bonds : angle 3.88159 / 2.79 ( 432) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.079 Fit side-chains REVERT: R 184 GLU cc_start: 0.5648 (OUTLIER) cc_final: 0.5354 (pm20) REVERT: R 201 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8241 (mp) REVERT: R 289 MET cc_start: 0.8188 (mmm) cc_final: 0.7834 (mmm) REVERT: R 307 ARG cc_start: 0.8632 (mtp85) cc_final: 0.8312 (mtm-85) outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 0.0622 time to fit residues: 4.6384 Evaluate side-chains 62 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 8 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.1832 > 50:) chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.168452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.134800 restraints weight = 2682.900| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.64 r_work: 0.3559 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2153 Z= 0.111 Angle : 0.552 7.277 2928 Z= 0.274 Chirality : 0.038 0.146 364 Planarity : 0.003 0.023 344 Dihedral : 4.159 23.777 285 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.53 % Allowed : 31.06 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.57), residues: 255 helix: 1.83 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.21 (1.10), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 302 TYR 0.011 0.001 TYR R 277 PHE 0.020 0.001 PHE R 197 TRP 0.007 0.001 TRP R 169 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 2151) covalent geometry : angle 0.55163 / 0.27 ( 2926) SS BOND : bond 0.00237 / 0.12 ( 1) SS BOND : angle 0.72877 / 0.42 ( 2) hydrogen bonds : bond 0.03758 / 2.59 ( 146) hydrogen bonds : angle 3.82511 / 2.72 ( 432) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.080 Fit side-chains REVERT: R 201 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8170 (mp) REVERT: R 289 MET cc_start: 0.8165 (mmm) cc_final: 0.7864 (mmm) outliers start: 13 outliers final: 10 residues processed: 61 average time/residue: 0.0624 time to fit residues: 4.4667 Evaluate side-chains 63 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.168572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134725 restraints weight = 2728.457| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.69 r_work: 0.3560 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2153 Z= 0.115 Angle : 0.564 7.720 2928 Z= 0.278 Chirality : 0.038 0.148 364 Planarity : 0.003 0.025 344 Dihedral : 4.142 23.383 285 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 6.81 % Allowed : 30.21 % Favored : 62.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.57), residues: 255 helix: 1.86 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.24 (1.09), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 302 TYR 0.011 0.001 TYR R 277 PHE 0.013 0.001 PHE R 197 TRP 0.007 0.001 TRP R 169 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 2151) covalent geometry : angle 0.56422 / 0.28 ( 2926) SS BOND : bond 0.00201 / 0.11 ( 1) SS BOND : angle 0.72047 / 0.42 ( 2) hydrogen bonds : bond 0.03825 / 2.64 ( 146) hydrogen bonds : angle 3.83286 / 2.72 ( 432) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.095 Fit side-chains REVERT: R 184 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.5121 (pm20) REVERT: R 201 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8235 (mp) REVERT: R 289 MET cc_start: 0.8164 (mmm) cc_final: 0.7841 (mmm) outliers start: 16 outliers final: 10 residues processed: 61 average time/residue: 0.0498 time to fit residues: 3.7034 Evaluate side-chains 64 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 116 MET Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.169503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135771 restraints weight = 2679.437| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.67 r_work: 0.3575 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2153 Z= 0.111 Angle : 0.583 8.502 2928 Z= 0.281 Chirality : 0.038 0.150 364 Planarity : 0.003 0.027 344 Dihedral : 4.089 22.959 285 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 6.81 % Allowed : 31.06 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.56), residues: 255 helix: 1.92 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.37 (1.06), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 302 TYR 0.010 0.001 TYR R 277 PHE 0.022 0.001 PHE R 197 TRP 0.007 0.001 TRP R 169 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 2151) covalent geometry : angle 0.58300 / 0.28 ( 2926) SS BOND : bond 0.00201 / 0.11 ( 1) SS BOND : angle 0.64385 / 0.37 ( 2) hydrogen bonds : bond 0.03677 / 2.53 ( 146) hydrogen bonds : angle 3.76086 / 2.66 ( 432) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.075 Fit side-chains REVERT: R 184 GLU cc_start: 0.5673 (OUTLIER) cc_final: 0.5140 (pm20) REVERT: R 201 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8180 (mp) outliers start: 16 outliers final: 12 residues processed: 61 average time/residue: 0.0470 time to fit residues: 3.5119 Evaluate side-chains 65 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 116 MET Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.169324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135570 restraints weight = 2696.639| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.66 r_work: 0.3564 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2153 Z= 0.115 Angle : 0.588 7.933 2928 Z= 0.285 Chirality : 0.038 0.154 364 Planarity : 0.003 0.027 344 Dihedral : 4.070 22.563 285 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 6.38 % Allowed : 31.49 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.56), residues: 255 helix: 1.96 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.41 (1.07), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 302 TYR 0.010 0.001 TYR R 277 PHE 0.013 0.001 PHE R 197 TRP 0.007 0.001 TRP R 169 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 2151) covalent geometry : angle 0.58785 / 0.28 ( 2926) SS BOND : bond 0.00212 / 0.11 ( 1) SS BOND : angle 0.67444 / 0.39 ( 2) hydrogen bonds : bond 0.03787 / 2.61 ( 146) hydrogen bonds : angle 3.80097 / 2.69 ( 432) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.078 Fit side-chains REVERT: R 184 GLU cc_start: 0.5702 (OUTLIER) cc_final: 0.5134 (pm20) REVERT: R 201 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8222 (mp) REVERT: R 289 MET cc_start: 0.8155 (mmm) cc_final: 0.7897 (mmm) outliers start: 15 outliers final: 12 residues processed: 59 average time/residue: 0.0459 time to fit residues: 3.3082 Evaluate side-chains 64 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 116 MET Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.168411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.134441 restraints weight = 2746.881| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.70 r_work: 0.3554 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2153 Z= 0.125 Angle : 0.604 7.845 2928 Z= 0.292 Chirality : 0.039 0.155 364 Planarity : 0.003 0.025 344 Dihedral : 4.089 22.553 285 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.96 % Allowed : 32.77 % Favored : 61.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.56), residues: 255 helix: 1.94 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.38 (1.07), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 302 TYR 0.010 0.001 TYR R 277 PHE 0.021 0.001 PHE R 197 TRP 0.007 0.001 TRP R 169 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 2151) covalent geometry : angle 0.60380 / 0.29 ( 2926) SS BOND : bond 0.00229 / 0.12 ( 1) SS BOND : angle 0.76590 / 0.45 ( 2) hydrogen bonds : bond 0.03971 / 2.74 ( 146) hydrogen bonds : angle 3.84450 / 2.71 ( 432) Misc. bond : bond 0.00008 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.090 Fit side-chains REVERT: R 184 GLU cc_start: 0.5636 (OUTLIER) cc_final: 0.5043 (pm20) REVERT: R 201 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8173 (mp) REVERT: R 289 MET cc_start: 0.8157 (mmm) cc_final: 0.7907 (mmm) outliers start: 14 outliers final: 11 residues processed: 57 average time/residue: 0.0559 time to fit residues: 3.8430 Evaluate side-chains 62 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 116 MET Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 0.0010 chunk 20 optimal weight: 0.0370 chunk 18 optimal weight: 0.0070 chunk 4 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.173251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.139797 restraints weight = 2745.694| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.71 r_work: 0.3623 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2153 Z= 0.101 Angle : 0.568 7.845 2928 Z= 0.274 Chirality : 0.037 0.154 364 Planarity : 0.003 0.028 344 Dihedral : 3.959 21.573 285 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.68 % Allowed : 33.62 % Favored : 61.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.56), residues: 255 helix: 2.00 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -0.28 (1.11), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 302 TYR 0.009 0.001 TYR R 277 PHE 0.010 0.001 PHE R 197 TRP 0.007 0.001 TRP R 169 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 2151) covalent geometry : angle 0.56803 / 0.27 ( 2926) SS BOND : bond 0.00130 / 0.07 ( 1) SS BOND : angle 0.39401 / 0.23 ( 2) hydrogen bonds : bond 0.03171 / 2.17 ( 146) hydrogen bonds : angle 3.68602 / 2.61 ( 432) Misc. bond : bond 0.00002 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 801.23 seconds wall clock time: 14 minutes 31.47 seconds (871.47 seconds total)