Starting phenix.real_space_refine on Wed Jul 1 20:45:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kig_37259/07_2026/8kig_37259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kig_37259/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kig_37259/07_2026/8kig_37259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kig_37259/07_2026/8kig_37259.map" model { file = "/net/cci-nas-00/data/ceres_data/8kig_37259/07_2026/8kig_37259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kig_37259/07_2026/8kig_37259.cif" } 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-dev-6108/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, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 0.93, per 1000 atoms: 0.44 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: 0.47 Conformation dependent library (CDL) restraints added in 159.5 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: 0.12 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: 0.42 Time building geometry restraints manager: 0.37 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 3.250 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 3.250 ... (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: 4.230 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.460 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:1.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.710 ------------------------------------------------------------------------------- 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 : 0.135 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: 0.0816 time to fit residues: 4.9392 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 : 0.087 ------------------------------------------------------------------------------- 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: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.163242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130065 restraints weight = 2790.673| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.68 r_work: 0.3514 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1509 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= 0.149 Angle : 0.611 6.540 2928 Z= 0.318 Chirality : 0.041 0.154 364 Planarity : 0.003 0.018 344 Dihedral : 5.150 26.757 286 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.96 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: 0.75 (0.56), residues: 255 helix: 0.78 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -0.63 (1.19), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 302 TYR 0.011 0.001 TYR R 277 PHE 0.018 0.001 PHE R 197 TRP 0.013 0.002 TRP R 169 HIS 0.002 0.000 HIS L 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 2151) covalent geometry : angle 0.61126 / 0.32 ( 2926) SS BOND : bond 0.00305 / 0.16 ( 1) SS BOND : angle 0.81013 / 0.48 ( 2) hydrogen bonds : bond 0.05121 / 3.45 ( 146) hydrogen bonds : angle 4.86418 / 3.46 ( 432) Misc. bond : bond 0.00013 / 0.01 ( 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 68 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.078 Fit side-chains REVERT: R 184 GLU cc_start: 0.5918 (OUTLIER) cc_final: 0.5683 (pm20) REVERT: R 307 ARG cc_start: 0.8689 (mtp85) cc_final: 0.8174 (mtm-85) outliers start: 13 outliers final: 5 residues processed: 63 average time/residue: 0.0624 time to fit residues: 4.6144 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 : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 158 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 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: 0.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.167482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134258 restraints weight = 2784.955| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.67 r_work: 0.3558 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1988 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= 0.133 Angle : 0.561 6.099 2928 Z= 0.292 Chirality : 0.039 0.129 364 Planarity : 0.003 0.016 344 Dihedral : 4.740 25.754 285 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.96 % Allowed : 31.06 % 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: 1.44 (0.56), residues: 255 helix: 1.24 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -0.31 (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 0.016 0.001 PHE R 197 TRP 0.010 0.002 TRP R 169 HIS 0.001 0.000 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 2151) covalent geometry : angle 0.56112 / 0.29 ( 2926) SS BOND : bond 0.00228 / 0.12 ( 1) SS BOND : angle 0.68270 / 0.40 ( 2) hydrogen bonds : bond 0.04398 / 3.01 ( 146) hydrogen bonds : angle 4.31761 / 3.06 ( 432) Misc. bond : bond 0.00009 / 0.00 ( 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 68 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.079 Fit side-chains REVERT: R 184 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.5492 (pm20) REVERT: R 197 PHE cc_start: 0.8051 (t80) cc_final: 0.7842 (t80) REVERT: R 201 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8250 (mp) REVERT: R 307 ARG cc_start: 0.8654 (mtp85) cc_final: 0.8108 (mtm-85) outliers start: 14 outliers final: 6 residues processed: 61 average time/residue: 0.0658 time to fit residues: 4.6709 Evaluate side-chains 62 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.077 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.0570 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.0370 chunk 12 optimal weight: 0.6980 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.171095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137784 restraints weight = 2728.916| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.65 r_work: 0.3611 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2153 Z= 0.108 Angle : 0.541 6.074 2928 Z= 0.278 Chirality : 0.038 0.135 364 Planarity : 0.003 0.016 344 Dihedral : 4.418 24.299 285 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.26 % Allowed : 31.06 % 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: 1.81 (0.57), residues: 255 helix: 1.48 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -0.09 (1.16), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 302 TYR 0.007 0.001 TYR R 277 PHE 0.016 0.001 PHE R 197 TRP 0.009 0.001 TRP R 169 HIS 0.001 0.000 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 2151) covalent geometry : angle 0.54096 / 0.28 ( 2926) SS BOND : bond 0.00210 / 0.11 ( 1) SS BOND : angle 0.59760 / 0.35 ( 2) hydrogen bonds : bond 0.03703 / 2.55 ( 146) hydrogen bonds : angle 3.99682 / 2.86 ( 432) Misc. bond : bond 0.00002 / 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 65 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.081 Fit side-chains REVERT: R 184 GLU cc_start: 0.5747 (OUTLIER) cc_final: 0.5487 (pm20) REVERT: R 201 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8208 (mp) REVERT: R 307 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8338 (mtm-85) outliers start: 10 outliers final: 6 residues processed: 60 average time/residue: 0.0614 time to fit residues: 4.3134 Evaluate side-chains 63 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 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 206 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: 1.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.166458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133378 restraints weight = 2710.391| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.64 r_work: 0.3584 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2153 Z= 0.148 Angle : 0.577 6.128 2928 Z= 0.296 Chirality : 0.040 0.139 364 Planarity : 0.003 0.021 344 Dihedral : 4.476 24.539 285 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.96 % Allowed : 29.79 % 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: 1.85 (0.57), residues: 255 helix: 1.53 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.23 (1.14), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 302 TYR 0.009 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 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 2151) covalent geometry : angle 0.57682 / 0.30 ( 2926) SS BOND : bond 0.00251 / 0.13 ( 1) SS BOND : angle 0.83574 / 0.49 ( 2) hydrogen bonds : bond 0.04502 / 3.10 ( 146) hydrogen bonds : angle 4.06016 / 2.88 ( 432) Misc. bond : bond 0.00015 / 0.01 ( 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 67 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.111 Fit side-chains REVERT: R 184 GLU cc_start: 0.5672 (OUTLIER) cc_final: 0.5395 (pm20) REVERT: R 201 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8207 (mp) REVERT: R 289 MET cc_start: 0.8161 (mmm) cc_final: 0.7864 (mmm) REVERT: R 307 ARG cc_start: 0.8652 (mtp85) cc_final: 0.8211 (mtm-85) outliers start: 14 outliers final: 7 residues processed: 62 average time/residue: 0.0635 time to fit residues: 4.6045 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 : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 MET 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 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: 0.6980 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.0770 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.171443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138229 restraints weight = 2673.259| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.64 r_work: 0.3608 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2153 Z= 0.107 Angle : 0.544 7.093 2928 Z= 0.276 Chirality : 0.038 0.144 364 Planarity : 0.003 0.020 344 Dihedral : 4.219 23.351 285 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 5.11 % Allowed : 31.49 % 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: 2.11 (0.57), residues: 255 helix: 1.71 (0.38), residues: 217 sheet: None (None), residues: 0 loop : -0.19 (1.13), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 302 TYR 0.009 0.001 TYR R 277 PHE 0.013 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 0.00232 / 0.11 ( 2151) covalent geometry : angle 0.54410 / 0.28 ( 2926) SS BOND : bond 0.00265 / 0.14 ( 1) SS BOND : angle 0.60597 / 0.35 ( 2) hydrogen bonds : bond 0.03613 / 2.49 ( 146) hydrogen bonds : angle 3.84952 / 2.76 ( 432) Misc. bond : bond 0.00003 / 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 69 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.081 Fit side-chains REVERT: R 163 THR cc_start: 0.8700 (p) cc_final: 0.8335 (t) REVERT: R 184 GLU cc_start: 0.5660 (OUTLIER) cc_final: 0.5363 (pm20) REVERT: R 201 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8241 (mp) REVERT: R 289 MET cc_start: 0.8161 (mmm) cc_final: 0.7842 (mmm) outliers start: 12 outliers final: 7 residues processed: 63 average time/residue: 0.0593 time to fit residues: 4.3918 Evaluate side-chains 63 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 184 GLU 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 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: 0.8980 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 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 = 0.4096 r_free = 0.4096 target = 0.170686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136252 restraints weight = 2740.689| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.73 r_work: 0.3588 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2153 Z= 0.119 Angle : 0.558 7.909 2928 Z= 0.279 Chirality : 0.039 0.136 364 Planarity : 0.003 0.024 344 Dihedral : 4.189 22.991 285 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.68 % Allowed : 33.19 % 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: 2.26 (0.57), residues: 255 helix: 1.83 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.25 (1.09), 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 0.021 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 0.00267 / 0.12 ( 2151) covalent geometry : angle 0.55798 / 0.28 ( 2926) SS BOND : bond 0.00161 / 0.08 ( 1) SS BOND : angle 0.82416 / 0.47 ( 2) hydrogen bonds : bond 0.03908 / 2.70 ( 146) hydrogen bonds : angle 3.84760 / 2.74 ( 432) Misc. bond : bond 0.00009 / 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 66 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.057 Fit side-chains REVERT: R 201 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8162 (mp) REVERT: R 289 MET cc_start: 0.8165 (mmm) cc_final: 0.7866 (mmm) REVERT: R 307 ARG cc_start: 0.8621 (mtp85) cc_final: 0.8159 (mtm-85) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.0554 time to fit residues: 3.9413 Evaluate side-chains 63 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.078 ------------------------------------------------------------------------------- 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 116 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.170157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136341 restraints weight = 2699.206| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.69 r_work: 0.3586 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2153 Z= 0.126 Angle : 0.586 7.878 2928 Z= 0.290 Chirality : 0.039 0.150 364 Planarity : 0.003 0.026 344 Dihedral : 4.164 22.847 285 Min Nonbonded Distance : 2.545 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: 2.22 (0.56), residues: 255 helix: 1.82 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.41 (1.06), 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 0.00287 / 0.13 ( 2151) covalent geometry : angle 0.58609 / 0.29 ( 2926) SS BOND : bond 0.00182 / 0.10 ( 1) SS BOND : angle 0.79385 / 0.46 ( 2) hydrogen bonds : bond 0.04024 / 2.79 ( 146) hydrogen bonds : angle 3.85217 / 2.73 ( 432) Misc. bond : bond 0.00008 / 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 68 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.074 Fit side-chains REVERT: R 184 GLU cc_start: 0.5594 (OUTLIER) cc_final: 0.5041 (pm20) REVERT: R 201 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8266 (mp) REVERT: R 289 MET cc_start: 0.8155 (mmm) cc_final: 0.7875 (mmm) REVERT: R 307 ARG cc_start: 0.8624 (mtp85) cc_final: 0.8158 (mtm-85) outliers start: 14 outliers final: 9 residues processed: 61 average time/residue: 0.0540 time to fit residues: 3.9090 Evaluate side-chains 65 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 116 MET Chi-restraints excluded: chain R residue 184 GLU 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: 0.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.0570 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.173153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.139570 restraints weight = 2704.876| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.68 r_work: 0.3624 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2153 Z= 0.107 Angle : 0.570 8.226 2928 Z= 0.278 Chirality : 0.038 0.152 364 Planarity : 0.003 0.026 344 Dihedral : 4.054 22.204 285 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 5.53 % Allowed : 33.62 % Favored : 60.85 % 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: 1.93 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.41 (1.06), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 302 TYR 0.007 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 0.00232 / 0.11 ( 2151) covalent geometry : angle 0.56961 / 0.28 ( 2926) SS BOND : bond 0.00146 / 0.08 ( 1) SS BOND : angle 0.55206 / 0.32 ( 2) hydrogen bonds : bond 0.03485 / 2.40 ( 146) hydrogen bonds : angle 3.73671 / 2.65 ( 432) Misc. bond : bond 0.00001 / 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 66 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.063 Fit side-chains REVERT: R 184 GLU cc_start: 0.5745 (OUTLIER) cc_final: 0.5172 (pm20) REVERT: R 201 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8143 (mp) outliers start: 13 outliers final: 10 residues processed: 60 average time/residue: 0.0395 time to fit residues: 2.8660 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 : 0.054 ------------------------------------------------------------------------------- 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 184 GLU 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: 0.9980 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.0000 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.173120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.138864 restraints weight = 2768.165| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.74 r_work: 0.3611 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2153 Z= 0.109 Angle : 0.575 8.085 2928 Z= 0.281 Chirality : 0.038 0.150 364 Planarity : 0.003 0.027 344 Dihedral : 3.999 21.913 285 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.11 % Allowed : 34.04 % Favored : 60.85 % 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: 2.43 (0.56), residues: 255 helix: 1.97 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -0.36 (1.07), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 302 TYR 0.015 0.001 TYR R 143 PHE 0.012 0.001 PHE R 197 TRP 0.007 0.001 TRP R 169 HIS 0.001 0.000 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 2151) covalent geometry : angle 0.57492 / 0.28 ( 2926) SS BOND : bond 0.00170 / 0.09 ( 1) SS BOND : angle 0.56334 / 0.33 ( 2) hydrogen bonds : bond 0.03586 / 2.48 ( 146) hydrogen bonds : angle 3.75822 / 2.66 ( 432) Misc. bond : bond 0.00005 / 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 64 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.049 Fit side-chains REVERT: R 184 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.5155 (pm20) REVERT: R 201 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8271 (mp) REVERT: R 289 MET cc_start: 0.8150 (mmm) cc_final: 0.7884 (mmm) outliers start: 12 outliers final: 10 residues processed: 58 average time/residue: 0.0377 time to fit residues: 2.6800 Evaluate side-chains 63 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 184 GLU 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: 0.8980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.170077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135812 restraints weight = 2792.619| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.74 r_work: 0.3577 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2882 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= 0.127 Angle : 0.590 7.892 2928 Z= 0.290 Chirality : 0.039 0.151 364 Planarity : 0.003 0.027 344 Dihedral : 4.063 22.202 285 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.11 % Allowed : 34.47 % Favored : 60.43 % 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: 2.37 (0.56), residues: 255 helix: 1.94 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -0.43 (1.06), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 302 TYR 0.015 0.001 TYR R 143 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 0.00289 / 0.13 ( 2151) covalent geometry : angle 0.59015 / 0.29 ( 2926) SS BOND : bond 0.00219 / 0.12 ( 1) SS BOND : angle 0.78092 / 0.45 ( 2) hydrogen bonds : bond 0.04035 / 2.79 ( 146) hydrogen bonds : angle 3.84572 / 2.71 ( 432) Misc. bond : bond 0.00009 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 763.41 seconds wall clock time: 13 minutes 56.67 seconds (836.67 seconds total)