Starting phenix.real_space_refine on Tue Aug 4 11:45:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v38_64751/08_2026/9v38_64751.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v38_64751/08_2026/9v38_64751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v38_64751/08_2026/9v38_64751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v38_64751/08_2026/9v38_64751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v38_64751/08_2026/9v38_64751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v38_64751/08_2026/9v38_64751.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 1274 2.51 5 N 331 2.21 5 O 309 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: 1930 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1883 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 236} Chain breaks: 1 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Classifications: {'peptide': 4} Link IDs: {'PTRANS': 1, 'TRANS': 2} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 0.67, per 1000 atoms: 0.35 Number of scatterers: 1930 At special positions: 0 Unit cell: (53.95, 54.9875, 80.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 309 8.00 N 331 7.00 C 1274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 133 " - pdb=" SG CYS R 219 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " DAL C 9 " - " LEU C 8 " Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 78.2 milliseconds 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL C 9 " Number of C-beta restraints generated: 478 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 1 sheets defined 84.5% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'R' and resid 37 through 64 Proline residue: R 51 - end of helix Processing helix chain 'R' and resid 65 through 66 No H-bonds generated for 'chain 'R' and resid 65 through 66' Processing helix chain 'R' and resid 67 through 68 No H-bonds generated for 'chain 'R' and resid 67 through 68' Processing helix chain 'R' and resid 69 through 85 removed outlier: 4.285A pdb=" N LEU R 73 " --> pdb=" O GLY R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 96 Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 102 through 137 Proline residue: R 111 - end of helix Processing helix chain 'R' and resid 143 through 172 removed outlier: 3.975A pdb=" N GLN R 152 " --> pdb=" O ALA R 148 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 195 through 209 removed outlier: 3.706A pdb=" N ALA R 199 " --> pdb=" O SER R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 225 Processing helix chain 'R' and resid 232 through 259 Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 263 through 294 Proline residue: R 274 - end of helix removed outlier: 4.552A pdb=" N SER R 284 " --> pdb=" O ALA R 280 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N CYS R 285 " --> pdb=" O LEU R 281 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing sheet with id=AA1, first strand: chain 'R' and resid 174 through 178 removed outlier: 3.713A pdb=" N MET C 6 " --> pdb=" O VAL R 188 " (cutoff:3.500A) 159 hydrogen bonds defined for protein. 471 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: 0.28 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 596 1.34 - 1.46: 431 1.46 - 1.58: 935 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 1982 Sorted by residual: bond pdb=" N DAL C 9 " pdb=" CA DAL C 9 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" CB THR R 117 " pdb=" CG2 THR R 117 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.36e+00 bond pdb=" C DAL C 9 " pdb=" O DAL C 9 " ideal model delta sigma weight residual 1.231 1.248 -0.017 2.00e-02 2.50e+03 7.61e-01 bond pdb=" CA ALA R 37 " pdb=" C ALA R 37 " ideal model delta sigma weight residual 1.525 1.540 -0.015 2.10e-02 2.27e+03 5.36e-01 bond pdb=" CA ASN R 287 " pdb=" C ASN R 287 " ideal model delta sigma weight residual 1.520 1.529 -0.009 1.23e-02 6.61e+03 5.33e-01 ... (remaining 1977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 2608 1.19 - 2.38: 75 2.38 - 3.57: 19 3.57 - 4.76: 7 4.76 - 5.95: 8 Bond angle restraints: 2717 Sorted by residual: angle pdb=" C VAL R 167 " pdb=" CA VAL R 167 " pdb=" CB VAL R 167 " ideal model delta sigma weight residual 113.70 110.24 3.46 9.50e-01 1.11e+00 1.33e+01 angle pdb=" C THR R 166 " pdb=" N VAL R 167 " pdb=" CA VAL R 167 " ideal model delta sigma weight residual 120.43 123.18 -2.75 9.60e-01 1.09e+00 8.19e+00 angle pdb=" CA DAL C 9 " pdb=" C DAL C 9 " pdb=" N ARG C 10 " ideal model delta sigma weight residual 116.20 119.88 -3.68 2.00e+00 2.50e-01 3.39e+00 angle pdb=" N HIS R 179 " pdb=" CA HIS R 179 " pdb=" C HIS R 179 " ideal model delta sigma weight residual 110.80 114.68 -3.88 2.13e+00 2.20e-01 3.31e+00 angle pdb=" CA LEU R 292 " pdb=" CB LEU R 292 " pdb=" CG LEU R 292 " ideal model delta sigma weight residual 116.30 122.25 -5.95 3.50e+00 8.16e-02 2.89e+00 ... (remaining 2712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 1049 16.53 - 33.06: 89 33.06 - 49.59: 14 49.59 - 66.12: 3 66.12 - 82.65: 3 Dihedral angle restraints: 1158 sinusoidal: 417 harmonic: 741 Sorted by residual: dihedral pdb=" CB CYS R 133 " pdb=" SG CYS R 133 " pdb=" SG CYS R 219 " pdb=" CB CYS R 219 " ideal model delta sinusoidal sigma weight residual 93.00 10.35 82.65 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CA ARG R 108 " pdb=" C ARG R 108 " pdb=" N ALA R 109 " pdb=" CA ALA R 109 " ideal model delta harmonic sigma weight residual -180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CG ARG R 147 " pdb=" CD ARG R 147 " pdb=" NE ARG R 147 " pdb=" CZ ARG R 147 " ideal model delta sinusoidal sigma weight residual 180.00 135.88 44.12 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 1155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 188 0.023 - 0.045: 68 0.045 - 0.067: 45 0.067 - 0.090: 14 0.090 - 0.112: 15 Chirality restraints: 330 Sorted by residual: chirality pdb=" CA TRP R 246 " pdb=" N TRP R 246 " pdb=" C TRP R 246 " pdb=" CB TRP R 246 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA PRO R 168 " pdb=" N PRO R 168 " pdb=" C PRO R 168 " pdb=" CB PRO R 168 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.11e-01 chirality pdb=" CA VAL R 188 " pdb=" N VAL R 188 " pdb=" C VAL R 188 " pdb=" CB VAL R 188 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.10e-01 ... (remaining 327 not shown) Planarity restraints: 333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 211 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO R 212 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO R 212 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 212 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 100 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO R 101 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO R 101 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 101 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 180 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO R 181 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO R 181 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 181 " 0.019 5.00e-02 4.00e+02 ... (remaining 330 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 346 2.77 - 3.31: 1893 3.31 - 3.84: 3287 3.84 - 4.37: 3335 4.37 - 4.90: 6330 Nonbonded interactions: 15191 Sorted by model distance: nonbonded pdb=" OG SER R 169 " pdb=" NH2 ARG R 204 " model vdw 2.243 3.120 nonbonded pdb=" NE2 GLN R 177 " pdb=" O GLU R 178 " model vdw 2.436 3.120 nonbonded pdb=" O SER R 218 " pdb=" OG SER R 221 " model vdw 2.470 3.040 nonbonded pdb=" OE2 GLU R 178 " pdb=" NE2 GLN R 185 " model vdw 2.522 3.120 nonbonded pdb=" O ILE R 89 " pdb=" OH TYR R 102 " model vdw 2.525 3.040 ... (remaining 15186 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: 1.410 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.930 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1985 Z= 0.139 Angle : 0.611 5.950 2724 Z= 0.304 Chirality : 0.038 0.112 330 Planarity : 0.006 0.047 332 Dihedral : 12.502 68.032 671 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.55), residues: 251 helix: 2.45 (0.36), residues: 206 sheet: -3.13 (1.07), residues: 12 loop : -2.09 (0.98), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 173 TYR 0.006 0.001 TYR R 119 PHE 0.007 0.001 PHE R 46 TRP 0.007 0.001 TRP R 246 HIS 0.002 0.001 HIS R 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 1982) covalent geometry : angle 0.60239 / 0.30 ( 2717) SS BOND : bond 0.00486 / 0.23 ( 2) SS BOND : angle 1.71295 / 0.95 ( 4) hydrogen bonds : bond 0.10183 / 6.40 ( 159) hydrogen bonds : angle 5.35831 / 3.89 ( 471) link_TRANS : bond 0.00547 / 0.29 ( 1) link_TRANS : angle 2.52695 / 1.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.075 Fit side-chains REVERT: R 80 ASP cc_start: 0.8205 (m-30) cc_final: 0.7955 (m-30) REVERT: R 149 CYS cc_start: 0.7331 (t) cc_final: 0.7011 (t) REVERT: R 285 CYS cc_start: 0.7985 (t) cc_final: 0.7662 (t) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0569 time to fit residues: 2.5756 Evaluate side-chains 32 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.0170 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.3416 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.187435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.148468 restraints weight = 2252.827| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.10 r_work: 0.3667 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 1985 Z= 0.140 Angle : 0.654 7.168 2724 Z= 0.298 Chirality : 0.042 0.241 330 Planarity : 0.006 0.048 332 Dihedral : 4.191 31.294 277 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.03 % Allowed : 8.63 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.68 (0.55), residues: 251 helix: 2.63 (0.36), residues: 206 sheet: -3.05 (1.13), residues: 12 loop : -2.10 (0.97), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 65 TYR 0.006 0.001 TYR R 102 PHE 0.010 0.001 PHE R 291 TRP 0.007 0.001 TRP R 142 HIS 0.003 0.001 HIS R 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 1982) covalent geometry : angle 0.64880 / 0.30 ( 2717) SS BOND : bond 0.00516 / 0.25 ( 2) SS BOND : angle 1.87165 / 1.02 ( 4) hydrogen bonds : bond 0.03861 / 2.66 ( 159) hydrogen bonds : angle 4.65613 / 3.38 ( 471) link_TRANS : bond 0.00250 / 0.13 ( 1) link_TRANS : angle 1.61909 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.068 Fit side-chains REVERT: R 80 ASP cc_start: 0.8208 (m-30) cc_final: 0.7923 (m-30) REVERT: R 149 CYS cc_start: 0.7337 (t) cc_final: 0.7023 (t) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 0.0564 time to fit residues: 2.1701 Evaluate side-chains 31 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 238 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 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 = 0.4172 r_free = 0.4172 target = 0.183726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.143914 restraints weight = 2311.662| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.13 r_work: 0.3618 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 1985 Z= 0.174 Angle : 0.684 6.082 2724 Z= 0.313 Chirality : 0.043 0.222 330 Planarity : 0.006 0.055 332 Dihedral : 4.171 28.447 277 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.05 % Allowed : 12.18 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.49 (0.54), residues: 251 helix: 2.45 (0.36), residues: 207 sheet: -3.14 (1.37), residues: 10 loop : -2.06 (0.95), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 173 TYR 0.006 0.001 TYR R 102 PHE 0.012 0.001 PHE R 46 TRP 0.008 0.001 TRP R 142 HIS 0.004 0.001 HIS R 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 1982) covalent geometry : angle 0.67871 / 0.31 ( 2717) SS BOND : bond 0.00615 / 0.29 ( 2) SS BOND : angle 1.92758 / 1.02 ( 4) hydrogen bonds : bond 0.03980 / 2.73 ( 159) hydrogen bonds : angle 4.64192 / 3.37 ( 471) link_TRANS : bond 0.00343 / 0.18 ( 1) link_TRANS : angle 1.69684 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.073 Fit side-chains REVERT: R 80 ASP cc_start: 0.8350 (m-30) cc_final: 0.8077 (m-30) REVERT: R 149 CYS cc_start: 0.7433 (t) cc_final: 0.7077 (t) REVERT: R 198 ASN cc_start: 0.8277 (t0) cc_final: 0.8027 (m-40) outliers start: 6 outliers final: 6 residues processed: 34 average time/residue: 0.0700 time to fit residues: 2.7667 Evaluate side-chains 36 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 257 THR Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.0470 chunk 21 optimal weight: 1.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.184807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.144833 restraints weight = 2231.114| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.15 r_work: 0.3617 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 1985 Z= 0.145 Angle : 0.640 7.229 2724 Z= 0.291 Chirality : 0.041 0.200 330 Planarity : 0.006 0.052 332 Dihedral : 4.111 28.175 277 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.06 % Allowed : 12.69 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.68 (0.54), residues: 251 helix: 2.58 (0.36), residues: 207 sheet: -3.30 (1.23), residues: 10 loop : -1.89 (0.96), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 65 TYR 0.006 0.001 TYR R 293 PHE 0.011 0.001 PHE R 46 TRP 0.007 0.001 TRP R 142 HIS 0.003 0.001 HIS R 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 1982) covalent geometry : angle 0.63464 / 0.29 ( 2717) SS BOND : bond 0.00576 / 0.28 ( 2) SS BOND : angle 1.83326 / 0.98 ( 4) hydrogen bonds : bond 0.03698 / 2.56 ( 159) hydrogen bonds : angle 4.51406 / 3.27 ( 471) link_TRANS : bond 0.00363 / 0.19 ( 1) link_TRANS : angle 1.72120 / 0.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.066 Fit side-chains REVERT: R 149 CYS cc_start: 0.7502 (t) cc_final: 0.7193 (t) REVERT: R 198 ASN cc_start: 0.8181 (t0) cc_final: 0.7945 (m-40) REVERT: R 238 ILE cc_start: 0.5533 (mm) cc_final: 0.5291 (mm) outliers start: 8 outliers final: 5 residues processed: 37 average time/residue: 0.0627 time to fit residues: 2.7194 Evaluate side-chains 34 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 1 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.183356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143349 restraints weight = 2228.482| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.11 r_work: 0.3593 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 1985 Z= 0.145 Angle : 0.644 7.527 2724 Z= 0.290 Chirality : 0.041 0.189 330 Planarity : 0.006 0.053 332 Dihedral : 4.122 28.278 277 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.55 % Allowed : 14.21 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.79 (0.54), residues: 251 helix: 2.65 (0.36), residues: 207 sheet: -3.43 (1.19), residues: 10 loop : -1.81 (0.97), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 173 TYR 0.004 0.001 TYR R 102 PHE 0.015 0.002 PHE R 291 TRP 0.006 0.001 TRP R 142 HIS 0.003 0.001 HIS R 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 1982) covalent geometry : angle 0.63749 / 0.29 ( 2717) SS BOND : bond 0.00493 / 0.24 ( 2) SS BOND : angle 1.96548 / 1.07 ( 4) hydrogen bonds : bond 0.03669 / 2.54 ( 159) hydrogen bonds : angle 4.53799 / 3.30 ( 471) link_TRANS : bond 0.00355 / 0.19 ( 1) link_TRANS : angle 1.70385 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.064 Fit side-chains REVERT: R 149 CYS cc_start: 0.7448 (t) cc_final: 0.7141 (t) REVERT: R 238 ILE cc_start: 0.5503 (mm) cc_final: 0.5250 (mm) outliers start: 7 outliers final: 5 residues processed: 35 average time/residue: 0.0539 time to fit residues: 2.2508 Evaluate side-chains 35 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 0.0030 chunk 4 optimal weight: 0.0980 chunk 6 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.0770 chunk 13 optimal weight: 0.0030 overall best weight: 0.1158 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.187222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.148079 restraints weight = 2230.509| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.10 r_work: 0.3665 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1985 Z= 0.120 Angle : 0.625 9.004 2724 Z= 0.274 Chirality : 0.039 0.156 330 Planarity : 0.006 0.047 332 Dihedral : 3.892 24.192 277 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.54 % Allowed : 14.21 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.55), residues: 251 helix: 2.98 (0.36), residues: 207 sheet: -3.41 (1.01), residues: 10 loop : -1.40 (1.04), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 65 TYR 0.003 0.001 TYR R 42 PHE 0.016 0.001 PHE R 291 TRP 0.006 0.001 TRP R 246 HIS 0.001 0.000 HIS R 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 1982) covalent geometry : angle 0.61949 / 0.27 ( 2717) SS BOND : bond 0.00524 / 0.25 ( 2) SS BOND : angle 1.81274 / 0.97 ( 4) hydrogen bonds : bond 0.03225 / 2.25 ( 159) hydrogen bonds : angle 4.43124 / 3.23 ( 471) link_TRANS : bond 0.00379 / 0.20 ( 1) link_TRANS : angle 1.63288 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.067 Fit side-chains REVERT: R 149 CYS cc_start: 0.7423 (t) cc_final: 0.7116 (t) REVERT: R 238 ILE cc_start: 0.5288 (mm) cc_final: 0.5074 (mm) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.0624 time to fit residues: 2.7023 Evaluate side-chains 35 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 285 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 5 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 = 0.4154 r_free = 0.4154 target = 0.183821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143650 restraints weight = 2228.275| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.12 r_work: 0.3581 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 1985 Z= 0.164 Angle : 0.680 7.583 2724 Z= 0.304 Chirality : 0.042 0.155 330 Planarity : 0.006 0.053 332 Dihedral : 4.097 29.011 277 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.55 % Allowed : 14.72 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.91 (0.53), residues: 251 helix: 2.71 (0.35), residues: 207 sheet: -3.62 (1.01), residues: 10 loop : -1.50 (1.03), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 173 TYR 0.005 0.001 TYR R 102 PHE 0.017 0.002 PHE R 291 TRP 0.004 0.001 TRP R 142 HIS 0.004 0.001 HIS R 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 1982) covalent geometry : angle 0.67397 / 0.30 ( 2717) SS BOND : bond 0.00359 / 0.18 ( 2) SS BOND : angle 2.17451 / 1.17 ( 4) hydrogen bonds : bond 0.03733 / 2.55 ( 159) hydrogen bonds : angle 4.56845 / 3.35 ( 471) link_TRANS : bond 0.00281 / 0.15 ( 1) link_TRANS : angle 1.46772 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.070 Fit side-chains REVERT: R 149 CYS cc_start: 0.7375 (t) cc_final: 0.7022 (t) REVERT: R 238 ILE cc_start: 0.5327 (mm) cc_final: 0.5090 (mm) outliers start: 7 outliers final: 7 residues processed: 35 average time/residue: 0.0539 time to fit residues: 2.2663 Evaluate side-chains 35 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.182832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142040 restraints weight = 2322.250| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.24 r_work: 0.3558 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 1985 Z= 0.175 Angle : 0.675 7.618 2724 Z= 0.306 Chirality : 0.042 0.147 330 Planarity : 0.006 0.056 332 Dihedral : 4.261 30.710 277 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.57 % Allowed : 14.21 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.74 (0.53), residues: 251 helix: 2.61 (0.35), residues: 207 sheet: -3.75 (1.01), residues: 10 loop : -1.67 (1.02), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 173 TYR 0.005 0.001 TYR R 102 PHE 0.016 0.002 PHE R 291 TRP 0.005 0.001 TRP R 142 HIS 0.004 0.001 HIS R 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 ( 1982) covalent geometry : angle 0.67037 / 0.30 ( 2717) SS BOND : bond 0.00458 / 0.22 ( 2) SS BOND : angle 2.04327 / 1.08 ( 4) hydrogen bonds : bond 0.03924 / 2.69 ( 159) hydrogen bonds : angle 4.65335 / 3.41 ( 471) link_TRANS : bond 0.00214 / 0.11 ( 1) link_TRANS : angle 1.22305 / 0.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.067 Fit side-chains REVERT: R 149 CYS cc_start: 0.7486 (t) cc_final: 0.7138 (t) REVERT: R 198 ASN cc_start: 0.8413 (m-40) cc_final: 0.8211 (m110) REVERT: R 238 ILE cc_start: 0.5454 (mm) cc_final: 0.5223 (mm) outliers start: 9 outliers final: 8 residues processed: 34 average time/residue: 0.0549 time to fit residues: 2.2375 Evaluate side-chains 34 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 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 = 0.4148 r_free = 0.4148 target = 0.183136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.142564 restraints weight = 2255.536| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.21 r_work: 0.3564 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 1985 Z= 0.163 Angle : 0.662 7.406 2724 Z= 0.301 Chirality : 0.041 0.141 330 Planarity : 0.007 0.068 332 Dihedral : 4.248 30.334 277 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.57 % Allowed : 14.21 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.70 (0.53), residues: 251 helix: 2.60 (0.35), residues: 207 sheet: -3.95 (0.91), residues: 10 loop : -1.71 (1.01), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 65 TYR 0.004 0.001 TYR R 102 PHE 0.016 0.002 PHE R 291 TRP 0.005 0.001 TRP R 142 HIS 0.003 0.001 HIS R 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 1982) covalent geometry : angle 0.65773 / 0.30 ( 2717) SS BOND : bond 0.00468 / 0.23 ( 2) SS BOND : angle 1.87997 / 0.99 ( 4) hydrogen bonds : bond 0.03784 / 2.59 ( 159) hydrogen bonds : angle 4.59980 / 3.35 ( 471) link_TRANS : bond 0.00188 / 0.10 ( 1) link_TRANS : angle 1.18200 / 0.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.069 Fit side-chains REVERT: R 149 CYS cc_start: 0.7479 (t) cc_final: 0.7142 (t) REVERT: R 198 ASN cc_start: 0.8409 (m-40) cc_final: 0.8205 (m110) REVERT: R 238 ILE cc_start: 0.5427 (mm) cc_final: 0.5199 (mm) outliers start: 9 outliers final: 9 residues processed: 35 average time/residue: 0.0501 time to fit residues: 2.1074 Evaluate side-chains 37 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 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 = 0.4151 r_free = 0.4151 target = 0.182663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.142621 restraints weight = 2325.541| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.16 r_work: 0.3568 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 1985 Z= 0.164 Angle : 0.664 7.458 2724 Z= 0.302 Chirality : 0.041 0.143 330 Planarity : 0.007 0.061 332 Dihedral : 4.250 30.026 277 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.57 % Allowed : 14.21 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.62 (0.53), residues: 251 helix: 2.55 (0.35), residues: 207 sheet: -3.94 (0.93), residues: 10 loop : -1.78 (0.99), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 65 TYR 0.005 0.001 TYR R 102 PHE 0.016 0.002 PHE R 291 TRP 0.005 0.001 TRP R 142 HIS 0.003 0.001 HIS R 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 1982) covalent geometry : angle 0.65898 / 0.30 ( 2717) SS BOND : bond 0.00507 / 0.25 ( 2) SS BOND : angle 2.05300 / 1.07 ( 4) hydrogen bonds : bond 0.03846 / 2.64 ( 159) hydrogen bonds : angle 4.58190 / 3.34 ( 471) link_TRANS : bond 0.00180 / 0.09 ( 1) link_TRANS : angle 1.10234 / 0.48 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.056 Fit side-chains REVERT: R 149 CYS cc_start: 0.7497 (t) cc_final: 0.7197 (t) REVERT: R 238 ILE cc_start: 0.5433 (mm) cc_final: 0.5201 (mm) outliers start: 9 outliers final: 9 residues processed: 33 average time/residue: 0.0556 time to fit residues: 2.2030 Evaluate side-chains 34 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.183907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144018 restraints weight = 2317.762| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.17 r_work: 0.3585 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 1985 Z= 0.146 Angle : 0.640 7.373 2724 Z= 0.291 Chirality : 0.040 0.125 330 Planarity : 0.007 0.058 332 Dihedral : 4.167 28.686 277 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.57 % Allowed : 14.21 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.78 (0.53), residues: 251 helix: 2.65 (0.35), residues: 207 sheet: -3.94 (0.88), residues: 10 loop : -1.68 (1.00), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 65 TYR 0.004 0.001 TYR R 293 PHE 0.016 0.002 PHE R 291 TRP 0.006 0.001 TRP R 142 HIS 0.003 0.001 HIS R 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 1982) covalent geometry : angle 0.63519 / 0.29 ( 2717) SS BOND : bond 0.00427 / 0.21 ( 2) SS BOND : angle 1.94530 / 1.04 ( 4) hydrogen bonds : bond 0.03685 / 2.54 ( 159) hydrogen bonds : angle 4.51780 / 3.28 ( 471) link_TRANS : bond 0.00179 / 0.09 ( 1) link_TRANS : angle 1.06585 / 0.47 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 690.12 seconds wall clock time: 12 minutes 53.26 seconds (773.26 seconds total)