Starting phenix.real_space_refine on Wed Sep 17 02:58:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bc5_12139/09_2025/7bc5_12139.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bc5_12139/09_2025/7bc5_12139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bc5_12139/09_2025/7bc5_12139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bc5_12139/09_2025/7bc5_12139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bc5_12139/09_2025/7bc5_12139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bc5_12139/09_2025/7bc5_12139.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 3 5.16 5 C 757 2.51 5 N 206 2.21 5 O 234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1200 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1200 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 9, 'TRANS': 151} Time building chain proxies: 0.56, per 1000 atoms: 0.47 Number of scatterers: 1200 At special positions: 0 Unit cell: (58.575, 54.315, 45.795, 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 3 16.00 O 234 8.00 N 206 7.00 C 757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.12 Conformation dependent library (CDL) restraints added in 33.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 288 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 53.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 149 through 157 removed outlier: 3.833A pdb=" N LEU A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 180 through 188 removed outlier: 3.663A pdb=" N LEU A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 4.205A pdb=" N ALA A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLN A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.923A pdb=" N ASN A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 251 removed outlier: 3.614A pdb=" N ALA A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.760A pdb=" N GLU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 293 removed outlier: 3.552A pdb=" N CYS A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) 37 hydrogen bonds defined for protein. 102 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: 0.08 Time building geometry restraints manager: 0.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 392 1.34 - 1.46: 140 1.46 - 1.57: 683 1.57 - 1.69: 0 1.69 - 1.80: 5 Bond restraints: 1220 Sorted by residual: bond pdb=" CG ARG A 274 " pdb=" CD ARG A 274 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.14e+00 bond pdb=" CG LEU A 264 " pdb=" CD1 LEU A 264 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CB GLN A 249 " pdb=" CG GLN A 249 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.08e+00 bond pdb=" CB PHE A 192 " pdb=" CG PHE A 192 " ideal model delta sigma weight residual 1.502 1.479 0.023 2.30e-02 1.89e+03 9.61e-01 bond pdb=" C MET A 235 " pdb=" N PRO A 236 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.22e-01 ... (remaining 1215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 1589 2.49 - 4.98: 48 4.98 - 7.47: 7 7.47 - 9.96: 1 9.96 - 12.45: 1 Bond angle restraints: 1646 Sorted by residual: angle pdb=" C PRO A 165 " pdb=" N LEU A 166 " pdb=" CA LEU A 166 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" CA LEU A 166 " pdb=" CB LEU A 166 " pdb=" CG LEU A 166 " ideal model delta sigma weight residual 116.30 128.75 -12.45 3.50e+00 8.16e-02 1.27e+01 angle pdb=" CA LEU A 207 " pdb=" CB LEU A 207 " pdb=" CG LEU A 207 " ideal model delta sigma weight residual 116.30 126.08 -9.78 3.50e+00 8.16e-02 7.80e+00 angle pdb=" C THR A 195 " pdb=" CA THR A 195 " pdb=" CB THR A 195 " ideal model delta sigma weight residual 108.88 112.72 -3.84 1.50e+00 4.44e-01 6.56e+00 angle pdb=" N SER A 194 " pdb=" CA SER A 194 " pdb=" C SER A 194 " ideal model delta sigma weight residual 110.80 116.15 -5.35 2.13e+00 2.20e-01 6.30e+00 ... (remaining 1641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.50: 629 14.50 - 29.00: 79 29.00 - 43.49: 34 43.49 - 57.99: 6 57.99 - 72.49: 2 Dihedral angle restraints: 750 sinusoidal: 300 harmonic: 450 Sorted by residual: dihedral pdb=" CA GLY A 193 " pdb=" C GLY A 193 " pdb=" N SER A 194 " pdb=" CA SER A 194 " ideal model delta harmonic sigma weight residual -180.00 -124.03 -55.97 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA GLN A 222 " pdb=" C GLN A 222 " pdb=" N THR A 223 " pdb=" CA THR A 223 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLU A 206 " pdb=" C GLU A 206 " pdb=" N LEU A 207 " pdb=" CA LEU A 207 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 95 0.034 - 0.067: 55 0.067 - 0.101: 28 0.101 - 0.134: 8 0.134 - 0.168: 2 Chirality restraints: 188 Sorted by residual: chirality pdb=" CB VAL A 243 " pdb=" CA VAL A 243 " pdb=" CG1 VAL A 243 " pdb=" CG2 VAL A 243 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CG LEU A 275 " pdb=" CB LEU A 275 " pdb=" CD1 LEU A 275 " pdb=" CD2 LEU A 275 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA PRO A 199 " pdb=" N PRO A 199 " pdb=" C PRO A 199 " pdb=" CB PRO A 199 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 185 not shown) Planarity restraints: 214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 211 " 0.013 2.00e-02 2.50e+03 1.57e-02 4.30e+00 pdb=" CG PHE A 211 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 211 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 211 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 211 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 211 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 211 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 166 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C LEU A 166 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU A 166 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A 167 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 193 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C GLY A 193 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY A 193 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A 194 " 0.010 2.00e-02 2.50e+03 ... (remaining 211 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 380 2.83 - 3.35: 1054 3.35 - 3.87: 1922 3.87 - 4.38: 2218 4.38 - 4.90: 3472 Nonbonded interactions: 9046 Sorted by model distance: nonbonded pdb=" O ARG A 229 " pdb=" OG SER A 233 " model vdw 2.314 3.040 nonbonded pdb=" O SER A 178 " pdb=" OG SER A 178 " model vdw 2.340 3.040 nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 286 " model vdw 2.381 3.040 nonbonded pdb=" O ARG A 251 " pdb=" NH1 ARG A 251 " model vdw 2.408 3.120 nonbonded pdb=" O PRO A 139 " pdb=" NE ARG A 258 " model vdw 2.409 3.120 ... (remaining 9041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 5.090 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: 0.010 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 2.590 Find NCS groups from input model: 0.000 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:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 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 : 0.005 0.055 1220 Z= 0.204 Angle : 1.045 12.451 1646 Z= 0.509 Chirality : 0.053 0.168 188 Planarity : 0.007 0.040 214 Dihedral : 15.919 72.490 462 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.76 % Allowed : 10.69 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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 aren not related in a simple way. whole: -5.64 (0.43), residues: 159 helix: -4.45 (0.28), residues: 77 sheet: None (None), residues: 0 loop : -3.00 (0.51), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 274 TYR 0.005 0.001 TYR A 247 PHE 0.036 0.004 PHE A 211 TRP 0.001 0.001 TRP A 252 HIS 0.004 0.002 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 1220) covalent geometry : angle 1.04534 ( 1646) hydrogen bonds : bond 0.33929 ( 37) hydrogen bonds : angle 11.05878 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.027 Fit side-chains REVERT: A 183 GLU cc_start: 0.7862 (tt0) cc_final: 0.7067 (mm-30) REVERT: A 228 ASN cc_start: 0.8306 (m110) cc_final: 0.7599 (t0) outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.0336 time to fit residues: 1.5405 Evaluate side-chains 36 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.202443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.198745 restraints weight = 2435.566| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 0.84 r_work: 0.4510 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.4464 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5776 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1220 Z= 0.134 Angle : 0.722 8.265 1646 Z= 0.343 Chirality : 0.042 0.116 188 Planarity : 0.005 0.033 214 Dihedral : 6.451 40.174 167 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 6.11 % Allowed : 17.56 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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 aren not related in a simple way. whole: -4.42 (0.51), residues: 159 helix: -3.46 (0.42), residues: 75 sheet: None (None), residues: 0 loop : -2.38 (0.56), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 258 TYR 0.005 0.001 TYR A 292 PHE 0.009 0.002 PHE A 215 TRP 0.002 0.001 TRP A 252 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 1220) covalent geometry : angle 0.72209 ( 1646) hydrogen bonds : bond 0.02863 ( 37) hydrogen bonds : angle 6.14892 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.029 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 0.0237 time to fit residues: 1.3549 Evaluate side-chains 45 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 7 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 15 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.199244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.195617 restraints weight = 2344.401| |-----------------------------------------------------------------------------| r_work (start): 0.4523 rms_B_bonded: 0.80 r_work: 0.4496 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.4450 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 1220 Z= 0.138 Angle : 0.712 7.829 1646 Z= 0.337 Chirality : 0.042 0.108 188 Planarity : 0.005 0.036 214 Dihedral : 6.297 40.084 167 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 6.87 % Allowed : 25.19 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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 aren not related in a simple way. whole: -4.00 (0.55), residues: 159 helix: -3.15 (0.42), residues: 83 sheet: None (None), residues: 0 loop : -1.93 (0.66), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 274 TYR 0.002 0.001 TYR A 292 PHE 0.009 0.002 PHE A 215 TRP 0.001 0.001 TRP A 252 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 1220) covalent geometry : angle 0.71232 ( 1646) hydrogen bonds : bond 0.03111 ( 37) hydrogen bonds : angle 5.86068 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.047 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 45 average time/residue: 0.0467 time to fit residues: 2.3991 Evaluate side-chains 45 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 10 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 13 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 1 optimal weight: 0.0370 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 overall best weight: 4.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.199577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.196149 restraints weight = 2472.900| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 0.78 r_work: 0.4512 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.4466 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1220 Z= 0.128 Angle : 0.696 8.058 1646 Z= 0.324 Chirality : 0.041 0.111 188 Planarity : 0.004 0.028 214 Dihedral : 5.972 34.845 167 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 6.11 % Allowed : 29.01 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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 aren not related in a simple way. whole: -3.53 (0.57), residues: 159 helix: -2.58 (0.47), residues: 81 sheet: None (None), residues: 0 loop : -1.98 (0.65), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 229 TYR 0.001 0.000 TYR A 292 PHE 0.007 0.002 PHE A 192 TRP 0.001 0.001 TRP A 252 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 1220) covalent geometry : angle 0.69649 ( 1646) hydrogen bonds : bond 0.02697 ( 37) hydrogen bonds : angle 5.43843 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.086 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 42 average time/residue: 0.0407 time to fit residues: 1.9990 Evaluate side-chains 45 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.204392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.201369 restraints weight = 2359.107| |-----------------------------------------------------------------------------| r_work (start): 0.4588 rms_B_bonded: 0.68 r_work: 0.4566 rms_B_bonded: 1.03 restraints_weight: 0.5000 r_work: 0.4527 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5670 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1220 Z= 0.104 Angle : 0.644 8.223 1646 Z= 0.296 Chirality : 0.040 0.103 188 Planarity : 0.004 0.027 214 Dihedral : 5.315 31.653 167 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 5.34 % Allowed : 32.06 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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 aren not related in a simple way. whole: -3.04 (0.59), residues: 159 helix: -2.08 (0.52), residues: 81 sheet: None (None), residues: 0 loop : -1.86 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 258 TYR 0.002 0.000 TYR A 292 PHE 0.012 0.002 PHE A 215 TRP 0.001 0.000 TRP A 252 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 1220) covalent geometry : angle 0.64358 ( 1646) hydrogen bonds : bond 0.02022 ( 37) hydrogen bonds : angle 5.10399 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.047 Fit side-chains REVERT: A 290 GLN cc_start: 0.6611 (mt0) cc_final: 0.6402 (mt0) outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.0304 time to fit residues: 1.5297 Evaluate side-chains 42 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 6 optimal weight: 40.0000 chunk 13 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.196535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.193368 restraints weight = 2397.114| |-----------------------------------------------------------------------------| r_work (start): 0.4526 rms_B_bonded: 0.74 r_work: 0.4501 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.4455 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 1220 Z= 0.158 Angle : 0.736 8.717 1646 Z= 0.340 Chirality : 0.045 0.122 188 Planarity : 0.004 0.027 214 Dihedral : 5.974 33.423 167 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 6.87 % Allowed : 31.30 % Favored : 61.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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 aren not related in a simple way. whole: -2.93 (0.62), residues: 159 helix: -2.10 (0.52), residues: 81 sheet: None (None), residues: 0 loop : -1.67 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 229 TYR 0.002 0.001 TYR A 292 PHE 0.012 0.003 PHE A 215 TRP 0.006 0.002 TRP A 252 HIS 0.003 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 1220) covalent geometry : angle 0.73615 ( 1646) hydrogen bonds : bond 0.02877 ( 37) hydrogen bonds : angle 5.32063 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.060 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 42 average time/residue: 0.0313 time to fit residues: 1.6120 Evaluate side-chains 45 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 0.0030 chunk 13 optimal weight: 40.0000 chunk 3 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 0.0670 overall best weight: 3.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.199224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.196152 restraints weight = 2413.695| |-----------------------------------------------------------------------------| r_work (start): 0.4550 rms_B_bonded: 0.70 r_work: 0.4526 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.4479 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1220 Z= 0.119 Angle : 0.683 9.305 1646 Z= 0.311 Chirality : 0.042 0.109 188 Planarity : 0.004 0.025 214 Dihedral : 5.629 30.919 167 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 5.34 % Allowed : 33.59 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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 aren not related in a simple way. whole: -2.78 (0.63), residues: 159 helix: -2.01 (0.53), residues: 81 sheet: None (None), residues: 0 loop : -1.55 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 229 TYR 0.001 0.001 TYR A 247 PHE 0.012 0.002 PHE A 215 TRP 0.001 0.000 TRP A 252 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 1220) covalent geometry : angle 0.68305 ( 1646) hydrogen bonds : bond 0.02445 ( 37) hydrogen bonds : angle 5.14550 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.049 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 42 average time/residue: 0.0409 time to fit residues: 2.0045 Evaluate side-chains 44 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.202862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.199915 restraints weight = 2423.800| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 0.69 r_work: 0.4567 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.4518 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.4518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1220 Z= 0.097 Angle : 0.594 5.469 1646 Z= 0.281 Chirality : 0.040 0.107 188 Planarity : 0.004 0.024 214 Dihedral : 5.085 27.625 167 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.58 % Allowed : 35.11 % Favored : 60.31 % 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 aren not related in a simple way. whole: -2.61 (0.64), residues: 159 helix: -1.77 (0.55), residues: 81 sheet: None (None), residues: 0 loop : -1.58 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 258 TYR 0.001 0.000 TYR A 292 PHE 0.010 0.002 PHE A 215 TRP 0.001 0.000 TRP A 252 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 1220) covalent geometry : angle 0.59352 ( 1646) hydrogen bonds : bond 0.02138 ( 37) hydrogen bonds : angle 4.99247 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.051 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 40 average time/residue: 0.0333 time to fit residues: 1.6121 Evaluate side-chains 43 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 13 optimal weight: 30.0000 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 30.0000 chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS A 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.198338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.195318 restraints weight = 2373.487| |-----------------------------------------------------------------------------| r_work (start): 0.4554 rms_B_bonded: 0.70 r_work: 0.4530 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.4494 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1220 Z= 0.129 Angle : 0.668 8.186 1646 Z= 0.315 Chirality : 0.042 0.118 188 Planarity : 0.004 0.022 214 Dihedral : 5.406 27.589 167 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.34 % Allowed : 33.59 % Favored : 61.07 % 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 aren not related in a simple way. whole: -2.40 (0.65), residues: 159 helix: -1.75 (0.54), residues: 80 sheet: None (None), residues: 0 loop : -1.30 (0.74), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 258 TYR 0.001 0.001 TYR A 292 PHE 0.010 0.002 PHE A 215 TRP 0.003 0.001 TRP A 252 HIS 0.003 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 1220) covalent geometry : angle 0.66845 ( 1646) hydrogen bonds : bond 0.02702 ( 37) hydrogen bonds : angle 5.20669 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.112 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 40 average time/residue: 0.0315 time to fit residues: 1.5417 Evaluate side-chains 44 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 15 optimal weight: 40.0000 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 11 optimal weight: 0.0070 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.203423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.200416 restraints weight = 2320.291| |-----------------------------------------------------------------------------| r_work (start): 0.4595 rms_B_bonded: 0.69 r_work: 0.4573 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.4528 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5716 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 1220 Z= 0.098 Angle : 0.594 5.211 1646 Z= 0.281 Chirality : 0.040 0.118 188 Planarity : 0.004 0.023 214 Dihedral : 4.835 23.106 167 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 6.11 % Allowed : 32.82 % Favored : 61.07 % 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 aren not related in a simple way. whole: -2.50 (0.64), residues: 159 helix: -1.68 (0.55), residues: 82 sheet: None (None), residues: 0 loop : -1.53 (0.70), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 258 TYR 0.003 0.001 TYR A 292 PHE 0.011 0.002 PHE A 215 TRP 0.001 0.000 TRP A 252 HIS 0.000 0.000 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 1220) covalent geometry : angle 0.59363 ( 1646) hydrogen bonds : bond 0.02142 ( 37) hydrogen bonds : angle 4.90134 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.052 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.0303 time to fit residues: 1.5928 Evaluate side-chains 44 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.197167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.194364 restraints weight = 2445.202| |-----------------------------------------------------------------------------| r_work (start): 0.4540 rms_B_bonded: 0.69 r_work: 0.4517 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.4467 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 1220 Z= 0.174 Angle : 0.702 6.068 1646 Z= 0.338 Chirality : 0.046 0.148 188 Planarity : 0.004 0.022 214 Dihedral : 5.894 26.948 167 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.34 % Allowed : 30.53 % Favored : 64.12 % 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 aren not related in a simple way. whole: -2.51 (0.65), residues: 159 helix: -1.85 (0.54), residues: 81 sheet: None (None), residues: 0 loop : -1.34 (0.73), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 229 TYR 0.002 0.001 TYR A 292 PHE 0.013 0.003 PHE A 215 TRP 0.007 0.002 TRP A 252 HIS 0.004 0.002 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 1220) covalent geometry : angle 0.70250 ( 1646) hydrogen bonds : bond 0.03326 ( 37) hydrogen bonds : angle 5.34586 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 678.36 seconds wall clock time: 13 minutes 5.10 seconds (785.10 seconds total)