Starting phenix.real_space_refine on Tue Aug 4 11:46:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v35_64749/08_2026/9v35_64749.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v35_64749/08_2026/9v35_64749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v35_64749/08_2026/9v35_64749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v35_64749/08_2026/9v35_64749.map" model { file = "/net/cci-nas-00/data/ceres_data/9v35_64749/08_2026/9v35_64749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v35_64749/08_2026/9v35_64749.cif" } resolution = 2.97 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 15 5.16 5 C 1294 2.51 5 N 334 2.21 5 O 316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 1959 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1959 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 249} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 1.19, per 1000 atoms: 0.61 Number of scatterers: 1959 At special positions: 0 Unit cell: (54.0685, 60.7085, 82.5256, 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 15 16.00 O 316 8.00 N 334 7.00 C 1294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 219 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.17 Conformation dependent library (CDL) restraints added in 135.0 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 492 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 1 sheets defined 83.1% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 37 through 65 Proline residue: A 51 - end of helix removed outlier: 4.041A pdb=" N ARG A 65 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 69 through 85 removed outlier: 3.866A pdb=" N LEU A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 96 removed outlier: 4.712A pdb=" N ILE A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 102 through 137 removed outlier: 3.854A pdb=" N GLY A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Proline residue: A 111 - end of helix removed outlier: 3.862A pdb=" N ILE A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 171 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 193 through 209 removed outlier: 3.663A pdb=" N ALA A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 Processing helix chain 'A' and resid 232 through 259 removed outlier: 3.818A pdb=" N THR A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 263 through 295 Proline residue: A 274 - end of helix removed outlier: 3.705A pdb=" N HIS A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N SER A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Proline residue: A 288 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 178 155 hydrogen bonds defined for protein. 459 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: 0.43 Time building geometry restraints manager: 0.25 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: 607 1.34 - 1.46: 440 1.46 - 1.58: 949 1.58 - 1.70: 0 1.70 - 1.81: 18 Bond restraints: 2014 Sorted by residual: bond pdb=" N CYS A 219 " pdb=" CA CYS A 219 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.19e-02 7.06e+03 7.05e+00 bond pdb=" C LEU A 39 " pdb=" N PRO A 40 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.74e+00 bond pdb=" C GLU A 273 " pdb=" N PRO A 274 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.38e-02 5.25e+03 2.49e+00 bond pdb=" C ALA A 37 " pdb=" N PRO A 38 " ideal model delta sigma weight residual 1.334 1.356 -0.022 1.51e-02 4.39e+03 2.17e+00 bond pdb=" CA VAL A 188 " pdb=" CB VAL A 188 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.01e+00 ... (remaining 2009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 2593 1.14 - 2.27: 135 2.27 - 3.41: 29 3.41 - 4.55: 4 4.55 - 5.69: 8 Bond angle restraints: 2769 Sorted by residual: angle pdb=" C CYS A 149 " pdb=" N GLY A 150 " pdb=" CA GLY A 150 " ideal model delta sigma weight residual 119.98 123.12 -3.14 1.11e+00 8.12e-01 7.99e+00 angle pdb=" N GLN A 146 " pdb=" CA GLN A 146 " pdb=" C GLN A 146 " ideal model delta sigma weight residual 110.97 108.28 2.69 1.09e+00 8.42e-01 6.09e+00 angle pdb=" C ALA A 272 " pdb=" N GLU A 273 " pdb=" CA GLU A 273 " ideal model delta sigma weight residual 120.58 123.61 -3.03 1.32e+00 5.74e-01 5.25e+00 angle pdb=" N SER A 194 " pdb=" CA SER A 194 " pdb=" C SER A 194 " ideal model delta sigma weight residual 113.01 110.28 2.73 1.20e+00 6.94e-01 5.17e+00 angle pdb=" N GLY A 191 " pdb=" CA GLY A 191 " pdb=" C GLY A 191 " ideal model delta sigma weight residual 115.63 112.37 3.26 1.49e+00 4.50e-01 4.79e+00 ... (remaining 2764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 1043 14.82 - 29.65: 93 29.65 - 44.47: 20 44.47 - 59.29: 8 59.29 - 74.12: 1 Dihedral angle restraints: 1165 sinusoidal: 401 harmonic: 764 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 219 " pdb=" CB CYS A 219 " ideal model delta sinusoidal sigma weight residual 93.00 167.12 -74.12 1 1.00e+01 1.00e-02 6.97e+01 dihedral pdb=" CA PHE A 209 " pdb=" C PHE A 209 " pdb=" N LEU A 210 " pdb=" CA LEU A 210 " ideal model delta harmonic sigma weight residual -180.00 -164.34 -15.66 0 5.00e+00 4.00e-02 9.81e+00 dihedral pdb=" SG CYS A 133 " pdb=" CB CYS A 219 " pdb=" SG CYS A 219 " pdb=" CA CYS A 219 " ideal model delta sinusoidal sigma weight residual 79.00 28.73 50.27 1 2.00e+01 2.50e-03 8.66e+00 ... (remaining 1162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 225 0.033 - 0.066: 74 0.066 - 0.098: 29 0.098 - 0.131: 6 0.131 - 0.163: 3 Chirality restraints: 337 Sorted by residual: chirality pdb=" CA CYS A 219 " pdb=" N CYS A 219 " pdb=" C CYS A 219 " pdb=" CB CYS A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA LEU A 110 " pdb=" N LEU A 110 " pdb=" C LEU A 110 " pdb=" CB LEU A 110 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA HIS A 179 " pdb=" N HIS A 179 " pdb=" C HIS A 179 " pdb=" CB HIS A 179 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 334 not shown) Planarity restraints: 340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 37 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A 38 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 141 " -0.015 2.00e-02 2.50e+03 1.24e-02 3.84e+00 pdb=" CG TRP A 141 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 141 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 141 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 141 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 141 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 141 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 141 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 141 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 141 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 146 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C GLN A 146 " 0.032 2.00e-02 2.50e+03 pdb=" O GLN A 146 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 147 " -0.011 2.00e-02 2.50e+03 ... (remaining 337 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 426 2.79 - 3.32: 1955 3.32 - 3.85: 3389 3.85 - 4.37: 3544 4.37 - 4.90: 6347 Nonbonded interactions: 15661 Sorted by model distance: nonbonded pdb=" O TRP A 141 " pdb=" NE2 GLN A 146 " model vdw 2.264 3.120 nonbonded pdb=" O ALA A 162 " pdb=" OG1 THR A 166 " model vdw 2.459 3.040 nonbonded pdb=" OG SER A 169 " pdb=" NH2 ARG A 204 " model vdw 2.477 3.120 nonbonded pdb=" O LEU A 254 " pdb=" OG1 THR A 257 " model vdw 2.503 3.040 nonbonded pdb=" NH1 ARG A 174 " pdb=" O LEU A 175 " model vdw 2.548 3.120 ... (remaining 15656 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: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.020 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 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 : 0.004 0.033 2016 Z= 0.185 Angle : 0.665 6.284 2773 Z= 0.386 Chirality : 0.041 0.163 337 Planarity : 0.007 0.052 340 Dihedral : 12.058 50.925 667 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.54), residues: 264 helix: 1.47 (0.38), residues: 206 sheet: -1.43 (1.26), residues: 10 loop : -1.40 (0.89), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.008 0.001 TYR A 42 PHE 0.009 0.001 PHE A 243 TRP 0.034 0.002 TRP A 141 HIS 0.006 0.002 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.19 ( 2014) covalent geometry : angle 0.65396 / 0.38 ( 2769) SS BOND : bond 0.00247 / 0.12 ( 2) SS BOND : angle 3.19550 / 1.87 ( 4) hydrogen bonds : bond 0.10529 / 7.68 ( 155) hydrogen bonds : angle 5.63299 / 4.14 ( 459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.070 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.6864 (mtt180) cc_final: 0.6594 (mtp85) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.5248 time to fit residues: 15.0526 Evaluate side-chains 22 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.192474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.146805 restraints weight = 2228.302| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.36 r_work: 0.3598 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2016 Z= 0.152 Angle : 0.580 5.529 2773 Z= 0.294 Chirality : 0.041 0.156 337 Planarity : 0.006 0.057 340 Dihedral : 4.059 14.338 284 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.54 % Allowed : 11.28 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.54), residues: 264 helix: 1.94 (0.37), residues: 205 sheet: -1.54 (1.25), residues: 10 loop : -1.05 (0.96), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.009 0.001 TYR A 42 PHE 0.008 0.001 PHE A 243 TRP 0.020 0.001 TRP A 141 HIS 0.005 0.002 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 2014) covalent geometry : angle 0.57953 / 0.29 ( 2769) SS BOND : bond 0.00294 / 0.14 ( 2) SS BOND : angle 0.90645 / 0.49 ( 4) hydrogen bonds : bond 0.04342 / 2.86 ( 155) hydrogen bonds : angle 4.23337 / 3.16 ( 459) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: A 58 TRP cc_start: 0.7200 (t60) cc_final: 0.6957 (t-100) REVERT: A 167 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7814 (m) outliers start: 3 outliers final: 1 residues processed: 22 average time/residue: 0.3223 time to fit residues: 7.3929 Evaluate side-chains 22 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.186368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.144314 restraints weight = 2247.980| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.94 r_work: 0.3499 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2016 Z= 0.135 Angle : 0.557 5.685 2773 Z= 0.278 Chirality : 0.040 0.151 337 Planarity : 0.006 0.056 340 Dihedral : 3.973 14.106 284 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.54 % Allowed : 11.28 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.54), residues: 264 helix: 2.23 (0.37), residues: 205 sheet: -1.44 (1.29), residues: 10 loop : -0.91 (0.97), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.007 0.001 TYR A 249 PHE 0.008 0.001 PHE A 243 TRP 0.015 0.001 TRP A 141 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 2014) covalent geometry : angle 0.55681 / 0.28 ( 2769) SS BOND : bond 0.00257 / 0.12 ( 2) SS BOND : angle 0.44150 / 0.21 ( 4) hydrogen bonds : bond 0.04047 / 2.66 ( 155) hydrogen bonds : angle 4.06205 / 3.04 ( 459) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: A 167 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7732 (m) REVERT: A 197 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7821 (tm-30) outliers start: 3 outliers final: 0 residues processed: 24 average time/residue: 0.2443 time to fit residues: 6.1618 Evaluate side-chains 23 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.191301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.147772 restraints weight = 2249.220| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.40 r_work: 0.3573 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2016 Z= 0.148 Angle : 0.572 5.724 2773 Z= 0.286 Chirality : 0.041 0.156 337 Planarity : 0.006 0.057 340 Dihedral : 3.982 14.116 284 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.54 % Allowed : 12.82 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.54), residues: 264 helix: 2.16 (0.37), residues: 207 sheet: -1.72 (1.29), residues: 10 loop : -0.90 (0.99), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.007 0.001 TYR A 249 PHE 0.008 0.001 PHE A 243 TRP 0.013 0.001 TRP A 141 HIS 0.005 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 2014) covalent geometry : angle 0.57124 / 0.29 ( 2769) SS BOND : bond 0.00264 / 0.13 ( 2) SS BOND : angle 0.79828 / 0.41 ( 4) hydrogen bonds : bond 0.04205 / 2.79 ( 155) hydrogen bonds : angle 4.07897 / 3.05 ( 459) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.067 Fit side-chains revert: symmetry clash REVERT: A 167 VAL cc_start: 0.8074 (OUTLIER) cc_final: 0.7840 (m) REVERT: A 197 GLU cc_start: 0.8275 (tm-30) cc_final: 0.8073 (tm-30) outliers start: 3 outliers final: 0 residues processed: 23 average time/residue: 0.2590 time to fit residues: 6.2482 Evaluate side-chains 22 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.190281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.147587 restraints weight = 2267.286| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.11 r_work: 0.3601 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2016 Z= 0.149 Angle : 0.567 5.777 2773 Z= 0.283 Chirality : 0.041 0.154 337 Planarity : 0.006 0.057 340 Dihedral : 3.986 14.176 284 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.08 % Allowed : 12.31 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.24 (0.54), residues: 264 helix: 2.19 (0.37), residues: 207 sheet: -1.79 (1.32), residues: 10 loop : -0.97 (0.96), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.007 0.001 TYR A 249 PHE 0.008 0.001 PHE A 243 TRP 0.011 0.001 TRP A 141 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 2014) covalent geometry : angle 0.56616 / 0.28 ( 2769) SS BOND : bond 0.00265 / 0.13 ( 2) SS BOND : angle 0.94667 / 0.52 ( 4) hydrogen bonds : bond 0.04197 / 2.78 ( 155) hydrogen bonds : angle 4.05684 / 3.03 ( 459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.065 Fit side-chains revert: symmetry clash REVERT: A 149 CYS cc_start: 0.5981 (OUTLIER) cc_final: 0.5162 (p) REVERT: A 167 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7831 (m) REVERT: A 197 GLU cc_start: 0.8243 (tm-30) cc_final: 0.8020 (tm-30) outliers start: 6 outliers final: 1 residues processed: 23 average time/residue: 0.2482 time to fit residues: 5.9904 Evaluate side-chains 24 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 178 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.189066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143294 restraints weight = 2229.060| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.07 r_work: 0.3624 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2016 Z= 0.126 Angle : 0.563 8.470 2773 Z= 0.271 Chirality : 0.039 0.146 337 Planarity : 0.006 0.057 340 Dihedral : 3.883 13.892 284 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.54 % Allowed : 15.38 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.51 (0.55), residues: 264 helix: 2.37 (0.37), residues: 207 sheet: -1.67 (1.33), residues: 10 loop : -0.85 (0.99), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.006 0.001 TYR A 249 PHE 0.007 0.001 PHE A 243 TRP 0.011 0.001 TRP A 141 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 ( 2014) covalent geometry : angle 0.56319 / 0.27 ( 2769) SS BOND : bond 0.00268 / 0.13 ( 2) SS BOND : angle 0.54771 / 0.28 ( 4) hydrogen bonds : bond 0.03857 / 2.55 ( 155) hydrogen bonds : angle 3.96503 / 2.96 ( 459) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: A 149 CYS cc_start: 0.5954 (m) cc_final: 0.5198 (p) REVERT: A 167 VAL cc_start: 0.8066 (OUTLIER) cc_final: 0.7826 (m) outliers start: 3 outliers final: 0 residues processed: 25 average time/residue: 0.2264 time to fit residues: 5.9335 Evaluate side-chains 24 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.190765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.148580 restraints weight = 2250.438| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.06 r_work: 0.3611 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2016 Z= 0.142 Angle : 0.580 7.567 2773 Z= 0.282 Chirality : 0.040 0.152 337 Planarity : 0.006 0.057 340 Dihedral : 3.897 13.938 284 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.54 % Allowed : 16.41 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.54), residues: 264 helix: 2.28 (0.37), residues: 207 sheet: -1.92 (1.30), residues: 10 loop : -0.85 (1.00), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.007 0.001 TYR A 249 PHE 0.008 0.001 PHE A 243 TRP 0.011 0.001 TRP A 141 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 2014) covalent geometry : angle 0.57847 / 0.28 ( 2769) SS BOND : bond 0.00314 / 0.15 ( 2) SS BOND : angle 1.13128 / 0.63 ( 4) hydrogen bonds : bond 0.04032 / 2.67 ( 155) hydrogen bonds : angle 4.00691 / 2.99 ( 459) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.106 Fit side-chains REVERT: A 149 CYS cc_start: 0.5929 (m) cc_final: 0.5123 (p) REVERT: A 167 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7863 (m) outliers start: 3 outliers final: 1 residues processed: 24 average time/residue: 0.3247 time to fit residues: 8.0793 Evaluate side-chains 25 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 178 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 13 optimal weight: 0.0170 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 4 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 overall best weight: 0.3018 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.189663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.148667 restraints weight = 2254.016| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.08 r_work: 0.3585 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2016 Z= 0.120 Angle : 0.566 7.517 2773 Z= 0.273 Chirality : 0.039 0.144 337 Planarity : 0.005 0.057 340 Dihedral : 3.827 13.909 284 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.03 % Allowed : 17.95 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.65 (0.55), residues: 264 helix: 2.48 (0.37), residues: 207 sheet: -1.74 (1.33), residues: 10 loop : -0.85 (0.99), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 67 TYR 0.005 0.001 TYR A 249 PHE 0.007 0.001 PHE A 46 TRP 0.010 0.001 TRP A 141 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 ( 2014) covalent geometry : angle 0.56518 / 0.27 ( 2769) SS BOND : bond 0.00296 / 0.14 ( 2) SS BOND : angle 0.82799 / 0.44 ( 4) hydrogen bonds : bond 0.03675 / 2.44 ( 155) hydrogen bonds : angle 3.90995 / 2.92 ( 459) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.066 Fit side-chains REVERT: A 58 TRP cc_start: 0.7248 (t60) cc_final: 0.7025 (t-100) REVERT: A 149 CYS cc_start: 0.5911 (m) cc_final: 0.5173 (p) REVERT: A 167 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7840 (m) outliers start: 2 outliers final: 0 residues processed: 25 average time/residue: 0.2760 time to fit residues: 7.1608 Evaluate side-chains 25 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.187765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.146393 restraints weight = 2233.395| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.22 r_work: 0.3607 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2016 Z= 0.134 Angle : 0.599 7.566 2773 Z= 0.291 Chirality : 0.040 0.147 337 Planarity : 0.006 0.057 340 Dihedral : 3.889 13.860 284 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.03 % Allowed : 17.95 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.54 (0.54), residues: 264 helix: 2.40 (0.37), residues: 207 sheet: -1.73 (1.36), residues: 10 loop : -0.89 (0.98), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 67 TYR 0.006 0.001 TYR A 249 PHE 0.007 0.001 PHE A 243 TRP 0.010 0.001 TRP A 141 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 2014) covalent geometry : angle 0.59858 / 0.29 ( 2769) SS BOND : bond 0.00270 / 0.13 ( 2) SS BOND : angle 0.77485 / 0.41 ( 4) hydrogen bonds : bond 0.03853 / 2.57 ( 155) hydrogen bonds : angle 3.93208 / 2.93 ( 459) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.065 Fit side-chains REVERT: A 58 TRP cc_start: 0.7229 (t60) cc_final: 0.6975 (t-100) REVERT: A 149 CYS cc_start: 0.5936 (m) cc_final: 0.5192 (p) REVERT: A 167 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7850 (m) outliers start: 2 outliers final: 0 residues processed: 25 average time/residue: 0.2517 time to fit residues: 6.5513 Evaluate side-chains 24 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.187764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.146452 restraints weight = 2293.191| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.26 r_work: 0.3608 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2016 Z= 0.133 Angle : 0.635 10.221 2773 Z= 0.309 Chirality : 0.040 0.147 337 Planarity : 0.007 0.087 340 Dihedral : 3.994 15.947 284 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.51 % Allowed : 18.97 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.54 (0.54), residues: 264 helix: 2.39 (0.37), residues: 207 sheet: -1.72 (1.37), residues: 10 loop : -0.78 (1.00), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 67 TYR 0.006 0.001 TYR A 249 PHE 0.007 0.001 PHE A 243 TRP 0.010 0.001 TRP A 141 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 2014) covalent geometry : angle 0.63513 / 0.31 ( 2769) SS BOND : bond 0.00263 / 0.13 ( 2) SS BOND : angle 0.71666 / 0.38 ( 4) hydrogen bonds : bond 0.03832 / 2.56 ( 155) hydrogen bonds : angle 3.93530 / 2.94 ( 459) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.041 Fit side-chains REVERT: A 58 TRP cc_start: 0.7232 (t60) cc_final: 0.6970 (t-100) REVERT: A 149 CYS cc_start: 0.5928 (m) cc_final: 0.5189 (p) REVERT: A 167 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7810 (m) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.2033 time to fit residues: 5.0628 Evaluate side-chains 25 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.0040 chunk 9 optimal weight: 0.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.189304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.145859 restraints weight = 2292.284| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.29 r_work: 0.3622 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2016 Z= 0.127 Angle : 0.616 10.827 2773 Z= 0.298 Chirality : 0.040 0.144 337 Planarity : 0.007 0.069 340 Dihedral : 3.951 15.847 284 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.51 % Allowed : 19.49 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.61 (0.55), residues: 264 helix: 2.43 (0.37), residues: 207 sheet: -1.62 (1.48), residues: 10 loop : -0.75 (1.02), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 67 TYR 0.005 0.001 TYR A 249 PHE 0.007 0.001 PHE A 243 TRP 0.010 0.001 TRP A 142 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 2014) covalent geometry : angle 0.61546 / 0.30 ( 2769) SS BOND : bond 0.00267 / 0.13 ( 2) SS BOND : angle 0.65425 / 0.34 ( 4) hydrogen bonds : bond 0.03731 / 2.49 ( 155) hydrogen bonds : angle 3.89031 / 2.91 ( 459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 833.49 seconds wall clock time: 14 minutes 53.18 seconds (893.18 seconds total)