Starting phenix.real_space_refine on Wed Sep 17 03:00:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ql2_14061/09_2025/7ql2_14061.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql2_14061/09_2025/7ql2_14061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ql2_14061/09_2025/7ql2_14061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql2_14061/09_2025/7ql2_14061.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ql2_14061/09_2025/7ql2_14061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql2_14061/09_2025/7ql2_14061.map" } resolution = 2.95 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 690 2.51 5 N 198 2.21 5 O 213 1.98 5 H 1179 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 2286 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 762 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "A" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 762 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "C" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 762 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Time building chain proxies: 0.71, per 1000 atoms: 0.31 Number of scatterers: 2286 At special positions: 0 Unit cell: (64.272, 57.68, 32.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 213 8.00 N 198 7.00 C 690 6.00 H 1179 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 322 " distance=1.99 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 322 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 322 " distance=2.01 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: 0.18 Conformation dependent library (CDL) restraints added in 57.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 270 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 59.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 276 through 291 removed outlier: 6.899A pdb=" N ILE B 277 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 278 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN B 279 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS A 280 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS B 281 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU A 282 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP B 283 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 284 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER B 285 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN A 286 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N GLN B 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N ASN C 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N ILE B 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N LYS C 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N LYS B 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 10.595A pdb=" N ASP C 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N SER C 285 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N LEU B 284 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N VAL C 287 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN B 286 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N SER C 289 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN B 288 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N CYS C 291 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS B 290 " --> pdb=" O CYS C 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 294 through 297 removed outlier: 6.782A pdb=" N ASP B 295 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN A 296 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N LYS B 294 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 9.736A pdb=" N ILE C 297 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASN B 296 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 305 through 310 removed outlier: 6.548A pdb=" N VAL B 306 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL A 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 308 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.570A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 323 removed outlier: 6.243A pdb=" N VAL B 318 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N LYS A 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER B 320 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLY A 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS B 322 " --> pdb=" O GLY A 323 " (cutoff:3.500A) 18 hydrogen bonds defined for protein. 51 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: 0.44 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 1179 1.13 - 1.30: 187 1.30 - 1.48: 382 1.48 - 1.65: 541 1.65 - 1.83: 6 Bond restraints: 2295 Sorted by residual: bond pdb=" NE2 GLN A 276 " pdb="HE21 GLN A 276 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N SER A 293 " pdb=" H SER A 293 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASN A 286 " pdb=" H ASN A 286 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" ND2 ASN A 286 " pdb="HD22 ASN A 286 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N SER C 316 " pdb=" H SER C 316 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 2290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 2899 1.78 - 3.56: 876 3.56 - 5.33: 271 5.33 - 7.11: 138 7.11 - 8.89: 19 Bond angle restraints: 4203 Sorted by residual: angle pdb=" CA ASP C 283 " pdb=" CB ASP C 283 " pdb=" CG ASP C 283 " ideal model delta sigma weight residual 112.60 119.29 -6.69 1.00e+00 1.00e+00 4.48e+01 angle pdb=" CA ASP B 283 " pdb=" CB ASP B 283 " pdb=" CG ASP B 283 " ideal model delta sigma weight residual 112.60 119.07 -6.47 1.00e+00 1.00e+00 4.19e+01 angle pdb=" CA ASP A 283 " pdb=" CB ASP A 283 " pdb=" CG ASP A 283 " ideal model delta sigma weight residual 112.60 118.79 -6.19 1.00e+00 1.00e+00 3.84e+01 angle pdb=" N VAL C 313 " pdb=" CA VAL C 313 " pdb=" C VAL C 313 " ideal model delta sigma weight residual 106.88 98.98 7.90 1.52e+00 4.33e-01 2.70e+01 angle pdb=" N CYS A 322 " pdb=" CA CYS A 322 " pdb=" CB CYS A 322 " ideal model delta sigma weight residual 111.53 102.64 8.89 1.86e+00 2.89e-01 2.29e+01 ... (remaining 4198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.60: 935 14.60 - 29.20: 63 29.20 - 43.80: 15 43.80 - 58.40: 29 58.40 - 73.00: 23 Dihedral angle restraints: 1065 sinusoidal: 624 harmonic: 441 Sorted by residual: dihedral pdb=" CA PRO B 312 " pdb=" C PRO B 312 " pdb=" N VAL B 313 " pdb=" CA VAL B 313 " ideal model delta harmonic sigma weight residual 180.00 149.41 30.59 0 5.00e+00 4.00e-02 3.74e+01 dihedral pdb=" CA LYS C 321 " pdb=" C LYS C 321 " pdb=" N CYS C 322 " pdb=" CA CYS C 322 " ideal model delta harmonic sigma weight residual 180.00 -152.99 -27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" C LYS A 311 " pdb=" N LYS A 311 " pdb=" CA LYS A 311 " pdb=" CB LYS A 311 " ideal model delta harmonic sigma weight residual -122.60 -135.34 12.74 0 2.50e+00 1.60e-01 2.60e+01 ... (remaining 1062 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.087: 105 0.087 - 0.173: 55 0.173 - 0.259: 16 0.259 - 0.345: 3 0.345 - 0.431: 1 Chirality restraints: 180 Sorted by residual: chirality pdb=" CA LYS A 311 " pdb=" N LYS A 311 " pdb=" C LYS A 311 " pdb=" CB LYS A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA LYS B 311 " pdb=" N LYS B 311 " pdb=" C LYS B 311 " pdb=" CB LYS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA LYS C 311 " pdb=" N LYS C 311 " pdb=" C LYS C 311 " pdb=" CB LYS C 311 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 177 not shown) Planarity restraints: 327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 296 " 0.021 2.00e-02 2.50e+03 1.08e-01 1.73e+02 pdb=" CG ASN C 296 " 0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN C 296 " -0.117 2.00e-02 2.50e+03 pdb=" ND2 ASN C 296 " 0.148 2.00e-02 2.50e+03 pdb="HD21 ASN C 296 " -0.159 2.00e-02 2.50e+03 pdb="HD22 ASN C 296 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 312 " -0.038 2.00e-02 2.50e+03 7.04e-02 4.95e+01 pdb=" N VAL B 313 " 0.122 2.00e-02 2.50e+03 pdb=" CA VAL B 313 " -0.035 2.00e-02 2.50e+03 pdb=" H VAL B 313 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 321 " 0.037 2.00e-02 2.50e+03 6.78e-02 4.60e+01 pdb=" N CYS C 322 " -0.117 2.00e-02 2.50e+03 pdb=" CA CYS C 322 " 0.033 2.00e-02 2.50e+03 pdb=" H CYS C 322 " 0.048 2.00e-02 2.50e+03 ... (remaining 324 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 326 2.30 - 2.88: 4770 2.88 - 3.45: 5620 3.45 - 4.03: 7215 4.03 - 4.60: 10481 Nonbonded interactions: 28412 Sorted by model distance: nonbonded pdb=" O CYS A 291 " pdb=" HG SER A 320 " model vdw 1.725 2.450 nonbonded pdb=" OD2 ASP B 295 " pdb=" HZ3 LYS B 298 " model vdw 1.752 2.450 nonbonded pdb=" HG3 LYS C 298 " pdb=" H HIS C 299 " model vdw 1.759 2.270 nonbonded pdb=" OD2 ASP A 295 " pdb=" HZ2 LYS A 298 " model vdw 1.760 2.450 nonbonded pdb="HE21 GLN B 276 " pdb="HD11 ILE B 278 " model vdw 1.764 2.270 ... (remaining 28407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 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: 0.020 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.620 Find NCS groups from input model: 0.030 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 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 : 0.010 0.039 1119 Z= 0.625 Angle : 2.109 8.891 1500 Z= 1.367 Chirality : 0.111 0.431 180 Planarity : 0.009 0.034 186 Dihedral : 10.984 47.071 432 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 1.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.71 % 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: -2.82 (0.58), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.44), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.052 0.018 TYR C 310 HIS 0.011 0.004 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.01016 ( 1116) covalent geometry : angle 2.10899 ( 1494) SS BOND : bond 0.02569 ( 3) SS BOND : angle 2.14439 ( 6) hydrogen bonds : bond 0.16788 ( 18) hydrogen bonds : angle 7.31295 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 1.9719 time to fit residues: 12.0080 Evaluate side-chains 6 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5320 r_free = 0.5320 target = 0.174891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5163 r_free = 0.5163 target = 0.152551 restraints weight = 3357.490| |-----------------------------------------------------------------------------| r_work (start): 0.5244 rms_B_bonded: 3.03 r_work: 0.5091 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.5091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1119 Z= 0.126 Angle : 0.590 3.687 1500 Z= 0.312 Chirality : 0.054 0.145 180 Planarity : 0.004 0.040 186 Dihedral : 6.921 19.577 150 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.48 % Allowed : 9.63 % Favored : 88.89 % 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: -3.08 (0.58), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.44), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR B 310 HIS 0.002 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 1116) covalent geometry : angle 0.58951 ( 1494) SS BOND : bond 0.00761 ( 3) SS BOND : angle 0.64980 ( 6) hydrogen bonds : bond 0.02490 ( 18) hydrogen bonds : angle 5.47515 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.070 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 9 average time/residue: 1.5989 time to fit residues: 14.5991 Evaluate side-chains 6 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.5304 r_free = 0.5304 target = 0.171613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5141 r_free = 0.5141 target = 0.147896 restraints weight = 3492.726| |-----------------------------------------------------------------------------| r_work (start): 0.5211 rms_B_bonded: 3.11 r_work: 0.5063 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.5063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1119 Z= 0.104 Angle : 0.539 3.586 1500 Z= 0.287 Chirality : 0.054 0.134 180 Planarity : 0.004 0.032 186 Dihedral : 6.211 18.309 150 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % 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: -3.23 (0.54), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR C 310 HIS 0.002 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 1116) covalent geometry : angle 0.53831 ( 1494) SS BOND : bond 0.00500 ( 3) SS BOND : angle 0.62384 ( 6) hydrogen bonds : bond 0.02421 ( 18) hydrogen bonds : angle 4.95043 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.070 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 1.6313 time to fit residues: 9.9630 Evaluate side-chains 5 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.5333 r_free = 0.5333 target = 0.176022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5157 r_free = 0.5157 target = 0.152256 restraints weight = 3339.093| |-----------------------------------------------------------------------------| r_work (start): 0.5140 rms_B_bonded: 2.94 r_work: 0.4993 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1119 Z= 0.126 Angle : 0.538 3.405 1500 Z= 0.284 Chirality : 0.054 0.136 180 Planarity : 0.004 0.032 186 Dihedral : 6.080 19.418 150 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.22 % Allowed : 10.37 % Favored : 87.41 % 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: -3.20 (0.53), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR C 310 HIS 0.003 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 1116) covalent geometry : angle 0.53838 ( 1494) SS BOND : bond 0.00471 ( 3) SS BOND : angle 0.55789 ( 6) hydrogen bonds : bond 0.01922 ( 18) hydrogen bonds : angle 4.92366 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 5 time to evaluate : 0.071 Fit side-chains REVERT: A 322 CYS cc_start: 0.5230 (OUTLIER) cc_final: 0.4985 (t) outliers start: 3 outliers final: 0 residues processed: 8 average time/residue: 1.2864 time to fit residues: 10.4934 Evaluate side-chains 6 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 5 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5342 r_free = 0.5342 target = 0.174515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5184 r_free = 0.5184 target = 0.152639 restraints weight = 3528.966| |-----------------------------------------------------------------------------| r_work (start): 0.5150 rms_B_bonded: 3.01 r_work: 0.5045 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.5045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1119 Z= 0.110 Angle : 0.515 3.202 1500 Z= 0.277 Chirality : 0.054 0.132 180 Planarity : 0.004 0.034 186 Dihedral : 5.792 18.311 150 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.22 % Allowed : 9.63 % Favored : 88.15 % 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: -3.26 (0.53), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR C 310 HIS 0.012 0.003 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 1116) covalent geometry : angle 0.51587 ( 1494) SS BOND : bond 0.00406 ( 3) SS BOND : angle 0.36819 ( 6) hydrogen bonds : bond 0.01846 ( 18) hydrogen bonds : angle 4.86589 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 5 time to evaluate : 0.059 Fit side-chains revert: symmetry clash REVERT: A 322 CYS cc_start: 0.5331 (OUTLIER) cc_final: 0.4920 (t) outliers start: 3 outliers final: 1 residues processed: 8 average time/residue: 1.2268 time to fit residues: 10.0343 Evaluate side-chains 7 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 5 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain C residue 322 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.5295 r_free = 0.5295 target = 0.171333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.149675 restraints weight = 3624.365| |-----------------------------------------------------------------------------| r_work (start): 0.5104 rms_B_bonded: 3.01 r_work: 0.5001 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.5001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1119 Z= 0.128 Angle : 0.527 3.333 1500 Z= 0.283 Chirality : 0.054 0.136 180 Planarity : 0.004 0.036 186 Dihedral : 5.818 19.023 150 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.22 % Allowed : 8.89 % Favored : 88.89 % 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: -3.27 (0.55), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.42), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR C 310 HIS 0.015 0.006 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 1116) covalent geometry : angle 0.52708 ( 1494) SS BOND : bond 0.00426 ( 3) SS BOND : angle 0.37344 ( 6) hydrogen bonds : bond 0.01831 ( 18) hydrogen bonds : angle 4.91044 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 5 time to evaluate : 0.066 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 8 average time/residue: 1.2336 time to fit residues: 10.0735 Evaluate side-chains 6 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 4 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain C residue 322 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.5311 r_free = 0.5311 target = 0.172721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.150897 restraints weight = 3657.518| |-----------------------------------------------------------------------------| r_work (start): 0.5127 rms_B_bonded: 3.05 r_work: 0.5026 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.5026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1119 Z= 0.118 Angle : 0.499 3.059 1500 Z= 0.270 Chirality : 0.054 0.133 180 Planarity : 0.004 0.036 186 Dihedral : 5.696 18.479 150 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 1.48 % Allowed : 10.37 % Favored : 88.15 % 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: -3.34 (0.54), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR C 310 HIS 0.008 0.003 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 1116) covalent geometry : angle 0.49960 ( 1494) SS BOND : bond 0.00402 ( 3) SS BOND : angle 0.33163 ( 6) hydrogen bonds : bond 0.01781 ( 18) hydrogen bonds : angle 4.94750 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 5 time to evaluate : 0.060 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 7 average time/residue: 0.9656 time to fit residues: 6.8948 Evaluate side-chains 6 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 4 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain C residue 322 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.5273 r_free = 0.5273 target = 0.170515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5117 r_free = 0.5117 target = 0.148666 restraints weight = 3573.210| |-----------------------------------------------------------------------------| r_work (start): 0.5090 rms_B_bonded: 2.98 r_work: 0.4993 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1119 Z= 0.129 Angle : 0.505 3.057 1500 Z= 0.272 Chirality : 0.053 0.134 180 Planarity : 0.004 0.036 186 Dihedral : 5.769 19.027 150 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.22 % Allowed : 10.37 % Favored : 87.41 % 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: -3.34 (0.54), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.003 TYR C 310 HIS 0.007 0.003 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 1116) covalent geometry : angle 0.50542 ( 1494) SS BOND : bond 0.00435 ( 3) SS BOND : angle 0.32157 ( 6) hydrogen bonds : bond 0.01823 ( 18) hydrogen bonds : angle 4.94320 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 4 time to evaluate : 0.067 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 7 average time/residue: 0.7624 time to fit residues: 5.4851 Evaluate side-chains 6 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 4 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain C residue 322 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.5323 r_free = 0.5323 target = 0.174343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5172 r_free = 0.5172 target = 0.152473 restraints weight = 3585.843| |-----------------------------------------------------------------------------| r_work (start): 0.5148 rms_B_bonded: 3.02 r_work: 0.5048 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.5048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1119 Z= 0.099 Angle : 0.478 3.005 1500 Z= 0.257 Chirality : 0.054 0.129 180 Planarity : 0.004 0.039 186 Dihedral : 5.486 17.824 150 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.48 % Allowed : 11.11 % Favored : 87.41 % 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: -3.28 (0.54), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR C 310 HIS 0.008 0.003 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 1116) covalent geometry : angle 0.47869 ( 1494) SS BOND : bond 0.00370 ( 3) SS BOND : angle 0.30904 ( 6) hydrogen bonds : bond 0.01602 ( 18) hydrogen bonds : angle 4.80480 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 8 average time/residue: 1.3405 time to fit residues: 10.8949 Evaluate side-chains 7 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 5 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain C residue 322 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.5162 r_free = 0.5162 target = 0.167883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.144176 restraints weight = 3818.834| |-----------------------------------------------------------------------------| r_work (start): 0.4938 rms_B_bonded: 3.25 r_work: 0.4837 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1119 Z= 0.143 Angle : 0.513 3.007 1500 Z= 0.276 Chirality : 0.054 0.136 180 Planarity : 0.004 0.037 186 Dihedral : 5.746 19.328 150 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 1.48 % Allowed : 11.11 % Favored : 87.41 % 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: -3.37 (0.53), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR C 310 HIS 0.006 0.003 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 1116) covalent geometry : angle 0.51314 ( 1494) SS BOND : bond 0.00448 ( 3) SS BOND : angle 0.33147 ( 6) hydrogen bonds : bond 0.01917 ( 18) hydrogen bonds : angle 5.01847 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 5 time to evaluate : 0.070 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 7 average time/residue: 1.2421 time to fit residues: 8.8715 Evaluate side-chains 7 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 5 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain C residue 322 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.5205 r_free = 0.5205 target = 0.171060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.147716 restraints weight = 3741.114| |-----------------------------------------------------------------------------| r_work (start): 0.4978 rms_B_bonded: 3.24 r_work: 0.4878 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1119 Z= 0.109 Angle : 0.484 3.062 1500 Z= 0.260 Chirality : 0.053 0.131 180 Planarity : 0.004 0.039 186 Dihedral : 5.507 18.276 150 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.48 % Allowed : 10.37 % Favored : 88.15 % 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: -3.43 (0.53), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.40), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR C 310 HIS 0.007 0.003 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 1116) covalent geometry : angle 0.48473 ( 1494) SS BOND : bond 0.00370 ( 3) SS BOND : angle 0.31004 ( 6) hydrogen bonds : bond 0.01649 ( 18) hydrogen bonds : angle 4.91815 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.23 seconds wall clock time: 25 minutes 42.93 seconds (1542.93 seconds total)