Starting phenix.real_space_refine on Wed Jun 4 11:06:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ql2_14061/06_2025/7ql2_14061.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql2_14061/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ql2_14061/06_2025/7ql2_14061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql2_14061/06_2025/7ql2_14061.map" model { file = "/net/cci-nas-00/data/ceres_data/7ql2_14061/06_2025/7ql2_14061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql2_14061/06_2025/7ql2_14061.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 2.16, per 1000 atoms: 0.94 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: 0.57 Conformation dependent library (CDL) restraints added in 214.9 milliseconds 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: 0.25 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: 0.65 Time building geometry restraints manager: 0.71 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: 0.01 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: 2.260 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: 0.050 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.270 Find NCS groups from input model: 0.060 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:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.490 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.011 0.004 HIS C 299 TYR 0.052 0.018 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.16788 ( 18) hydrogen bonds : angle 7.31295 ( 51) SS BOND : bond 0.02569 ( 3) SS BOND : angle 2.14439 ( 6) covalent geometry : bond 0.01016 ( 1116) covalent geometry : angle 2.10899 ( 1494) *********************** 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 : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 3.4723 time to fit residues: 21.2604 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 : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.5314 r_free = 0.5314 target = 0.174420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5157 r_free = 0.5157 target = 0.152383 restraints weight = 3324.585| |-----------------------------------------------------------------------------| r_work (start): 0.5236 rms_B_bonded: 2.98 r_work: 0.5085 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.5085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1119 Z= 0.130 Angle : 0.595 3.695 1500 Z= 0.314 Chirality : 0.054 0.144 180 Planarity : 0.004 0.040 186 Dihedral : 6.982 19.943 150 Min Nonbonded Distance : 2.560 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.58), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.44), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 TYR 0.011 0.003 TYR B 310 Details of bonding type rmsd hydrogen bonds : bond 0.02597 ( 18) hydrogen bonds : angle 5.47027 ( 51) SS BOND : bond 0.00721 ( 3) SS BOND : angle 0.65271 ( 6) covalent geometry : bond 0.00311 ( 1116) covalent geometry : angle 0.59480 ( 1494) *********************** 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 9 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.198 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 8 average time/residue: 2.7684 time to fit residues: 22.6411 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 : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 0.0030 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 overall best weight: 0.9194 ------------------------------------------------------------------------------- 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 = 0.5292 r_free = 0.5292 target = 0.171116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5129 r_free = 0.5129 target = 0.147480 restraints weight = 3371.391| |-----------------------------------------------------------------------------| r_work (start): 0.5196 rms_B_bonded: 3.06 r_work: 0.5047 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.5047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3323 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= 0.109 Angle : 0.550 3.649 1500 Z= 0.293 Chirality : 0.055 0.135 180 Planarity : 0.004 0.033 186 Dihedral : 6.180 18.480 150 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 11.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.54), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.42), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 299 TYR 0.013 0.003 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.02418 ( 18) hydrogen bonds : angle 4.92640 ( 51) SS BOND : bond 0.00536 ( 3) SS BOND : angle 0.68877 ( 6) covalent geometry : bond 0.00231 ( 1116) covalent geometry : angle 0.54895 ( 1494) *********************** 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 : 0.200 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 3.1142 time to fit residues: 19.1665 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 : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.5350 r_free = 0.5350 target = 0.175178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.154210 restraints weight = 3544.214| |-----------------------------------------------------------------------------| r_work (start): 0.5174 rms_B_bonded: 2.97 r_work: 0.5023 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.5023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1119 Z= 0.114 Angle : 0.519 3.379 1500 Z= 0.273 Chirality : 0.054 0.135 180 Planarity : 0.004 0.033 186 Dihedral : 5.942 18.717 150 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.54), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 299 TYR 0.010 0.002 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.01941 ( 18) hydrogen bonds : angle 4.77121 ( 51) SS BOND : bond 0.00475 ( 3) SS BOND : angle 0.47372 ( 6) covalent geometry : bond 0.00241 ( 1116) covalent geometry : angle 0.51927 ( 1494) *********************** 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: 2 poor density : 6 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 322 CYS cc_start: 0.5165 (OUTLIER) cc_final: 0.4915 (t) outliers start: 2 outliers final: 1 residues processed: 8 average time/residue: 2.6924 time to fit residues: 22.0485 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 : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 HIS 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 10 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 = 0.5310 r_free = 0.5310 target = 0.171385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5161 r_free = 0.5161 target = 0.148993 restraints weight = 3527.661| |-----------------------------------------------------------------------------| r_work (start): 0.5200 rms_B_bonded: 3.06 r_work: 0.5052 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.5052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1119 Z= 0.094 Angle : 0.482 3.246 1500 Z= 0.255 Chirality : 0.054 0.130 180 Planarity : 0.004 0.038 186 Dihedral : 5.563 17.528 150 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.54), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.42), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 299 TYR 0.009 0.002 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.01752 ( 18) hydrogen bonds : angle 4.70106 ( 51) SS BOND : bond 0.00376 ( 3) SS BOND : angle 0.35863 ( 6) covalent geometry : bond 0.00209 ( 1116) covalent geometry : angle 0.48291 ( 1494) *********************** 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: 2 poor density : 6 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 322 CYS cc_start: 0.5163 (OUTLIER) cc_final: 0.4752 (t) outliers start: 2 outliers final: 1 residues processed: 8 average time/residue: 2.6643 time to fit residues: 21.8055 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 : 0.200 ------------------------------------------------------------------------------- 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 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 0 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.5367 r_free = 0.5367 target = 0.175812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5235 r_free = 0.5235 target = 0.155053 restraints weight = 3590.816| |-----------------------------------------------------------------------------| r_work (start): 0.5187 rms_B_bonded: 2.96 r_work: 0.5040 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.5040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.4347 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 : 0.485 3.252 1500 Z= 0.256 Chirality : 0.054 0.133 180 Planarity : 0.004 0.040 186 Dihedral : 5.461 18.016 150 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.55), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.42), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 299 TYR 0.009 0.002 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.01796 ( 18) hydrogen bonds : angle 4.66300 ( 51) SS BOND : bond 0.00398 ( 3) SS BOND : angle 0.35417 ( 6) covalent geometry : bond 0.00214 ( 1116) covalent geometry : angle 0.48522 ( 1494) *********************** 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: 2 poor density : 6 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 8 average time/residue: 2.7613 time to fit residues: 22.5684 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 : 0.185 ------------------------------------------------------------------------------- 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 11 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.5153 r_free = 0.5153 target = 0.167136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.143045 restraints weight = 3826.699| |-----------------------------------------------------------------------------| r_work (start): 0.4890 rms_B_bonded: 3.30 r_work: 0.4778 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4419 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= 0.156 Angle : 0.529 2.989 1500 Z= 0.283 Chirality : 0.054 0.139 180 Planarity : 0.004 0.035 186 Dihedral : 5.861 19.919 150 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 2.96 % Allowed : 8.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.54), 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 HIS 0.005 0.003 HIS C 299 TYR 0.014 0.003 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.01994 ( 18) hydrogen bonds : angle 5.06255 ( 51) SS BOND : bond 0.00413 ( 3) SS BOND : angle 0.49952 ( 6) covalent geometry : bond 0.00324 ( 1116) covalent geometry : angle 0.52943 ( 1494) *********************** 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 11 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 11 average time/residue: 1.9852 time to fit residues: 22.3752 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 : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 HIS 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 8 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.5187 r_free = 0.5187 target = 0.169910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5014 r_free = 0.5014 target = 0.145561 restraints weight = 3823.872| |-----------------------------------------------------------------------------| r_work (start): 0.4908 rms_B_bonded: 3.26 r_work: 0.4801 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1119 Z= 0.146 Angle : 0.527 3.399 1500 Z= 0.284 Chirality : 0.054 0.139 180 Planarity : 0.004 0.037 186 Dihedral : 5.888 19.550 150 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.96 % Allowed : 9.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.54), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 299 TYR 0.011 0.003 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.02025 ( 18) hydrogen bonds : angle 4.92483 ( 51) SS BOND : bond 0.00457 ( 3) SS BOND : angle 0.38314 ( 6) covalent geometry : bond 0.00299 ( 1116) covalent geometry : angle 0.52720 ( 1494) *********************** 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 10 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 6 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 10 average time/residue: 2.1212 time to fit residues: 21.7230 Evaluate side-chains 9 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 HIS 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 12 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.5225 r_free = 0.5225 target = 0.171776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5058 r_free = 0.5058 target = 0.148208 restraints weight = 3649.066| |-----------------------------------------------------------------------------| r_work (start): 0.4970 rms_B_bonded: 3.20 r_work: 0.4866 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.4692 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= 0.096 Angle : 0.476 3.131 1500 Z= 0.255 Chirality : 0.054 0.129 180 Planarity : 0.005 0.040 186 Dihedral : 5.438 17.630 150 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.54), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 299 TYR 0.009 0.002 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.01556 ( 18) hydrogen bonds : angle 4.78203 ( 51) SS BOND : bond 0.00345 ( 3) SS BOND : angle 0.30487 ( 6) covalent geometry : bond 0.00202 ( 1116) covalent geometry : angle 0.47703 ( 1494) *********************** 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 7 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 5 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 7 average time/residue: 2.4050 time to fit residues: 17.2896 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 : 0.184 ------------------------------------------------------------------------------- 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 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.5243 r_free = 0.5243 target = 0.173472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.149656 restraints weight = 3692.855| |-----------------------------------------------------------------------------| r_work (start): 0.4966 rms_B_bonded: 3.23 r_work: 0.4859 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4747 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= 0.106 Angle : 0.486 2.946 1500 Z= 0.261 Chirality : 0.053 0.132 180 Planarity : 0.004 0.039 186 Dihedral : 5.479 18.198 150 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (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 HIS 0.002 0.001 HIS C 299 TYR 0.010 0.002 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.01781 ( 18) hydrogen bonds : angle 4.77716 ( 51) SS BOND : bond 0.00368 ( 3) SS BOND : angle 0.27433 ( 6) covalent geometry : bond 0.00221 ( 1116) covalent geometry : angle 0.48622 ( 1494) ********************** 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 : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 7 average time/residue: 2.3626 time to fit residues: 17.0801 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 : 0.201 ------------------------------------------------------------------------------- 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 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.5208 r_free = 0.5208 target = 0.170505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.147031 restraints weight = 3723.184| |-----------------------------------------------------------------------------| r_work (start): 0.4966 rms_B_bonded: 3.22 r_work: 0.4861 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.4809 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= 0.106 Angle : 0.477 2.869 1500 Z= 0.255 Chirality : 0.053 0.131 180 Planarity : 0.004 0.038 186 Dihedral : 5.409 18.126 150 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 1.75 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.54), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 299 TYR 0.010 0.002 TYR C 310 Details of bonding type rmsd hydrogen bonds : bond 0.01558 ( 18) hydrogen bonds : angle 4.80744 ( 51) SS BOND : bond 0.00356 ( 3) SS BOND : angle 0.29106 ( 6) covalent geometry : bond 0.00218 ( 1116) covalent geometry : angle 0.47724 ( 1494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2689.84 seconds wall clock time: 46 minutes 18.83 seconds (2778.83 seconds total)