Starting phenix.real_space_refine on Mon Feb 10 20:32:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ql2_14061/02_2025/7ql2_14061.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql2_14061/02_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_14061/02_2025/7ql2_14061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql2_14061/02_2025/7ql2_14061.map" model { file = "/net/cci-nas-00/data/ceres_data/7ql2_14061/02_2025/7ql2_14061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql2_14061/02_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 0.52 Conformation dependent library (CDL) restraints added in 166.5 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: 0.21 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: 0.65 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: 2.780 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: 0.040 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.610 Find NCS groups from input model: 0.050 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:9.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.290 ------------------------------------------------------------------------------- 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 0.034 1116 Z= 0.684 Angle : 2.109 8.891 1494 Z= 1.368 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 *********************** 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 : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 3.4958 time to fit residues: 21.3912 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 ------------------------------------------------------------------------------- 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: 1.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.5307 r_free = 0.5307 target = 0.174133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5149 r_free = 0.5149 target = 0.152032 restraints weight = 3326.002| |-----------------------------------------------------------------------------| r_work (start): 0.5232 rms_B_bonded: 2.99 r_work: 0.5126 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.5126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1116 Z= 0.202 Angle : 0.604 3.699 1494 Z= 0.321 Chirality : 0.054 0.147 180 Planarity : 0.004 0.041 186 Dihedral : 7.067 20.391 150 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.48 % Allowed : 8.89 % Favored : 89.63 % 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: -3.09 (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 0.012 0.003 TYR B 310 *********************** 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 : 0.183 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 8 average time/residue: 2.8466 time to fit residues: 23.2763 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.5436 r_free = 0.5436 target = 0.183612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5261 r_free = 0.5261 target = 0.158896 restraints weight = 3118.443| |-----------------------------------------------------------------------------| r_work (start): 0.5234 rms_B_bonded: 2.99 r_work: 0.5082 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.5082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1116 Z= 0.139 Angle : 0.531 3.697 1494 Z= 0.283 Chirality : 0.055 0.136 180 Planarity : 0.004 0.035 186 Dihedral : 6.118 17.734 150 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % 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: -3.18 (0.55), 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 0.002 0.001 HIS C 299 TYR 0.012 0.002 TYR C 310 *********************** 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 7 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.188 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 3.2687 time to fit residues: 23.3888 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 : 0.191 ------------------------------------------------------------------------------- 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: 0.0770 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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 = 0.5412 r_free = 0.5412 target = 0.178646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5273 r_free = 0.5273 target = 0.156829 restraints weight = 3432.062| |-----------------------------------------------------------------------------| r_work (start): 0.5253 rms_B_bonded: 3.05 r_work: 0.5104 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.5104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1116 Z= 0.133 Angle : 0.487 3.481 1494 Z= 0.255 Chirality : 0.054 0.131 180 Planarity : 0.004 0.039 186 Dihedral : 5.703 17.397 150 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: -3.09 (0.55), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.42), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 299 TYR 0.008 0.002 TYR C 310 *********************** 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 6 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.198 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 3.6551 time to fit residues: 22.3883 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 : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 0.0020 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 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: 3.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 = 0.5392 r_free = 0.5392 target = 0.177100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5261 r_free = 0.5261 target = 0.155830 restraints weight = 3497.944| |-----------------------------------------------------------------------------| r_work (start): 0.5242 rms_B_bonded: 3.02 r_work: 0.5096 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.5096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1116 Z= 0.131 Angle : 0.472 3.203 1494 Z= 0.249 Chirality : 0.053 0.130 180 Planarity : 0.004 0.040 186 Dihedral : 5.424 17.400 150 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.74 % Allowed : 11.11 % 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: -3.08 (0.56), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.43), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 299 TYR 0.010 0.002 TYR C 310 *********************** 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 6 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 5 time to evaluate : 0.189 Fit side-chains REVERT: A 322 CYS cc_start: 0.5036 (OUTLIER) cc_final: 0.4673 (t) outliers start: 1 outliers final: 0 residues processed: 6 average time/residue: 2.8810 time to fit residues: 17.7075 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 : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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: 3.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.5254 r_free = 0.5254 target = 0.172995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.148945 restraints weight = 3706.896| |-----------------------------------------------------------------------------| r_work (start): 0.5012 rms_B_bonded: 3.28 r_work: 0.4897 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1116 Z= 0.160 Angle : 0.495 3.053 1494 Z= 0.263 Chirality : 0.054 0.136 180 Planarity : 0.004 0.037 186 Dihedral : 5.618 18.736 150 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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 (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: -3.15 (0.54), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.42), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 299 TYR 0.010 0.003 TYR C 310 *********************** 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 : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 CYS cc_start: 0.5284 (OUTLIER) cc_final: 0.4696 (t) outliers start: 3 outliers final: 2 residues processed: 8 average time/residue: 2.3041 time to fit residues: 18.8901 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 : 0.199 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.5279 r_free = 0.5279 target = 0.175010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.151202 restraints weight = 3676.042| |-----------------------------------------------------------------------------| r_work (start): 0.5075 rms_B_bonded: 3.31 r_work: 0.4965 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1116 Z= 0.134 Angle : 0.465 2.981 1494 Z= 0.246 Chirality : 0.053 0.129 180 Planarity : 0.004 0.038 186 Dihedral : 5.393 17.378 150 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 1.75 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 (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: -3.24 (0.54), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 299 TYR 0.008 0.002 TYR C 310 *********************** 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 8 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 8 average time/residue: 2.7420 time to fit residues: 22.4122 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 : 0.176 ------------------------------------------------------------------------------- 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 8 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.5210 r_free = 0.5210 target = 0.170754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.146768 restraints weight = 3808.635| |-----------------------------------------------------------------------------| r_work (start): 0.5014 rms_B_bonded: 3.36 r_work: 0.4899 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1116 Z= 0.170 Angle : 0.492 2.931 1494 Z= 0.262 Chirality : 0.054 0.134 180 Planarity : 0.004 0.036 186 Dihedral : 5.619 19.090 150 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % 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: -3.24 (0.55), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.42), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 299 TYR 0.011 0.003 TYR C 310 *********************** 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 8 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 8 average time/residue: 2.2437 time to fit residues: 18.4321 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 : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain C residue 322 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 0.0670 overall best weight: 0.6320 ------------------------------------------------------------------------------- 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 = 0.5255 r_free = 0.5255 target = 0.173844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.149906 restraints weight = 3617.598| |-----------------------------------------------------------------------------| r_work (start): 0.4995 rms_B_bonded: 3.25 r_work: 0.4884 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1116 Z= 0.128 Angle : 0.463 2.953 1494 Z= 0.245 Chirality : 0.053 0.129 180 Planarity : 0.004 0.039 186 Dihedral : 5.335 17.701 150 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % 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 (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: -3.25 (0.55), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.42), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 299 TYR 0.007 0.002 TYR C 310 *********************** 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: 3 poor density : 5 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 8 average time/residue: 2.3001 time to fit residues: 18.8904 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 : 0.189 ------------------------------------------------------------------------------- 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: 2.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.5220 r_free = 0.5220 target = 0.171566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.147653 restraints weight = 3718.950| |-----------------------------------------------------------------------------| r_work (start): 0.4979 rms_B_bonded: 3.30 r_work: 0.4864 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1116 Z= 0.147 Angle : 0.477 2.945 1494 Z= 0.252 Chirality : 0.053 0.132 180 Planarity : 0.004 0.037 186 Dihedral : 5.430 18.498 150 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.19 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 (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: -3.28 (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 HIS 0.002 0.001 HIS C 299 TYR 0.011 0.002 TYR C 310 ********************** 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 : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 7 average time/residue: 2.5109 time to fit residues: 18.0252 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 : 0.177 ------------------------------------------------------------------------------- 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: 0.4980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.5234 r_free = 0.5234 target = 0.172723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.149191 restraints weight = 3687.583| |-----------------------------------------------------------------------------| r_work (start): 0.4991 rms_B_bonded: 3.27 r_work: 0.4881 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1116 Z= 0.134 Angle : 0.461 2.878 1494 Z= 0.243 Chirality : 0.053 0.129 180 Planarity : 0.004 0.039 186 Dihedral : 5.294 17.810 150 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % 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: -3.30 (0.54), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.42), 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2827.89 seconds wall clock time: 50 minutes 33.77 seconds (3033.77 seconds total)