Starting phenix.real_space_refine on Mon Jan 13 16:32:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5h_38069/01_2025/8x5h_38069.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5h_38069/01_2025/8x5h_38069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x5h_38069/01_2025/8x5h_38069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5h_38069/01_2025/8x5h_38069.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5h_38069/01_2025/8x5h_38069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5h_38069/01_2025/8x5h_38069.cif" } resolution = 3.47 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2082 2.51 5 N 519 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Restraints were copied for chains: C, B Time building chain proxies: 3.32, per 1000 atoms: 1.02 Number of scatterers: 3258 At special positions: 0 Unit cell: (100.43, 97.94, 34.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 636 8.00 N 519 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.02 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: 0.75 Conformation dependent library (CDL) restraints added in 372.9 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.664A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 137 removed outlier: 6.589A pdb=" N SER B 134 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL C 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASP B 136 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 144 removed outlier: 6.536A pdb=" N ILE B 142 " --> pdb=" O TYR C 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 156 removed outlier: 6.564A pdb=" N ASN B 155 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 164 removed outlier: 6.985A pdb=" N GLU B 163 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 167 through 169 removed outlier: 6.555A pdb=" N GLN B 168 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 185 through 187 removed outlier: 6.495A pdb=" N THR B 185 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 190 through 192 removed outlier: 6.466A pdb=" N ASP B 191 " --> pdb=" O MET C 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 201 through 213 removed outlier: 8.949A pdb=" N VAL B 202 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 9.868A pdb=" N GLU A 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 204 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N MET A 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU B 206 " --> pdb=" O MET A 207 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR A 209 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER B 208 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N TYR A 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET B 210 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE A 213 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP B 212 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL C 202 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 203 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA C 204 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 222 through 230 removed outlier: 7.012A pdb=" N VAL B 230 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN B 223 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU C 226 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N MET C 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N MET B 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL C 230 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLN B 229 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 242 through 244 removed outlier: 6.310A pdb=" N GLN B 242 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 251 through 253 removed outlier: 6.434A pdb=" N ASP B 252 " --> pdb=" O CYS A 253 " (cutoff:3.500A) 36 hydrogen bonds defined for protein. 108 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: 0.70 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1017 1.33 - 1.45: 426 1.45 - 1.57: 1833 1.57 - 1.68: 0 1.68 - 1.80: 36 Bond restraints: 3312 Sorted by residual: bond pdb=" CG LEU A 144 " pdb=" CD2 LEU A 144 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.27e+00 bond pdb=" CG LEU B 144 " pdb=" CD2 LEU B 144 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.26e+00 bond pdb=" CG LEU C 144 " pdb=" CD2 LEU C 144 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.18e+00 bond pdb=" CA ILE A 146 " pdb=" CB ILE A 146 " ideal model delta sigma weight residual 1.549 1.525 0.024 1.88e-02 2.83e+03 1.56e+00 bond pdb=" CA ILE C 146 " pdb=" CB ILE C 146 " ideal model delta sigma weight residual 1.549 1.525 0.023 1.88e-02 2.83e+03 1.56e+00 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 4022 1.20 - 2.41: 412 2.41 - 3.61: 45 3.61 - 4.82: 19 4.82 - 6.02: 5 Bond angle restraints: 4503 Sorted by residual: angle pdb=" C LEU A 144 " pdb=" N ASN A 145 " pdb=" CA ASN A 145 " ideal model delta sigma weight residual 122.82 127.69 -4.87 1.42e+00 4.96e-01 1.17e+01 angle pdb=" C LEU C 144 " pdb=" N ASN C 145 " pdb=" CA ASN C 145 " ideal model delta sigma weight residual 122.82 127.65 -4.83 1.42e+00 4.96e-01 1.16e+01 angle pdb=" C LEU B 144 " pdb=" N ASN B 145 " pdb=" CA ASN B 145 " ideal model delta sigma weight residual 122.82 127.64 -4.82 1.42e+00 4.96e-01 1.15e+01 angle pdb=" C ARG A 140 " pdb=" CA ARG A 140 " pdb=" CB ARG A 140 " ideal model delta sigma weight residual 111.86 107.99 3.87 1.34e+00 5.57e-01 8.33e+00 angle pdb=" C ARG C 140 " pdb=" CA ARG C 140 " pdb=" CB ARG C 140 " ideal model delta sigma weight residual 111.86 108.01 3.85 1.34e+00 5.57e-01 8.25e+00 ... (remaining 4498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 1763 16.50 - 33.01: 199 33.01 - 49.51: 15 49.51 - 66.02: 9 66.02 - 82.52: 3 Dihedral angle restraints: 1989 sinusoidal: 771 harmonic: 1218 Sorted by residual: dihedral pdb=" CA GLN C 138 " pdb=" C GLN C 138 " pdb=" N LYS C 139 " pdb=" CA LYS C 139 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA GLN B 138 " pdb=" C GLN B 138 " pdb=" N LYS B 139 " pdb=" CA LYS B 139 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA GLN A 138 " pdb=" C GLN A 138 " pdb=" N LYS A 139 " pdb=" CA LYS A 139 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 1986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 376 0.053 - 0.107: 123 0.107 - 0.160: 38 0.160 - 0.213: 3 0.213 - 0.266: 3 Chirality restraints: 543 Sorted by residual: chirality pdb=" CB ILE A 186 " pdb=" CA ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CG2 ILE A 186 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB ILE C 186 " pdb=" CA ILE C 186 " pdb=" CG1 ILE C 186 " pdb=" CG2 ILE C 186 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE B 186 " pdb=" CA ILE B 186 " pdb=" CG1 ILE B 186 " pdb=" CG2 ILE B 186 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 540 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 143 " 0.012 2.00e-02 2.50e+03 8.59e-03 1.48e+00 pdb=" CG TYR A 143 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 143 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 143 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 143 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 143 " 0.011 2.00e-02 2.50e+03 8.55e-03 1.46e+00 pdb=" CG TYR B 143 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 143 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 143 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 143 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 143 " 0.011 2.00e-02 2.50e+03 8.48e-03 1.44e+00 pdb=" CG TYR C 143 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 143 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 143 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 143 " 0.002 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 25 2.60 - 3.17: 2915 3.17 - 3.75: 4438 3.75 - 4.32: 6545 4.32 - 4.90: 12269 Nonbonded interactions: 26192 Sorted by model distance: nonbonded pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS A 214 " pdb=" SG CYS A 253 " model vdw 2.023 3.760 nonbonded pdb=" OH TYR A 236 " pdb=" O HIS A 239 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR C 236 " pdb=" O HIS C 239 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR B 236 " pdb=" O HIS B 239 " model vdw 2.265 3.040 ... (remaining 26187 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.900 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.500 Find NCS groups from input model: 0.060 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 : 0.009 0.050 3312 Z= 0.584 Angle : 0.803 6.025 4503 Z= 0.472 Chirality : 0.059 0.266 543 Planarity : 0.003 0.009 558 Dihedral : 14.226 82.523 1206 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % 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: -5.99 (0.28), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.21), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 222 PHE 0.015 0.003 PHE C 213 TYR 0.021 0.003 TYR B 250 ARG 0.005 0.001 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.356 Fit side-chains REVERT: B 161 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8092 (mm-30) REVERT: B 192 MET cc_start: 0.8360 (mtt) cc_final: 0.8094 (mtp) REVERT: B 210 MET cc_start: 0.8090 (mtt) cc_final: 0.7831 (mtt) REVERT: B 220 LYS cc_start: 0.8308 (mttt) cc_final: 0.7985 (mtpt) REVERT: A 161 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7865 (mm-30) REVERT: A 192 MET cc_start: 0.8610 (mtt) cc_final: 0.8296 (mtp) REVERT: A 207 MET cc_start: 0.6981 (ttm) cc_final: 0.6779 (ttm) REVERT: A 210 MET cc_start: 0.8415 (mtt) cc_final: 0.8180 (mtt) REVERT: C 161 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7157 (mm-30) REVERT: C 220 LYS cc_start: 0.8335 (mttt) cc_final: 0.7973 (mtpt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.2045 time to fit residues: 7.7560 Evaluate side-chains 30 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 35 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 223 ASN C 155 ASN C 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.138292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.121067 restraints weight = 3852.077| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.50 r_work: 0.3907 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3312 Z= 0.145 Angle : 0.552 4.287 4503 Z= 0.314 Chirality : 0.052 0.151 543 Planarity : 0.002 0.020 558 Dihedral : 6.116 20.558 447 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 1.32 % Allowed : 12.96 % Favored : 85.71 % 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: -5.57 (0.28), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.24 (0.22), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 239 PHE 0.004 0.001 PHE A 237 TYR 0.013 0.001 TYR B 250 ARG 0.001 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.358 Fit side-chains REVERT: B 210 MET cc_start: 0.8334 (mtt) cc_final: 0.8086 (mtt) REVERT: B 220 LYS cc_start: 0.8260 (mttt) cc_final: 0.7886 (mtpt) REVERT: A 180 ARG cc_start: 0.7044 (ptp-170) cc_final: 0.6736 (ptp90) REVERT: A 192 MET cc_start: 0.8722 (mtt) cc_final: 0.8449 (mtp) REVERT: A 207 MET cc_start: 0.7178 (ttm) cc_final: 0.6930 (ttm) REVERT: A 210 MET cc_start: 0.8469 (mtt) cc_final: 0.8197 (mtt) REVERT: C 220 LYS cc_start: 0.8331 (mttt) cc_final: 0.7969 (mtpt) outliers start: 5 outliers final: 2 residues processed: 41 average time/residue: 0.1908 time to fit residues: 9.4489 Evaluate side-chains 34 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain A residue 175 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 0.0050 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.139822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.122336 restraints weight = 3653.135| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.58 r_work: 0.3810 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3312 Z= 0.243 Angle : 0.578 3.772 4503 Z= 0.328 Chirality : 0.052 0.158 543 Planarity : 0.002 0.021 558 Dihedral : 6.085 19.549 447 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 1.85 % Allowed : 15.08 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.43 (0.29), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.22), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 239 PHE 0.008 0.002 PHE A 237 TYR 0.018 0.002 TYR A 143 ARG 0.001 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.348 Fit side-chains REVERT: B 210 MET cc_start: 0.8420 (mtt) cc_final: 0.8001 (mtt) REVERT: B 220 LYS cc_start: 0.8297 (mttt) cc_final: 0.7919 (mtpt) REVERT: A 180 ARG cc_start: 0.7195 (ptp-170) cc_final: 0.6806 (ptp90) REVERT: A 192 MET cc_start: 0.8697 (mtt) cc_final: 0.8451 (mtp) REVERT: A 207 MET cc_start: 0.7298 (ttm) cc_final: 0.7065 (ttm) REVERT: A 210 MET cc_start: 0.8503 (mtt) cc_final: 0.8273 (mtm) REVERT: C 220 LYS cc_start: 0.8397 (mttt) cc_final: 0.8003 (mtpt) outliers start: 7 outliers final: 5 residues processed: 38 average time/residue: 0.1870 time to fit residues: 8.7107 Evaluate side-chains 37 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 244 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.137145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.119243 restraints weight = 3864.691| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.56 r_work: 0.3923 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3312 Z= 0.157 Angle : 0.513 3.706 4503 Z= 0.292 Chirality : 0.051 0.156 543 Planarity : 0.002 0.021 558 Dihedral : 5.671 17.600 447 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.91 % Allowed : 15.34 % Favored : 81.75 % 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: -5.25 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 239 PHE 0.007 0.001 PHE A 237 TYR 0.011 0.001 TYR A 143 ARG 0.000 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.374 Fit side-chains REVERT: B 146 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8495 (pt) REVERT: B 210 MET cc_start: 0.8440 (mtt) cc_final: 0.8059 (mtt) REVERT: B 220 LYS cc_start: 0.8314 (mttt) cc_final: 0.7947 (mtpt) REVERT: A 180 ARG cc_start: 0.7130 (ptp-170) cc_final: 0.6739 (ptp90) REVERT: A 192 MET cc_start: 0.8612 (mtt) cc_final: 0.8390 (mtp) REVERT: A 207 MET cc_start: 0.7318 (ttm) cc_final: 0.7086 (ttm) REVERT: A 210 MET cc_start: 0.8423 (mtt) cc_final: 0.8153 (mtt) REVERT: C 146 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8461 (pt) REVERT: C 220 LYS cc_start: 0.8374 (mttt) cc_final: 0.7979 (mtpt) outliers start: 11 outliers final: 6 residues processed: 40 average time/residue: 0.1920 time to fit residues: 9.3378 Evaluate side-chains 38 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.132043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.114761 restraints weight = 3926.285| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.49 r_work: 0.3836 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3312 Z= 0.265 Angle : 0.570 4.645 4503 Z= 0.327 Chirality : 0.052 0.171 543 Planarity : 0.002 0.019 558 Dihedral : 5.903 18.965 447 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 3.44 % Allowed : 15.61 % Favored : 80.95 % 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: -5.21 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 239 PHE 0.010 0.002 PHE A 237 TYR 0.021 0.002 TYR B 143 ARG 0.001 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.335 Fit side-chains REVERT: B 146 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8499 (pt) REVERT: B 210 MET cc_start: 0.8444 (mtt) cc_final: 0.8059 (mtt) REVERT: A 207 MET cc_start: 0.7483 (ttm) cc_final: 0.7279 (ttm) REVERT: A 210 MET cc_start: 0.8547 (mtt) cc_final: 0.8325 (mtt) REVERT: C 146 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8463 (pt) REVERT: C 220 LYS cc_start: 0.8374 (mttt) cc_final: 0.7958 (mtpt) outliers start: 13 outliers final: 9 residues processed: 43 average time/residue: 0.1678 time to fit residues: 8.8868 Evaluate side-chains 42 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.135224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.117310 restraints weight = 4002.272| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.64 r_work: 0.3873 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3312 Z= 0.221 Angle : 0.560 6.920 4503 Z= 0.315 Chirality : 0.052 0.167 543 Planarity : 0.002 0.018 558 Dihedral : 5.828 18.444 447 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 4.50 % Allowed : 15.61 % Favored : 79.89 % 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: -5.17 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 239 PHE 0.009 0.002 PHE A 237 TYR 0.019 0.002 TYR B 143 ARG 0.000 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 28 time to evaluate : 0.472 Fit side-chains REVERT: B 146 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8424 (pt) REVERT: B 210 MET cc_start: 0.8418 (mtt) cc_final: 0.8051 (mtt) REVERT: A 141 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8740 (p) REVERT: A 146 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8602 (pt) REVERT: A 207 MET cc_start: 0.7485 (ttm) cc_final: 0.7267 (ttm) REVERT: A 210 MET cc_start: 0.8550 (mtt) cc_final: 0.8247 (mtt) REVERT: C 146 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8409 (pt) REVERT: C 220 LYS cc_start: 0.8375 (mttt) cc_final: 0.7966 (mtpt) outliers start: 17 outliers final: 12 residues processed: 44 average time/residue: 0.1797 time to fit residues: 9.7670 Evaluate side-chains 43 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 27 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 186 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.139830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.122177 restraints weight = 3913.501| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.49 r_work: 0.3944 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3312 Z= 0.277 Angle : 0.597 7.230 4503 Z= 0.337 Chirality : 0.053 0.171 543 Planarity : 0.002 0.017 558 Dihedral : 6.008 20.964 447 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 5.29 % Allowed : 15.08 % Favored : 79.63 % 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: -5.17 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 239 PHE 0.009 0.002 PHE A 237 TYR 0.022 0.002 TYR B 143 ARG 0.001 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 32 time to evaluate : 0.391 Fit side-chains REVERT: B 146 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8457 (pt) REVERT: B 210 MET cc_start: 0.8421 (mtt) cc_final: 0.8018 (mtt) REVERT: A 146 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8664 (pt) REVERT: A 207 MET cc_start: 0.7507 (ttm) cc_final: 0.7297 (ttm) REVERT: A 210 MET cc_start: 0.8546 (mtt) cc_final: 0.8273 (mtt) REVERT: C 146 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8429 (pt) REVERT: C 220 LYS cc_start: 0.8359 (mttt) cc_final: 0.7942 (mtpt) outliers start: 20 outliers final: 13 residues processed: 50 average time/residue: 0.1649 time to fit residues: 10.2730 Evaluate side-chains 47 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 244 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.139955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.122494 restraints weight = 3804.070| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.57 r_work: 0.3967 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3312 Z= 0.248 Angle : 0.587 7.825 4503 Z= 0.329 Chirality : 0.053 0.170 543 Planarity : 0.002 0.017 558 Dihedral : 5.949 20.244 447 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 4.50 % Allowed : 16.40 % Favored : 79.10 % 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: -5.15 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 239 PHE 0.009 0.002 PHE A 237 TYR 0.021 0.002 TYR A 143 ARG 0.001 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.337 Fit side-chains REVERT: B 146 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8417 (pt) REVERT: B 180 ARG cc_start: 0.7209 (ptp-170) cc_final: 0.6796 (ptm160) REVERT: B 210 MET cc_start: 0.8391 (mtt) cc_final: 0.7990 (mtt) REVERT: A 146 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8619 (pt) REVERT: A 207 MET cc_start: 0.7552 (ttm) cc_final: 0.7346 (ttm) REVERT: A 210 MET cc_start: 0.8555 (mtt) cc_final: 0.8298 (mtt) REVERT: C 146 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8395 (pt) REVERT: C 220 LYS cc_start: 0.8355 (mttt) cc_final: 0.7943 (mtpt) outliers start: 17 outliers final: 13 residues processed: 45 average time/residue: 0.1897 time to fit residues: 10.3084 Evaluate side-chains 45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 29 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 244 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.142089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.124324 restraints weight = 3805.040| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.62 r_work: 0.4000 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3312 Z= 0.217 Angle : 0.577 8.037 4503 Z= 0.321 Chirality : 0.052 0.165 543 Planarity : 0.002 0.018 558 Dihedral : 5.832 20.364 447 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 4.23 % Allowed : 16.93 % Favored : 78.84 % 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: -5.07 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 239 PHE 0.009 0.002 PHE A 237 TYR 0.019 0.002 TYR A 143 ARG 0.001 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 30 time to evaluate : 0.372 Fit side-chains REVERT: B 146 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8403 (pt) REVERT: B 180 ARG cc_start: 0.7255 (ptp-170) cc_final: 0.6826 (ptm160) REVERT: B 210 MET cc_start: 0.8394 (mtt) cc_final: 0.8007 (mtt) REVERT: A 146 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8580 (pt) REVERT: A 207 MET cc_start: 0.7523 (ttm) cc_final: 0.7306 (ttm) REVERT: A 210 MET cc_start: 0.8577 (mtt) cc_final: 0.8324 (mtt) REVERT: C 146 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8389 (pt) REVERT: C 220 LYS cc_start: 0.8338 (mttt) cc_final: 0.7906 (mtpt) outliers start: 16 outliers final: 12 residues processed: 44 average time/residue: 0.1911 time to fit residues: 10.1927 Evaluate side-chains 44 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 186 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.141708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.124512 restraints weight = 3748.682| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.52 r_work: 0.3859 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3312 Z= 0.265 Angle : 0.617 8.474 4503 Z= 0.343 Chirality : 0.053 0.171 543 Planarity : 0.002 0.019 558 Dihedral : 5.962 21.439 447 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 4.76 % Allowed : 16.93 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.07 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 239 PHE 0.010 0.002 PHE A 237 TYR 0.022 0.002 TYR A 143 ARG 0.001 0.000 ARG A 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 27 time to evaluate : 0.337 Fit side-chains REVERT: B 146 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8449 (pt) REVERT: B 180 ARG cc_start: 0.7320 (ptp-170) cc_final: 0.6861 (ptm160) REVERT: B 210 MET cc_start: 0.8390 (mtt) cc_final: 0.7994 (mtt) REVERT: A 146 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8617 (pt) REVERT: A 210 MET cc_start: 0.8545 (mtt) cc_final: 0.8316 (mtt) REVERT: C 146 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8427 (pt) REVERT: C 220 LYS cc_start: 0.8348 (mttt) cc_final: 0.7922 (mtpt) outliers start: 18 outliers final: 13 residues processed: 43 average time/residue: 0.1845 time to fit residues: 9.7824 Evaluate side-chains 43 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 27 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 186 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.147760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.129856 restraints weight = 3756.709| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.62 r_work: 0.4071 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3312 Z= 0.156 Angle : 0.565 7.981 4503 Z= 0.312 Chirality : 0.051 0.160 543 Planarity : 0.002 0.021 558 Dihedral : 5.591 20.798 447 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.23 % Allowed : 16.67 % Favored : 79.10 % 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: -5.03 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 239 PHE 0.007 0.001 PHE A 237 TYR 0.014 0.001 TYR A 143 ARG 0.001 0.000 ARG A 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2106.48 seconds wall clock time: 38 minutes 33.61 seconds (2313.61 seconds total)