Starting phenix.real_space_refine on Sun Mar 10 14:31:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/03_2024/7dwv_30887.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/03_2024/7dwv_30887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/03_2024/7dwv_30887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/03_2024/7dwv_30887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/03_2024/7dwv_30887.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/03_2024/7dwv_30887.pdb" } resolution = 3.07 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= 0.001 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 30 5.16 5 C 1278 2.51 5 N 354 2.21 5 O 402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 200": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "F GLU 200": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2064 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "B" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "C" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "D" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "E" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "F" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Time building chain proxies: 1.43, per 1000 atoms: 0.69 Number of scatterers: 2064 At special positions: 0 Unit cell: (98.358, 84.162, 31.434, 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 30 16.00 O 402 8.00 N 354 7.00 C 1278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 214 " distance=2.02 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 214 " distance=2.02 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 214 " distance=2.02 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 214 " distance=2.02 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 214 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 0.77 Conformation dependent library (CDL) restraints added in 383.0 milliseconds 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 504 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 182 Processing sheet with id=AA2, first strand: chain 'D' and resid 180 through 182 8 hydrogen bonds defined for protein. 24 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: 0.34 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 672 1.34 - 1.45: 200 1.45 - 1.57: 1162 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 2082 Sorted by residual: bond pdb=" CB THR A 193 " pdb=" CG2 THR A 193 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CB THR D 193 " pdb=" CG2 THR D 193 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.72e+00 bond pdb=" CB THR C 193 " pdb=" CG2 THR C 193 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" CB THR F 193 " pdb=" CG2 THR F 193 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" CB THR E 193 " pdb=" CG2 THR E 193 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 ... (remaining 2077 not shown) Histogram of bond angle deviations from ideal: 100.34 - 106.54: 30 106.54 - 112.75: 1254 112.75 - 118.95: 535 118.95 - 125.15: 971 125.15 - 131.36: 12 Bond angle restraints: 2802 Sorted by residual: angle pdb=" N ASN C 181 " pdb=" CA ASN C 181 " pdb=" C ASN C 181 " ideal model delta sigma weight residual 107.93 112.24 -4.31 1.65e+00 3.67e-01 6.82e+00 angle pdb=" N ASN D 181 " pdb=" CA ASN D 181 " pdb=" C ASN D 181 " ideal model delta sigma weight residual 107.93 112.21 -4.28 1.65e+00 3.67e-01 6.74e+00 angle pdb=" N ASN F 181 " pdb=" CA ASN F 181 " pdb=" C ASN F 181 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.71e+00 angle pdb=" N ASN A 181 " pdb=" CA ASN A 181 " pdb=" C ASN A 181 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.70e+00 angle pdb=" N ASN B 181 " pdb=" CA ASN B 181 " pdb=" C ASN B 181 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.69e+00 ... (remaining 2797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.64: 984 11.64 - 23.29: 210 23.29 - 34.93: 90 34.93 - 46.57: 6 46.57 - 58.21: 6 Dihedral angle restraints: 1296 sinusoidal: 540 harmonic: 756 Sorted by residual: dihedral pdb=" CA MET C 206 " pdb=" C MET C 206 " pdb=" N GLU C 207 " pdb=" CA GLU C 207 " ideal model delta harmonic sigma weight residual -180.00 -165.64 -14.36 0 5.00e+00 4.00e-02 8.25e+00 dihedral pdb=" CA MET E 206 " pdb=" C MET E 206 " pdb=" N GLU E 207 " pdb=" CA GLU E 207 " ideal model delta harmonic sigma weight residual -180.00 -165.65 -14.35 0 5.00e+00 4.00e-02 8.24e+00 dihedral pdb=" CA MET A 206 " pdb=" C MET A 206 " pdb=" N GLU A 207 " pdb=" CA GLU A 207 " ideal model delta harmonic sigma weight residual -180.00 -165.65 -14.35 0 5.00e+00 4.00e-02 8.24e+00 ... (remaining 1293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 115 0.030 - 0.060: 127 0.060 - 0.091: 62 0.091 - 0.121: 32 0.121 - 0.151: 24 Chirality restraints: 360 Sorted by residual: chirality pdb=" CB THR C 183 " pdb=" CA THR C 183 " pdb=" OG1 THR C 183 " pdb=" CG2 THR C 183 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CB THR A 183 " pdb=" CA THR A 183 " pdb=" OG1 THR A 183 " pdb=" CG2 THR A 183 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CB THR D 183 " pdb=" CA THR D 183 " pdb=" OG1 THR D 183 " pdb=" CG2 THR D 183 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 357 not shown) Planarity restraints: 342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 187 " -0.009 2.00e-02 2.50e+03 9.09e-03 1.24e+00 pdb=" CG HIS C 187 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS C 187 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS C 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 187 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS C 187 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 187 " -0.010 2.00e-02 2.50e+03 9.07e-03 1.23e+00 pdb=" CG HIS E 187 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS E 187 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS E 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS E 187 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS E 187 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 187 " -0.009 2.00e-02 2.50e+03 8.96e-03 1.20e+00 pdb=" CG HIS B 187 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS B 187 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS B 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS B 187 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 187 " -0.004 2.00e-02 2.50e+03 ... (remaining 339 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 485 2.79 - 3.31: 2050 3.31 - 3.84: 3171 3.84 - 4.37: 3321 4.37 - 4.90: 7268 Nonbonded interactions: 16295 Sorted by model distance: nonbonded pdb=" OD1 ASN B 197 " pdb=" OG1 THR B 199 " model vdw 2.258 2.440 nonbonded pdb=" OD1 ASN A 197 " pdb=" OG1 THR A 199 " model vdw 2.258 2.440 nonbonded pdb=" OD1 ASN C 197 " pdb=" OG1 THR C 199 " model vdw 2.258 2.440 nonbonded pdb=" OD1 ASN F 197 " pdb=" OG1 THR F 199 " model vdw 2.258 2.440 nonbonded pdb=" OD1 ASN E 197 " pdb=" OG1 THR E 199 " model vdw 2.258 2.440 ... (remaining 16290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 12.360 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.290 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 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 : 0.007 0.055 2082 Z= 0.445 Angle : 0.799 4.308 2802 Z= 0.475 Chirality : 0.062 0.151 360 Planarity : 0.003 0.009 342 Dihedral : 14.691 58.214 774 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.83 % Favored : 73.17 % Rotamer: Outliers : 0.00 % Allowed : 28.57 % Favored : 71.43 % 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: -7.45 (0.29), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.67 (0.22), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS D 187 PHE 0.007 0.002 PHE D 175 ARG 0.001 0.000 ARG E 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.258 Fit side-chains REVERT: A 194 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8526 (tppp) REVERT: D 212 GLN cc_start: 0.8385 (mt0) cc_final: 0.8012 (mt0) REVERT: E 217 GLN cc_start: 0.7454 (mt0) cc_final: 0.7237 (mt0) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1320 time to fit residues: 10.0906 Evaluate side-chains 63 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS C 217 GLN F 177 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2082 Z= 0.188 Angle : 0.576 5.167 2802 Z= 0.327 Chirality : 0.051 0.136 360 Planarity : 0.002 0.012 342 Dihedral : 5.257 11.456 258 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.17 % Favored : 76.83 % Rotamer: Outliers : 14.29 % Allowed : 23.41 % Favored : 62.30 % 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: -6.76 (0.34), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.15 (0.26), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 187 PHE 0.004 0.001 PHE F 175 ARG 0.000 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 65 time to evaluate : 0.250 Fit side-chains REVERT: A 194 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8375 (tppp) REVERT: D 181 ASN cc_start: 0.7837 (p0) cc_final: 0.7636 (p0) REVERT: F 177 HIS cc_start: 0.6469 (m-70) cc_final: 0.6258 (m170) outliers start: 36 outliers final: 22 residues processed: 91 average time/residue: 0.1073 time to fit residues: 11.6420 Evaluate side-chains 86 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 64 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 192 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS F 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2082 Z= 0.185 Angle : 0.618 4.596 2802 Z= 0.349 Chirality : 0.051 0.132 360 Planarity : 0.002 0.012 342 Dihedral : 5.098 12.444 258 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.54 % Favored : 78.46 % Rotamer: Outliers : 13.89 % Allowed : 26.98 % Favored : 59.13 % 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: -6.46 (0.36), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.91 (0.27), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 187 PHE 0.004 0.001 PHE C 175 ARG 0.000 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 66 time to evaluate : 0.259 Fit side-chains REVERT: A 194 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8457 (tppp) REVERT: F 177 HIS cc_start: 0.6421 (m-70) cc_final: 0.6151 (m170) outliers start: 35 outliers final: 30 residues processed: 95 average time/residue: 0.1054 time to fit residues: 11.9635 Evaluate side-chains 94 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 64 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS F 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2082 Z= 0.218 Angle : 0.623 4.217 2802 Z= 0.351 Chirality : 0.051 0.132 360 Planarity : 0.003 0.013 342 Dihedral : 5.248 14.784 258 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.98 % Favored : 76.02 % Rotamer: Outliers : 15.48 % Allowed : 26.59 % Favored : 57.94 % 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: -6.41 (0.36), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.88 (0.28), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 187 PHE 0.005 0.001 PHE C 175 ARG 0.000 0.000 ARG F 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 63 time to evaluate : 0.256 Fit side-chains REVERT: A 194 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8408 (tppp) REVERT: D 194 LYS cc_start: 0.8878 (tptm) cc_final: 0.8671 (tppp) REVERT: D 206 MET cc_start: 0.7152 (mtt) cc_final: 0.6612 (mtt) REVERT: F 177 HIS cc_start: 0.6464 (m-70) cc_final: 0.6191 (m170) outliers start: 39 outliers final: 37 residues processed: 95 average time/residue: 0.1044 time to fit residues: 11.9105 Evaluate side-chains 100 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 63 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2082 Z= 0.280 Angle : 0.657 4.534 2802 Z= 0.371 Chirality : 0.053 0.134 360 Planarity : 0.003 0.013 342 Dihedral : 5.729 13.990 258 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.61 % Favored : 74.39 % Rotamer: Outliers : 20.24 % Allowed : 26.19 % Favored : 53.57 % 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: -6.44 (0.36), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.90 (0.27), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 187 PHE 0.007 0.002 PHE F 175 ARG 0.001 0.000 ARG F 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 61 time to evaluate : 0.229 Fit side-chains REVERT: A 194 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8425 (tppp) REVERT: D 194 LYS cc_start: 0.8869 (tptm) cc_final: 0.8662 (tppp) REVERT: D 206 MET cc_start: 0.7240 (mtt) cc_final: 0.6755 (mtt) REVERT: D 212 GLN cc_start: 0.8352 (mt0) cc_final: 0.8052 (mt0) REVERT: E 181 ASN cc_start: 0.7453 (OUTLIER) cc_final: 0.7237 (p0) outliers start: 51 outliers final: 48 residues processed: 102 average time/residue: 0.0979 time to fit residues: 12.1276 Evaluate side-chains 111 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 62 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2082 Z= 0.303 Angle : 0.681 4.670 2802 Z= 0.384 Chirality : 0.053 0.134 360 Planarity : 0.003 0.013 342 Dihedral : 5.929 14.670 258 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.80 % Favored : 75.20 % Rotamer: Outliers : 22.22 % Allowed : 24.60 % Favored : 53.17 % 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: -6.45 (0.36), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.91 (0.27), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS E 187 PHE 0.008 0.002 PHE B 175 ARG 0.000 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 59 time to evaluate : 0.297 Fit side-chains REVERT: A 194 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8418 (tppp) REVERT: D 206 MET cc_start: 0.7274 (mtt) cc_final: 0.6819 (mtt) REVERT: D 212 GLN cc_start: 0.8375 (mt0) cc_final: 0.8067 (mt0) REVERT: F 190 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7665 (m) outliers start: 56 outliers final: 52 residues processed: 103 average time/residue: 0.0988 time to fit residues: 12.3772 Evaluate side-chains 112 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 59 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 209 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 2082 Z= 0.401 Angle : 0.756 5.156 2802 Z= 0.427 Chirality : 0.057 0.137 360 Planarity : 0.003 0.013 342 Dihedral : 6.594 16.336 258 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.42 % Favored : 73.58 % Rotamer: Outliers : 25.40 % Allowed : 24.21 % Favored : 50.40 % 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: -6.61 (0.35), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.03 (0.27), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS E 187 PHE 0.011 0.002 PHE B 175 ARG 0.000 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 58 time to evaluate : 0.247 Fit side-chains REVERT: A 187 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.7477 (p-80) REVERT: A 194 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8490 (tppp) REVERT: B 214 CYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6802 (m) REVERT: D 206 MET cc_start: 0.7355 (mtt) cc_final: 0.6944 (mtt) REVERT: F 177 HIS cc_start: 0.6712 (m-70) cc_final: 0.6391 (m170) REVERT: F 202 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.7881 (p0) outliers start: 64 outliers final: 56 residues processed: 109 average time/residue: 0.0904 time to fit residues: 12.0208 Evaluate side-chains 116 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 57 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 187 HIS Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 209 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2082 Z= 0.198 Angle : 0.642 4.938 2802 Z= 0.362 Chirality : 0.051 0.132 360 Planarity : 0.003 0.015 342 Dihedral : 5.353 14.668 258 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.39 % Favored : 75.61 % Rotamer: Outliers : 19.84 % Allowed : 30.56 % Favored : 49.60 % 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: -6.39 (0.37), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.87 (0.28), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 187 PHE 0.008 0.001 PHE E 175 ARG 0.000 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 64 time to evaluate : 0.251 Fit side-chains REVERT: A 194 LYS cc_start: 0.8665 (mmmt) cc_final: 0.8373 (tppp) REVERT: D 206 MET cc_start: 0.7106 (mtt) cc_final: 0.6686 (mtt) REVERT: F 177 HIS cc_start: 0.6515 (m-70) cc_final: 0.6062 (m170) REVERT: F 202 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7771 (p0) outliers start: 50 outliers final: 46 residues processed: 105 average time/residue: 0.1048 time to fit residues: 13.2142 Evaluate side-chains 111 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 64 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 187 HIS Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 209 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.0470 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.0000 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2082 Z= 0.161 Angle : 0.635 5.013 2802 Z= 0.357 Chirality : 0.050 0.130 360 Planarity : 0.003 0.015 342 Dihedral : 4.935 14.953 258 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.14 % Favored : 78.86 % Rotamer: Outliers : 14.68 % Allowed : 36.11 % Favored : 49.21 % 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: -6.12 (0.39), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.66 (0.30), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 187 PHE 0.009 0.001 PHE E 175 ARG 0.000 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 61 time to evaluate : 0.263 Fit side-chains REVERT: A 194 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8328 (tppp) REVERT: D 194 LYS cc_start: 0.8861 (tptm) cc_final: 0.8644 (tppp) REVERT: D 206 MET cc_start: 0.6984 (mtt) cc_final: 0.6584 (mtt) REVERT: F 177 HIS cc_start: 0.6384 (m-70) cc_final: 0.5985 (m170) REVERT: F 202 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7890 (p0) outliers start: 37 outliers final: 33 residues processed: 96 average time/residue: 0.1029 time to fit residues: 11.8229 Evaluate side-chains 95 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 61 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2082 Z= 0.202 Angle : 0.698 7.738 2802 Z= 0.387 Chirality : 0.051 0.127 360 Planarity : 0.003 0.014 342 Dihedral : 5.231 17.882 258 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.51 % Favored : 80.49 % Rotamer: Outliers : 15.87 % Allowed : 35.32 % Favored : 48.81 % 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: -6.06 (0.40), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.61 (0.31), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 187 PHE 0.009 0.001 PHE E 175 ARG 0.000 0.000 ARG C 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 61 time to evaluate : 0.268 Fit side-chains REVERT: A 194 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8318 (tppp) REVERT: D 206 MET cc_start: 0.7090 (mtt) cc_final: 0.6700 (mtt) REVERT: F 177 HIS cc_start: 0.6397 (m-70) cc_final: 0.5925 (m170) outliers start: 40 outliers final: 39 residues processed: 96 average time/residue: 0.1037 time to fit residues: 11.9275 Evaluate side-chains 100 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 61 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 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 177 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 = 0.4404 r_free = 0.4404 target = 0.133696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.124179 restraints weight = 3482.846| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 2.72 r_work: 0.4183 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2082 Z= 0.272 Angle : 0.740 7.988 2802 Z= 0.410 Chirality : 0.052 0.132 360 Planarity : 0.003 0.013 342 Dihedral : 5.776 19.462 258 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % Rotamer: Outliers : 19.44 % Allowed : 30.95 % Favored : 49.60 % 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: -6.14 (0.40), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.67 (0.30), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS C 187 PHE 0.008 0.001 PHE E 175 ARG 0.000 0.000 ARG B 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1241.37 seconds wall clock time: 22 minutes 59.33 seconds (1379.33 seconds total)