Starting phenix.real_space_refine on Wed Mar 5 14:48:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dwv_30887/03_2025/7dwv_30887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dwv_30887/03_2025/7dwv_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/cci-nas-00/data/ceres_data/7dwv_30887/03_2025/7dwv_30887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dwv_30887/03_2025/7dwv_30887.map" model { file = "/net/cci-nas-00/data/ceres_data/7dwv_30887/03_2025/7dwv_30887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dwv_30887/03_2025/7dwv_30887.cif" } 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. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2064 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.57, per 1000 atoms: 1.25 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 C 179 " - pdb=" SG CYS C 214 " distance=2.02 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 214 " distance=2.02 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 214 " distance=2.02 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 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 - 3.00 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: 0.46 Conformation dependent library (CDL) restraints added in 240.8 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: 0.16 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: 0.36 Time building geometry restraints manager: 0.57 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: 0.00 - 0.86: 2269 0.86 - 1.72: 410 1.72 - 2.58: 93 2.58 - 3.45: 12 3.45 - 4.31: 18 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 3.040 nonbonded pdb=" OD1 ASN A 197 " pdb=" OG1 THR A 199 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN C 197 " pdb=" OG1 THR C 199 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN F 197 " pdb=" OG1 THR F 199 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN E 197 " pdb=" OG1 THR E 199 " model vdw 2.258 3.040 ... (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 Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 3.130 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.920 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.226 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: 0.1328 time to fit residues: 10.1340 Evaluate side-chains 63 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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: 0.5980 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 GLN F 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.136433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.127665 restraints weight = 3400.426| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 2.65 r_work: 0.4218 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2082 Z= 0.206 Angle : 0.637 5.081 2802 Z= 0.366 Chirality : 0.052 0.137 360 Planarity : 0.003 0.012 342 Dihedral : 5.357 11.665 258 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.98 % Favored : 76.02 % Rotamer: Outliers : 9.92 % Allowed : 25.00 % Favored : 65.08 % 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: -6.81 (0.33), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.18 (0.25), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 187 PHE 0.005 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 90 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.225 Fit side-chains REVERT: A 194 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8428 (tppp) REVERT: F 177 HIS cc_start: 0.6772 (m-70) cc_final: 0.6506 (m170) outliers start: 25 outliers final: 18 residues processed: 85 average time/residue: 0.1059 time to fit residues: 10.7658 Evaluate side-chains 82 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 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 C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL 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 E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 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 192 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.140573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.131291 restraints weight = 3360.300| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 2.67 r_work: 0.4247 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2082 Z= 0.198 Angle : 0.615 4.037 2802 Z= 0.352 Chirality : 0.052 0.136 360 Planarity : 0.003 0.013 342 Dihedral : 5.083 11.426 258 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.39 % Favored : 75.61 % Rotamer: Outliers : 14.68 % Allowed : 24.60 % Favored : 60.71 % 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: -6.63 (0.35), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.05 (0.26), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 187 PHE 0.005 0.001 PHE A 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 102 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 0.229 Fit side-chains REVERT: A 194 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8535 (tppp) REVERT: F 177 HIS cc_start: 0.6793 (m-70) cc_final: 0.6518 (m170) outliers start: 37 outliers final: 26 residues processed: 97 average time/residue: 0.0982 time to fit residues: 11.4467 Evaluate side-chains 90 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 183 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 176 VAL 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 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 F residue 176 VAL 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 206 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.139416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.129964 restraints weight = 3376.990| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 2.71 r_work: 0.4248 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2371 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= 0.186 Angle : 0.651 4.097 2802 Z= 0.371 Chirality : 0.051 0.133 360 Planarity : 0.003 0.013 342 Dihedral : 4.969 12.045 258 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.14 % Favored : 78.86 % Rotamer: Outliers : 14.29 % Allowed : 24.21 % Favored : 61.51 % 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 0.006 0.002 HIS B 187 PHE 0.004 0.001 PHE F 175 ARG 0.000 0.000 ARG B 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 98 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 62 time to evaluate : 0.229 Fit side-chains REVERT: A 194 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8454 (tppp) REVERT: D 206 MET cc_start: 0.7236 (mtt) cc_final: 0.6793 (mtt) REVERT: F 177 HIS cc_start: 0.6786 (m-70) cc_final: 0.6496 (m170) outliers start: 36 outliers final: 32 residues processed: 93 average time/residue: 0.0999 time to fit residues: 11.1938 Evaluate side-chains 93 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 191 THR Chi-restraints excluded: chain C residue 176 VAL 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 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 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 209 VAL Chi-restraints excluded: chain F residue 176 VAL 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 Chi-restraints excluded: chain F residue 206 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.139627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.130313 restraints weight = 3395.656| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 2.69 r_work: 0.4247 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2532 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= 0.187 Angle : 0.620 4.430 2802 Z= 0.353 Chirality : 0.051 0.133 360 Planarity : 0.003 0.013 342 Dihedral : 4.900 11.506 258 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.36 % Favored : 77.64 % Rotamer: Outliers : 14.29 % Allowed : 26.59 % 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: -6.30 (0.37), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.79 (0.28), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 187 PHE 0.004 0.001 PHE F 175 ARG 0.000 0.000 ARG B 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 97 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 61 time to evaluate : 0.232 Fit side-chains REVERT: A 194 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8452 (tppp) REVERT: D 206 MET cc_start: 0.7276 (mtt) cc_final: 0.6808 (mtt) REVERT: F 177 HIS cc_start: 0.6805 (m-70) cc_final: 0.6504 (m170) outliers start: 36 outliers final: 32 residues processed: 92 average time/residue: 0.0948 time to fit residues: 10.5693 Evaluate side-chains 92 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 B residue 176 VAL 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 C residue 176 VAL 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 203 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 190 THR 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 209 VAL Chi-restraints excluded: chain F residue 176 VAL 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 Chi-restraints excluded: chain F residue 206 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 22 optimal weight: 0.0670 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.136272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.127201 restraints weight = 3405.569| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.64 r_work: 0.4205 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2082 Z= 0.240 Angle : 0.654 4.641 2802 Z= 0.372 Chirality : 0.052 0.134 360 Planarity : 0.003 0.014 342 Dihedral : 5.348 12.572 258 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.98 % Favored : 76.02 % Rotamer: Outliers : 17.86 % Allowed : 26.19 % Favored : 55.95 % 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: -6.29 (0.37), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.79 (0.28), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 187 PHE 0.006 0.001 PHE D 198 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 105 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 60 time to evaluate : 0.229 Fit side-chains REVERT: A 194 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8475 (tppp) REVERT: D 206 MET cc_start: 0.7393 (mtt) cc_final: 0.6972 (mtt) REVERT: D 212 GLN cc_start: 0.8452 (mt0) cc_final: 0.8140 (mt0) REVERT: F 177 HIS cc_start: 0.6828 (m90) cc_final: 0.6626 (m-70) outliers start: 45 outliers final: 43 residues processed: 97 average time/residue: 0.0957 time to fit residues: 11.4486 Evaluate side-chains 103 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 60 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 190 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 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 206 MET 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 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 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 206 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 176 VAL 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 Chi-restraints excluded: chain F residue 206 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.133947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.125022 restraints weight = 3501.149| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 2.65 r_work: 0.4174 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2582 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= 0.282 Angle : 0.699 4.868 2802 Z= 0.396 Chirality : 0.053 0.136 360 Planarity : 0.003 0.014 342 Dihedral : 5.701 13.672 258 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.61 % Favored : 74.39 % Rotamer: Outliers : 19.84 % Allowed : 24.60 % Favored : 55.56 % 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: -6.30 (0.37), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.80 (0.28), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS E 187 PHE 0.007 0.002 PHE D 198 ARG 0.000 0.000 ARG B 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 109 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 59 time to evaluate : 0.263 Fit side-chains REVERT: A 194 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8489 (tppp) REVERT: D 206 MET cc_start: 0.7472 (mtt) cc_final: 0.7129 (mtt) REVERT: D 212 GLN cc_start: 0.8472 (mt0) cc_final: 0.8165 (mt0) outliers start: 50 outliers final: 49 residues processed: 100 average time/residue: 0.0918 time to fit residues: 11.2877 Evaluate side-chains 108 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 59 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 190 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 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 206 MET 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 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 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 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 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 206 MET 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 13 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.139569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.130115 restraints weight = 3498.956| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 2.88 r_work: 0.4242 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2082 Z= 0.177 Angle : 0.660 5.173 2802 Z= 0.369 Chirality : 0.051 0.133 360 Planarity : 0.003 0.015 342 Dihedral : 4.988 13.909 258 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.92 % Favored : 80.08 % Rotamer: Outliers : 15.87 % Allowed : 29.37 % Favored : 54.76 % 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: -6.13 (0.39), 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 0.005 0.002 HIS B 187 PHE 0.009 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 100 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 60 time to evaluate : 0.273 Fit side-chains REVERT: A 194 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8421 (tppp) REVERT: A 213 MET cc_start: 0.6784 (ttt) cc_final: 0.6380 (ttt) REVERT: C 213 MET cc_start: 0.7211 (ttt) cc_final: 0.6945 (ttt) REVERT: D 206 MET cc_start: 0.7277 (mtt) cc_final: 0.6882 (mtt) REVERT: D 212 GLN cc_start: 0.8350 (mt0) cc_final: 0.8062 (mt0) REVERT: F 177 HIS cc_start: 0.6752 (m-70) cc_final: 0.6325 (m170) outliers start: 40 outliers final: 38 residues processed: 96 average time/residue: 0.1007 time to fit residues: 11.7894 Evaluate side-chains 98 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 60 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 190 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 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 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 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 190 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 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 209 VAL Chi-restraints excluded: chain F residue 176 VAL 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 Chi-restraints excluded: chain F residue 206 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.134245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.125338 restraints weight = 3541.473| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 2.64 r_work: 0.4174 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2729 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 : 0.746 7.003 2802 Z= 0.417 Chirality : 0.054 0.136 360 Planarity : 0.003 0.014 342 Dihedral : 5.786 15.137 258 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.02 % Favored : 73.98 % Rotamer: Outliers : 19.44 % Allowed : 26.19 % Favored : 54.37 % 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: -6.22 (0.38), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.74 (0.29), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS E 187 PHE 0.008 0.002 PHE D 198 ARG 0.001 0.000 ARG C 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 108 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 59 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8479 (tppp) REVERT: A 213 MET cc_start: 0.7353 (ttt) cc_final: 0.7039 (ttt) REVERT: D 206 MET cc_start: 0.7644 (mtt) cc_final: 0.7349 (mtt) REVERT: F 177 HIS cc_start: 0.6932 (m-70) cc_final: 0.6400 (m170) outliers start: 49 outliers final: 46 residues processed: 101 average time/residue: 0.0945 time to fit residues: 11.8153 Evaluate side-chains 104 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 58 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 190 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 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 206 MET 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 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 209 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 192 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 214 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4421 r_free = 0.4421 target = 0.136012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.126815 restraints weight = 3423.719| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.79 r_work: 0.4197 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2082 Z= 0.253 Angle : 0.723 6.782 2802 Z= 0.404 Chirality : 0.053 0.136 360 Planarity : 0.003 0.014 342 Dihedral : 5.558 15.171 258 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.54 % Favored : 78.46 % Rotamer: Outliers : 18.65 % Allowed : 26.59 % Favored : 54.76 % 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: -6.20 (0.39), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.72 (0.30), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 187 PHE 0.008 0.002 PHE E 175 ARG 0.000 0.000 ARG B 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 107 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 60 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8420 (tppp) REVERT: A 213 MET cc_start: 0.7126 (ttt) cc_final: 0.6793 (ttt) REVERT: D 206 MET cc_start: 0.7448 (mtt) cc_final: 0.7140 (mtt) REVERT: F 177 HIS cc_start: 0.6763 (m-70) cc_final: 0.6199 (m170) outliers start: 47 outliers final: 45 residues processed: 102 average time/residue: 0.0895 time to fit residues: 11.1567 Evaluate side-chains 104 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 59 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 209 VAL Chi-restraints excluded: chain B residue 176 VAL 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 206 MET 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 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 187 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 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 192 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 214 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.4431 r_free = 0.4431 target = 0.136646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.127712 restraints weight = 3429.831| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.68 r_work: 0.4194 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2807 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= 0.263 Angle : 0.729 6.936 2802 Z= 0.407 Chirality : 0.053 0.137 360 Planarity : 0.003 0.014 342 Dihedral : 5.637 14.797 258 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.80 % Favored : 75.20 % Rotamer: Outliers : 19.44 % Allowed : 26.19 % Favored : 54.37 % 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: -6.21 (0.39), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.72 (0.30), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 187 PHE 0.008 0.002 PHE E 175 ARG 0.000 0.000 ARG C 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1778.56 seconds wall clock time: 31 minutes 20.91 seconds (1880.91 seconds total)