Starting phenix.real_space_refine on Wed Jun 4 10:19:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dwv_30887/06_2025/7dwv_30887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dwv_30887/06_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_30887/06_2025/7dwv_30887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dwv_30887/06_2025/7dwv_30887.map" model { file = "/net/cci-nas-00/data/ceres_data/7dwv_30887/06_2025/7dwv_30887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dwv_30887/06_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-5710/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: 2.34, per 1000 atoms: 1.13 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 233.4 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: 0.35 Time building geometry restraints manager: 0.56 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: 2.530 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.440 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.190 ------------------------------------------------------------------------------- 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 2088 Z= 0.286 Angle : 0.798 4.308 2814 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 Details of bonding type rmsd hydrogen bonds : bond 0.41923 ( 8) hydrogen bonds : angle 13.54441 ( 24) SS BOND : bond 0.00659 ( 6) SS BOND : angle 0.65468 ( 12) covalent geometry : bond 0.00672 ( 2082) covalent geometry : angle 0.79902 ( 2802) *********************** 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 : 0.263 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: 0.1307 time to fit residues: 10.0213 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 : 0.251 ------------------------------------------------------------------------------- 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 2088 Z= 0.141 Angle : 0.637 5.081 2814 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 Details of bonding type rmsd hydrogen bonds : bond 0.06413 ( 8) hydrogen bonds : angle 8.38653 ( 24) SS BOND : bond 0.00283 ( 6) SS BOND : angle 0.63371 ( 12) covalent geometry : bond 0.00309 ( 2082) covalent geometry : angle 0.63678 ( 2802) *********************** 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 : 0.239 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: 0.1067 time to fit residues: 10.8521 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 : 0.260 ------------------------------------------------------------------------------- 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 2088 Z= 0.134 Angle : 0.614 4.037 2814 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 Details of bonding type rmsd hydrogen bonds : bond 0.06007 ( 8) hydrogen bonds : angle 7.79053 ( 24) SS BOND : bond 0.00184 ( 6) SS BOND : angle 0.54134 ( 12) covalent geometry : bond 0.00298 ( 2082) covalent geometry : angle 0.61458 ( 2802) *********************** 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 : 0.241 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: 0.1015 time to fit residues: 11.8407 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 : 0.246 ------------------------------------------------------------------------------- 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 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 2088 Z= 0.130 Angle : 0.651 4.097 2814 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 Details of bonding type rmsd hydrogen bonds : bond 0.05421 ( 8) hydrogen bonds : angle 7.51403 ( 24) SS BOND : bond 0.00186 ( 6) SS BOND : angle 0.45298 ( 12) covalent geometry : bond 0.00279 ( 2082) covalent geometry : angle 0.65142 ( 2802) *********************** 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 : 0.251 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: 0.1058 time to fit residues: 11.7948 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 : 0.250 ------------------------------------------------------------------------------- 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 2088 Z= 0.128 Angle : 0.619 4.430 2814 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 Details of bonding type rmsd hydrogen bonds : bond 0.05432 ( 8) hydrogen bonds : angle 7.39237 ( 24) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.41626 ( 12) covalent geometry : bond 0.00280 ( 2082) covalent geometry : angle 0.61967 ( 2802) *********************** 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 : 0.250 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: 0.0941 time to fit residues: 10.4899 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 : 0.250 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.7720 ------------------------------------------------------------------------------- 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 = 0.4464 r_free = 0.4464 target = 0.139045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.129700 restraints weight = 3373.962| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 2.78 r_work: 0.4240 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2088 Z= 0.133 Angle : 0.620 4.509 2814 Z= 0.352 Chirality : 0.050 0.132 360 Planarity : 0.003 0.014 342 Dihedral : 4.955 11.770 258 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.54 % Favored : 78.46 % Rotamer: Outliers : 17.06 % Allowed : 26.59 % Favored : 56.35 % 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 (0.37), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.73 (0.29), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 187 PHE 0.005 0.001 PHE F 175 ARG 0.000 0.000 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 8) hydrogen bonds : angle 7.72500 ( 24) SS BOND : bond 0.00332 ( 6) SS BOND : angle 0.88327 ( 12) covalent geometry : bond 0.00292 ( 2082) covalent geometry : angle 0.61858 ( 2802) *********************** 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 103 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 60 time to evaluate : 0.247 Fit side-chains REVERT: A 194 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8434 (tppp) REVERT: D 206 MET cc_start: 0.7322 (mtt) cc_final: 0.6876 (mtt) REVERT: F 177 HIS cc_start: 0.6815 (m90) cc_final: 0.6523 (m170) outliers start: 43 outliers final: 41 residues processed: 96 average time/residue: 0.0907 time to fit residues: 10.6574 Evaluate side-chains 100 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 59 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 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 193 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 206 MET 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 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=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: 2.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.132034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.123045 restraints weight = 3541.391| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 2.66 r_work: 0.4160 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2088 Z= 0.233 Angle : 0.737 5.986 2814 Z= 0.417 Chirality : 0.055 0.138 360 Planarity : 0.003 0.013 342 Dihedral : 6.103 14.802 258 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.83 % Favored : 73.17 % Rotamer: Outliers : 21.03 % Allowed : 24.21 % 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: -6.38 (0.36), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.86 (0.28), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS E 187 PHE 0.010 0.002 PHE D 198 ARG 0.001 0.000 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.05889 ( 8) hydrogen bonds : angle 8.42053 ( 24) SS BOND : bond 0.00742 ( 6) SS BOND : angle 0.72431 ( 12) covalent geometry : bond 0.00528 ( 2082) covalent geometry : angle 0.73745 ( 2802) *********************** 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 110 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 57 time to evaluate : 0.274 Fit side-chains REVERT: A 194 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8546 (tppp) REVERT: D 206 MET cc_start: 0.7535 (mtt) cc_final: 0.7202 (mtt) outliers start: 53 outliers final: 47 residues processed: 99 average time/residue: 0.0922 time to fit residues: 11.2468 Evaluate side-chains 103 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 56 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 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 D 212 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.135889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.126652 restraints weight = 3541.603| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 2.74 r_work: 0.4197 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2088 Z= 0.179 Angle : 0.748 6.319 2814 Z= 0.413 Chirality : 0.053 0.137 360 Planarity : 0.003 0.014 342 Dihedral : 5.622 13.791 258 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % Rotamer: Outliers : 18.65 % Allowed : 25.79 % 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: -6.25 (0.38), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.76 (0.29), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 187 PHE 0.007 0.002 PHE B 175 ARG 0.000 0.000 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.05503 ( 8) hydrogen bonds : angle 8.22595 ( 24) SS BOND : bond 0.00630 ( 6) SS BOND : angle 2.15241 ( 12) covalent geometry : bond 0.00396 ( 2082) covalent geometry : angle 0.73604 ( 2802) *********************** 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 106 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 59 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8738 (mmmt) cc_final: 0.8466 (tppp) REVERT: A 213 MET cc_start: 0.7135 (ttt) cc_final: 0.6780 (ttt) REVERT: D 206 MET cc_start: 0.7462 (mtt) cc_final: 0.7135 (mtt) REVERT: D 212 GLN cc_start: 0.8456 (mt0) cc_final: 0.8103 (mt0) REVERT: F 177 HIS cc_start: 0.6746 (m-70) cc_final: 0.6346 (m170) REVERT: F 190 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7781 (m) outliers start: 47 outliers final: 44 residues processed: 100 average time/residue: 0.0918 time to fit residues: 11.3323 Evaluate side-chains 103 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 58 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 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 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 190 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.0020 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.9392 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.136509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.127488 restraints weight = 3509.305| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 2.71 r_work: 0.4208 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2088 Z= 0.160 Angle : 0.730 7.007 2814 Z= 0.403 Chirality : 0.052 0.137 360 Planarity : 0.003 0.014 342 Dihedral : 5.389 15.253 258 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.39 % Favored : 75.61 % Rotamer: Outliers : 19.05 % Allowed : 25.79 % Favored : 55.16 % 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: -6.15 (0.38), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.68 (0.29), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 187 PHE 0.006 0.001 PHE B 175 ARG 0.000 0.000 ARG F 208 Details of bonding type rmsd hydrogen bonds : bond 0.05159 ( 8) hydrogen bonds : angle 8.17142 ( 24) SS BOND : bond 0.00555 ( 6) SS BOND : angle 1.87166 ( 12) covalent geometry : bond 0.00349 ( 2082) covalent geometry : angle 0.72170 ( 2802) *********************** 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 106 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 58 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8451 (tppp) REVERT: A 213 MET cc_start: 0.7072 (ttt) cc_final: 0.6733 (ttt) REVERT: D 206 MET cc_start: 0.7396 (mtt) cc_final: 0.7063 (mtt) REVERT: F 177 HIS cc_start: 0.6783 (m-70) cc_final: 0.6207 (m170) REVERT: F 190 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7773 (m) outliers start: 48 outliers final: 45 residues processed: 101 average time/residue: 0.0870 time to fit residues: 10.8255 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 : 0.231 ------------------------------------------------------------------------------- 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 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 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 190 THR 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 214 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 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 ** 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 = 0.4505 r_free = 0.4505 target = 0.141612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.132458 restraints weight = 3338.888| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 2.80 r_work: 0.4264 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2088 Z= 0.134 Angle : 0.683 5.897 2814 Z= 0.378 Chirality : 0.051 0.133 360 Planarity : 0.003 0.015 342 Dihedral : 4.993 13.565 258 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.36 % Favored : 77.64 % Rotamer: Outliers : 16.67 % Allowed : 28.17 % Favored : 55.16 % 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: -6.05 (0.40), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.60 (0.30), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 187 PHE 0.004 0.001 PHE B 175 ARG 0.001 0.000 ARG D 208 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 8) hydrogen bonds : angle 7.98024 ( 24) SS BOND : bond 0.00445 ( 6) SS BOND : angle 1.59188 ( 12) covalent geometry : bond 0.00287 ( 2082) covalent geometry : angle 0.67657 ( 2802) ********************** 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 102 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 60 time to evaluate : 0.267 Fit side-chains REVERT: A 194 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8368 (tppp) REVERT: A 213 MET cc_start: 0.6982 (ttt) cc_final: 0.6580 (ttt) REVERT: C 213 MET cc_start: 0.7284 (ttt) cc_final: 0.6936 (ttt) REVERT: D 206 MET cc_start: 0.7287 (mtt) cc_final: 0.6964 (mtt) REVERT: E 177 HIS cc_start: 0.7079 (m-70) cc_final: 0.6797 (m-70) REVERT: F 177 HIS cc_start: 0.6705 (m-70) cc_final: 0.6112 (m170) outliers start: 42 outliers final: 41 residues processed: 99 average time/residue: 0.1026 time to fit residues: 12.5220 Evaluate side-chains 100 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 59 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 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 203 VAL 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 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 9 optimal weight: 0.0030 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.139690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.130588 restraints weight = 3462.882| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 2.81 r_work: 0.4238 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2088 Z= 0.142 Angle : 0.695 5.972 2814 Z= 0.385 Chirality : 0.051 0.134 360 Planarity : 0.003 0.015 342 Dihedral : 5.062 12.843 258 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.98 % Favored : 76.02 % Rotamer: Outliers : 17.46 % Allowed : 26.98 % 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: -6.00 (0.40), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.31), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 187 PHE 0.005 0.001 PHE B 175 ARG 0.000 0.000 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.04957 ( 8) hydrogen bonds : angle 7.89068 ( 24) SS BOND : bond 0.00475 ( 6) SS BOND : angle 1.42843 ( 12) covalent geometry : bond 0.00307 ( 2082) covalent geometry : angle 0.69025 ( 2802) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.14 seconds wall clock time: 33 minutes 14.99 seconds (1994.99 seconds total)