Starting phenix.real_space_refine on Mon Sep 23 11:51:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/09_2024/7dwv_30887.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/09_2024/7dwv_30887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/09_2024/7dwv_30887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/09_2024/7dwv_30887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/09_2024/7dwv_30887.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/09_2024/7dwv_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-5461/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: 1.86, per 1000 atoms: 0.90 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 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: 0.47 Conformation dependent library (CDL) restraints added in 798.8 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: 0.35 Time building geometry restraints manager: 0.55 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: 979 11.64 - 23.29: 200 23.29 - 34.93: 90 34.93 - 46.57: 6 46.57 - 58.21: 6 Dihedral angle restraints: 1281 sinusoidal: 525 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 1278 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: 2.02 - 2.60: 38 2.60 - 3.17: 1904 3.17 - 3.75: 2913 3.75 - 4.32: 3792 4.32 - 4.90: 7663 Nonbonded interactions: 16310 Sorted by model distance: nonbonded pdb=" SG CYS C 179 " pdb=" SG CYS C 214 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS B 179 " pdb=" SG CYS B 214 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS D 179 " pdb=" SG CYS D 214 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS E 179 " pdb=" SG CYS E 214 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS F 179 " pdb=" SG CYS F 214 " model vdw 2.025 3.760 ... (remaining 16305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.730 Find NCS groups from input model: 0.070 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 2082 Z= 0.469 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 : 2.024 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.83 % Favored : 73.17 % Rotamer: Outliers : 0.00 % Allowed : 28.57 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.45 (0.29), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.67 (0.22), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS D 187 PHE 0.007 0.002 PHE D 175 ARG 0.001 0.000 ARG E 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.192 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: 0.1077 time to fit residues: 8.2114 Evaluate side-chains 63 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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: 2.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS C 217 GLN F 177 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.1800 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= 0.214 Angle : 0.636 5.113 2802 Z= 0.364 Chirality : 0.052 0.137 360 Planarity : 0.002 0.012 342 Dihedral : 5.148 11.740 258 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.61 % Favored : 74.39 % Rotamer: Outliers : 9.92 % Allowed : 25.40 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.61 (0.35), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.03 (0.27), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 187 PHE 0.004 0.001 PHE F 175 ARG 0.000 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 65 time to evaluate : 0.242 Fit side-chains REVERT: A 194 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8398 (tppp) REVERT: D 212 GLN cc_start: 0.8475 (mt0) cc_final: 0.8112 (mt0) REVERT: F 177 HIS cc_start: 0.6469 (m-70) cc_final: 0.6207 (m170) outliers start: 25 outliers final: 20 residues processed: 85 average time/residue: 0.1107 time to fit residues: 11.2536 Evaluate side-chains 83 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 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 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 181 ASN 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 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.0050 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS E 217 GLN F 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2082 Z= 0.166 Angle : 0.592 3.945 2802 Z= 0.336 Chirality : 0.050 0.134 360 Planarity : 0.002 0.013 342 Dihedral : 4.485 10.049 258 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.39 % Favored : 75.61 % Rotamer: Outliers : 13.49 % Allowed : 26.19 % Favored : 60.32 % 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 (0.39), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.76 (0.30), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 187 PHE 0.003 0.001 PHE F 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 99 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 65 time to evaluate : 0.242 Fit side-chains REVERT: A 194 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8440 (tppp) REVERT: B 181 ASN cc_start: 0.7167 (OUTLIER) cc_final: 0.6958 (p0) REVERT: D 212 GLN cc_start: 0.8499 (mt0) cc_final: 0.8154 (mt0) REVERT: F 177 HIS cc_start: 0.6432 (m-70) cc_final: 0.6213 (m170) outliers start: 34 outliers final: 18 residues processed: 91 average time/residue: 0.1027 time to fit residues: 11.2241 Evaluate side-chains 83 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 183 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 209 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN C 177 HIS F 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2082 Z= 0.336 Angle : 0.772 6.568 2802 Z= 0.436 Chirality : 0.056 0.138 360 Planarity : 0.003 0.012 342 Dihedral : 5.760 14.486 258 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.42 % Favored : 73.58 % Rotamer: Outliers : 17.06 % Allowed : 25.79 % Favored : 57.14 % 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: -6.42 (0.36), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.89 (0.28), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS B 187 PHE 0.009 0.002 PHE F 175 ARG 0.000 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 59 time to evaluate : 0.258 Fit side-chains REVERT: A 194 LYS cc_start: 0.8757 (mmmt) cc_final: 0.8463 (tppp) REVERT: D 206 MET cc_start: 0.7254 (mtt) cc_final: 0.6859 (mtt) REVERT: D 212 GLN cc_start: 0.8372 (mt0) cc_final: 0.8015 (mt0) REVERT: F 177 HIS cc_start: 0.6576 (m-70) cc_final: 0.6352 (m-70) outliers start: 43 outliers final: 39 residues processed: 94 average time/residue: 0.0951 time to fit residues: 10.8917 Evaluate side-chains 97 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 58 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 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 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.0270 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN C 177 HIS F 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2082 Z= 0.272 Angle : 0.714 6.457 2802 Z= 0.402 Chirality : 0.054 0.137 360 Planarity : 0.003 0.013 342 Dihedral : 5.550 12.755 258 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.80 % Favored : 75.20 % Rotamer: Outliers : 19.44 % Allowed : 24.60 % 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: -6.31 (0.37), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.81 (0.28), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 187 PHE 0.007 0.002 PHE B 175 ARG 0.000 0.000 ARG C 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 108 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 59 time to evaluate : 0.304 Fit side-chains REVERT: A 194 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8436 (tppp) REVERT: D 206 MET cc_start: 0.7219 (mtt) cc_final: 0.6842 (mtt) REVERT: D 212 GLN cc_start: 0.8422 (mt0) cc_final: 0.8051 (mt0) outliers start: 49 outliers final: 46 residues processed: 102 average time/residue: 0.0919 time to fit residues: 11.4902 Evaluate side-chains 105 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 59 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 193 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 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 183 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 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 209 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN C 177 HIS F 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2725 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= 0.189 Angle : 0.659 5.927 2802 Z= 0.371 Chirality : 0.051 0.134 360 Planarity : 0.003 0.013 342 Dihedral : 4.863 14.028 258 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.39 % Favored : 75.61 % Rotamer: Outliers : 15.08 % Allowed : 27.38 % Favored : 57.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.14 (0.39), 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 0.004 0.001 PHE D 198 ARG 0.000 0.000 ARG C 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 99 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 61 time to evaluate : 0.254 Fit side-chains REVERT: A 194 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8384 (tppp) REVERT: A 216 THR cc_start: 0.7769 (m) cc_final: 0.7487 (m) REVERT: D 194 LYS cc_start: 0.8850 (tptm) cc_final: 0.8650 (tppp) REVERT: D 206 MET cc_start: 0.7061 (mtt) cc_final: 0.6694 (mtt) REVERT: D 212 GLN cc_start: 0.8429 (mt0) cc_final: 0.8083 (mt0) REVERT: F 177 HIS cc_start: 0.6504 (m-70) cc_final: 0.6099 (m170) outliers start: 38 outliers final: 36 residues processed: 97 average time/residue: 0.0957 time to fit residues: 11.3138 Evaluate side-chains 98 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 62 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 181 ASN Chi-restraints excluded: chain B residue 183 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 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 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 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 209 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN C 177 HIS F 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2082 Z= 0.344 Angle : 0.768 7.023 2802 Z= 0.431 Chirality : 0.056 0.141 360 Planarity : 0.003 0.012 342 Dihedral : 5.872 14.690 258 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.64 % Favored : 72.36 % Rotamer: Outliers : 20.63 % Allowed : 23.81 % 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: -6.29 (0.38), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.78 (0.29), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS E 187 PHE 0.009 0.002 PHE D 198 ARG 0.000 0.000 ARG F 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 113 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 61 time to evaluate : 0.254 Fit side-chains REVERT: A 194 LYS cc_start: 0.8694 (mmmt) cc_final: 0.8426 (tppp) REVERT: D 206 MET cc_start: 0.7308 (mtt) cc_final: 0.6980 (mtt) REVERT: D 212 GLN cc_start: 0.8373 (mt0) cc_final: 0.8016 (mt0) REVERT: F 177 HIS cc_start: 0.6488 (m-70) cc_final: 0.6102 (m170) outliers start: 52 outliers final: 51 residues processed: 103 average time/residue: 0.0943 time to fit residues: 11.8248 Evaluate side-chains 112 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 61 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 193 THR Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain 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 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 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 190 THR Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 212 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2082 Z= 0.227 Angle : 0.685 6.413 2802 Z= 0.384 Chirality : 0.052 0.137 360 Planarity : 0.003 0.013 342 Dihedral : 5.233 14.909 258 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.39 % Favored : 75.61 % Rotamer: Outliers : 19.44 % Allowed : 26.59 % Favored : 53.97 % 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: -6.16 (0.39), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.69 (0.30), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 187 PHE 0.008 0.001 PHE E 175 ARG 0.000 0.000 ARG F 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 111 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 62 time to evaluate : 0.219 Fit side-chains REVERT: A 194 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8352 (tppp) REVERT: D 206 MET cc_start: 0.7141 (mtt) cc_final: 0.6823 (mtt) REVERT: D 212 GLN cc_start: 0.8445 (mt0) cc_final: 0.8099 (mt0) REVERT: F 177 HIS cc_start: 0.6513 (m-70) cc_final: 0.6070 (m170) outliers start: 49 outliers final: 45 residues processed: 107 average time/residue: 0.0912 time to fit residues: 11.9135 Evaluate side-chains 107 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 62 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 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 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 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 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 209 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN F 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3009 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= 0.194 Angle : 0.660 6.169 2802 Z= 0.369 Chirality : 0.051 0.135 360 Planarity : 0.003 0.013 342 Dihedral : 4.841 13.584 258 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.20 % Favored : 74.80 % Rotamer: Outliers : 17.06 % Allowed : 28.57 % 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: -6.02 (0.40), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.58 (0.31), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 187 PHE 0.009 0.001 PHE E 175 ARG 0.000 0.000 ARG B 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 106 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 63 time to evaluate : 0.249 Fit side-chains REVERT: A 194 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8359 (tppp) REVERT: D 194 LYS cc_start: 0.8872 (tptm) cc_final: 0.8659 (tppp) REVERT: D 206 MET cc_start: 0.7046 (mtt) cc_final: 0.6734 (mtt) REVERT: D 212 GLN cc_start: 0.8457 (mt0) cc_final: 0.8124 (mt0) REVERT: F 177 HIS cc_start: 0.6521 (m-70) cc_final: 0.6046 (m170) outliers start: 43 outliers final: 40 residues processed: 103 average time/residue: 0.1015 time to fit residues: 12.7784 Evaluate side-chains 103 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 63 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 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 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 181 ASN 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 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 212 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3060 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= 0.190 Angle : 0.679 6.308 2802 Z= 0.378 Chirality : 0.051 0.135 360 Planarity : 0.003 0.014 342 Dihedral : 4.813 13.259 258 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.76 % Favored : 77.24 % Rotamer: Outliers : 16.67 % Allowed : 28.57 % 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: -5.95 (0.41), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.53 (0.31), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 187 PHE 0.009 0.001 PHE E 175 ARG 0.001 0.000 ARG C 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 62 time to evaluate : 0.250 Fit side-chains REVERT: A 194 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8348 (tppp) REVERT: C 213 MET cc_start: 0.6919 (ttt) cc_final: 0.6678 (ttt) REVERT: D 194 LYS cc_start: 0.8862 (tptm) cc_final: 0.8652 (tppp) REVERT: D 206 MET cc_start: 0.7014 (mtt) cc_final: 0.6687 (mtt) REVERT: D 212 GLN cc_start: 0.8458 (mt0) cc_final: 0.8105 (mt0) REVERT: E 177 HIS cc_start: 0.6904 (m-70) cc_final: 0.6684 (m-70) REVERT: F 177 HIS cc_start: 0.6470 (m-70) cc_final: 0.6043 (m170) outliers start: 42 outliers final: 41 residues processed: 101 average time/residue: 0.0987 time to fit residues: 12.1564 Evaluate side-chains 103 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 62 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 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 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 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 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 209 VAL Chi-restraints excluded: chain F residue 212 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 23 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.0030 chunk 10 optimal weight: 1.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.147332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.137165 restraints weight = 3594.851| |-----------------------------------------------------------------------------| r_work (start): 0.4598 rms_B_bonded: 3.31 r_work: 0.4479 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2082 Z= 0.153 Angle : 0.639 5.709 2802 Z= 0.358 Chirality : 0.049 0.131 360 Planarity : 0.003 0.014 342 Dihedral : 4.220 11.382 258 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.48 % Favored : 82.52 % Rotamer: Outliers : 14.68 % Allowed : 30.16 % 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: -5.79 (0.42), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.41 (0.32), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 187 PHE 0.009 0.001 PHE E 175 ARG 0.001 0.000 ARG C 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1222.88 seconds wall clock time: 27 minutes 30.99 seconds (1650.99 seconds total)