Starting phenix.real_space_refine on Fri May 9 13:02:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxy_38765/05_2025/8xxy_38765.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxy_38765/05_2025/8xxy_38765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xxy_38765/05_2025/8xxy_38765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxy_38765/05_2025/8xxy_38765.map" model { file = "/net/cci-nas-00/data/ceres_data/8xxy_38765/05_2025/8xxy_38765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxy_38765/05_2025/8xxy_38765.cif" } resolution = 3.68 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= 1.000 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 14 5.16 5 C 1216 2.51 5 N 314 2.21 5 O 294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 1838 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1838 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 7, 'TRANS': 229} Chain breaks: 3 Time building chain proxies: 2.12, per 1000 atoms: 1.15 Number of scatterers: 1838 At special positions: 0 Unit cell: (58.1, 66.4, 73.6625, 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 14 16.00 O 294 8.00 N 314 7.00 C 1216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 223.5 milliseconds 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 446 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'R' and resid 59 through 80 Processing helix chain 'R' and resid 86 through 110 removed outlier: 3.531A pdb=" N THR R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU R 106 " --> pdb=" O LEU R 102 " (cutoff:3.500A) Proline residue: R 107 - end of helix Processing helix chain 'R' and resid 127 through 154 Processing helix chain 'R' and resid 168 through 188 Proline residue: R 185 - end of helix Processing helix chain 'R' and resid 209 through 224 removed outlier: 4.010A pdb=" N PHE R 224 " --> pdb=" O LEU R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 244 Processing helix chain 'R' and resid 249 through 284 Proline residue: R 270 - end of helix removed outlier: 3.531A pdb=" N VAL R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 319 Proline residue: R 315 - end of helix Processing helix chain 'R' and resid 322 through 332 removed outlier: 3.588A pdb=" N ARG R 326 " --> pdb=" O GLY R 322 " (cutoff:3.500A) 158 hydrogen bonds defined for protein. 474 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: 0.50 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: 1.23 - 1.35: 569 1.35 - 1.46: 446 1.46 - 1.58: 839 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 1874 Sorted by residual: bond pdb=" N LEU R 59 " pdb=" CA LEU R 59 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.11e+00 bond pdb=" CA TYR R 271 " pdb=" CB TYR R 271 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.63e-02 3.76e+03 3.89e-01 bond pdb=" CA PRO R 270 " pdb=" C PRO R 270 " ideal model delta sigma weight residual 1.516 1.526 -0.010 1.61e-02 3.86e+03 3.61e-01 bond pdb=" CA TRP R 268 " pdb=" C TRP R 268 " ideal model delta sigma weight residual 1.519 1.526 -0.007 1.22e-02 6.72e+03 3.08e-01 bond pdb=" N GLY R 67 " pdb=" CA GLY R 67 " ideal model delta sigma weight residual 1.454 1.447 0.007 1.24e-02 6.50e+03 3.06e-01 ... (remaining 1869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 2367 0.83 - 1.65: 157 1.65 - 2.48: 19 2.48 - 3.31: 5 3.31 - 4.14: 3 Bond angle restraints: 2551 Sorted by residual: angle pdb=" N VAL R 244 " pdb=" CA VAL R 244 " pdb=" C VAL R 244 " ideal model delta sigma weight residual 112.29 109.13 3.16 9.40e-01 1.13e+00 1.13e+01 angle pdb=" C VAL R 296 " pdb=" CA VAL R 296 " pdb=" CB VAL R 296 " ideal model delta sigma weight residual 112.22 109.83 2.39 1.38e+00 5.25e-01 2.99e+00 angle pdb=" C TRP R 176 " pdb=" N GLY R 177 " pdb=" CA GLY R 177 " ideal model delta sigma weight residual 120.00 121.83 -1.83 1.10e+00 8.26e-01 2.78e+00 angle pdb=" N VAL R 296 " pdb=" CA VAL R 296 " pdb=" C VAL R 296 " ideal model delta sigma weight residual 110.72 112.37 -1.65 1.01e+00 9.80e-01 2.66e+00 angle pdb=" C VAL R 298 " pdb=" CA VAL R 298 " pdb=" CB VAL R 298 " ideal model delta sigma weight residual 112.14 110.05 2.09 1.35e+00 5.49e-01 2.40e+00 ... (remaining 2546 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 13.94: 926 13.94 - 27.87: 114 27.87 - 41.80: 47 41.80 - 55.74: 7 55.74 - 69.67: 2 Dihedral angle restraints: 1096 sinusoidal: 408 harmonic: 688 Sorted by residual: dihedral pdb=" CA ARG R 255 " pdb=" CB ARG R 255 " pdb=" CG ARG R 255 " pdb=" CD ARG R 255 " ideal model delta sinusoidal sigma weight residual -180.00 -123.43 -56.57 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CG ARG R 246 " pdb=" CD ARG R 246 " pdb=" NE ARG R 246 " pdb=" CZ ARG R 246 " ideal model delta sinusoidal sigma weight residual -90.00 -130.31 40.31 2 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" N LYS R 324 " pdb=" CA LYS R 324 " pdb=" CB LYS R 324 " pdb=" CG LYS R 324 " ideal model delta sinusoidal sigma weight residual -180.00 -130.40 -49.60 3 1.50e+01 4.44e-03 8.80e+00 ... (remaining 1093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 215 0.022 - 0.044: 52 0.044 - 0.066: 27 0.066 - 0.087: 22 0.087 - 0.109: 5 Chirality restraints: 321 Sorted by residual: chirality pdb=" CA PRO R 270 " pdb=" N PRO R 270 " pdb=" C PRO R 270 " pdb=" CB PRO R 270 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.98e-01 chirality pdb=" CA ILE R 279 " pdb=" N ILE R 279 " pdb=" C ILE R 279 " pdb=" CB ILE R 279 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.42e-01 chirality pdb=" CA VAL R 244 " pdb=" N VAL R 244 " pdb=" C VAL R 244 " pdb=" CB VAL R 244 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.38e-01 ... (remaining 318 not shown) Planarity restraints: 303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 184 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO R 185 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO R 185 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 185 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 314 " -0.013 5.00e-02 4.00e+02 2.01e-02 6.46e-01 pdb=" N PRO R 315 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO R 315 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO R 315 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 226 " -0.013 5.00e-02 4.00e+02 1.95e-02 6.10e-01 pdb=" N PRO R 227 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO R 227 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO R 227 " -0.011 5.00e-02 4.00e+02 ... (remaining 300 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 545 2.83 - 3.35: 1951 3.35 - 3.87: 2946 3.87 - 4.38: 3240 4.38 - 4.90: 5438 Nonbonded interactions: 14120 Sorted by model distance: nonbonded pdb=" O ALA R 96 " pdb=" OG1 THR R 100 " model vdw 2.314 3.040 nonbonded pdb=" OE1 GLN R 219 " pdb=" OH TYR R 271 " model vdw 2.352 3.040 nonbonded pdb=" O ALA R 265 " pdb=" OG1 THR R 269 " model vdw 2.374 3.040 nonbonded pdb=" O LEU R 242 " pdb=" OG SER R 245 " model vdw 2.392 3.040 nonbonded pdb=" O LEU R 102 " pdb=" OG1 THR R 105 " model vdw 2.407 3.040 ... (remaining 14115 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 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 : 0.002 0.034 1874 Z= 0.118 Angle : 0.474 4.137 2551 Z= 0.298 Chirality : 0.032 0.109 321 Planarity : 0.003 0.027 303 Dihedral : 14.533 69.667 650 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % 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: 2.29 (0.57), residues: 229 helix: 2.16 (0.38), residues: 198 sheet: None (None), residues: 0 loop : -3.01 (0.84), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 268 HIS 0.004 0.001 HIS R 272 PHE 0.003 0.001 PHE R 147 TYR 0.004 0.001 TYR R 233 ARG 0.001 0.000 ARG R 249 Details of bonding type rmsd hydrogen bonds : bond 0.19393 ( 158) hydrogen bonds : angle 5.77294 ( 474) covalent geometry : bond 0.00219 ( 1874) covalent geometry : angle 0.47361 ( 2551) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.196 Fit side-chains REVERT: R 86 SER cc_start: 0.9025 (t) cc_final: 0.8294 (p) REVERT: R 132 ASN cc_start: 0.8277 (m-40) cc_final: 0.7996 (m110) REVERT: R 135 PHE cc_start: 0.8082 (t80) cc_final: 0.7122 (t80) REVERT: R 182 PHE cc_start: 0.7510 (t80) cc_final: 0.6636 (t80) REVERT: R 268 TRP cc_start: 0.7383 (m100) cc_final: 0.6709 (m100) REVERT: R 278 ASP cc_start: 0.8258 (t70) cc_final: 0.7897 (m-30) REVERT: R 311 CYS cc_start: 0.8217 (m) cc_final: 0.7978 (p) REVERT: R 313 LEU cc_start: 0.9019 (mt) cc_final: 0.8815 (mp) REVERT: R 318 TYR cc_start: 0.8664 (m-80) cc_final: 0.7903 (m-80) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1509 time to fit residues: 12.9126 Evaluate side-chains 45 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 134 ASN ** 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 = 0.3889 r_free = 0.3889 target = 0.122200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.099447 restraints weight = 4666.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.101825 restraints weight = 2965.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.103225 restraints weight = 2299.954| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1874 Z= 0.154 Angle : 0.645 8.556 2551 Z= 0.312 Chirality : 0.038 0.137 321 Planarity : 0.004 0.030 303 Dihedral : 3.513 14.318 259 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 5.13 % Allowed : 21.03 % Favored : 73.85 % 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: 2.51 (0.57), residues: 229 helix: 2.17 (0.37), residues: 204 sheet: None (None), residues: 0 loop : -2.87 (1.05), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 268 HIS 0.004 0.002 HIS R 272 PHE 0.020 0.002 PHE R 131 TYR 0.013 0.002 TYR R 136 ARG 0.005 0.001 ARG R 167 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 158) hydrogen bonds : angle 4.37368 ( 474) covalent geometry : bond 0.00318 ( 1874) covalent geometry : angle 0.64465 ( 2551) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.166 Fit side-chains REVERT: R 95 LEU cc_start: 0.9221 (tp) cc_final: 0.8998 (tt) REVERT: R 135 PHE cc_start: 0.8293 (t80) cc_final: 0.7601 (t80) REVERT: R 268 TRP cc_start: 0.7321 (m100) cc_final: 0.6727 (m100) outliers start: 10 outliers final: 5 residues processed: 62 average time/residue: 0.0911 time to fit residues: 6.9720 Evaluate side-chains 43 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 241 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.121361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.099954 restraints weight = 4812.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.102368 restraints weight = 2940.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.103822 restraints weight = 2240.470| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1874 Z= 0.138 Angle : 0.660 9.223 2551 Z= 0.306 Chirality : 0.037 0.133 321 Planarity : 0.004 0.024 303 Dihedral : 3.435 13.575 259 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.15 % Allowed : 23.08 % Favored : 70.77 % 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: 2.46 (0.57), residues: 229 helix: 2.03 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.75 (1.16), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 268 HIS 0.005 0.001 HIS R 272 PHE 0.017 0.002 PHE R 131 TYR 0.008 0.001 TYR R 136 ARG 0.003 0.000 ARG R 167 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 158) hydrogen bonds : angle 4.23186 ( 474) covalent geometry : bond 0.00274 ( 1874) covalent geometry : angle 0.65986 ( 2551) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: R 132 ASN cc_start: 0.8051 (m-40) cc_final: 0.7792 (m-40) REVERT: R 135 PHE cc_start: 0.8221 (t80) cc_final: 0.7487 (t80) REVERT: R 268 TRP cc_start: 0.7307 (m100) cc_final: 0.6617 (m100) outliers start: 12 outliers final: 4 residues processed: 52 average time/residue: 0.0848 time to fit residues: 5.5931 Evaluate side-chains 42 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 241 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 22 optimal weight: 0.0060 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.119502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.099640 restraints weight = 4877.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.101642 restraints weight = 3205.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.102904 restraints weight = 2546.052| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1874 Z= 0.173 Angle : 0.712 7.475 2551 Z= 0.328 Chirality : 0.039 0.138 321 Planarity : 0.004 0.023 303 Dihedral : 3.608 12.983 259 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 7.18 % Allowed : 22.56 % Favored : 70.26 % 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: 2.12 (0.57), residues: 229 helix: 1.81 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -2.86 (1.19), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 268 HIS 0.004 0.002 HIS R 272 PHE 0.013 0.002 PHE R 131 TYR 0.013 0.002 TYR R 136 ARG 0.003 0.000 ARG R 149 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 158) hydrogen bonds : angle 4.31889 ( 474) covalent geometry : bond 0.00379 ( 1874) covalent geometry : angle 0.71192 ( 2551) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: R 102 LEU cc_start: 0.8793 (tp) cc_final: 0.8537 (tt) REVERT: R 132 ASN cc_start: 0.8039 (m-40) cc_final: 0.7802 (m-40) REVERT: R 135 PHE cc_start: 0.8239 (t80) cc_final: 0.7484 (t80) REVERT: R 245 SER cc_start: 0.7701 (p) cc_final: 0.7157 (t) REVERT: R 254 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7296 (mpp) REVERT: R 268 TRP cc_start: 0.7263 (m100) cc_final: 0.6654 (m100) outliers start: 14 outliers final: 8 residues processed: 52 average time/residue: 0.0749 time to fit residues: 5.0017 Evaluate side-chains 52 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 282 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 237 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.119792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.098718 restraints weight = 4905.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.101031 restraints weight = 3089.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.102318 restraints weight = 2376.466| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1874 Z= 0.155 Angle : 0.693 8.114 2551 Z= 0.318 Chirality : 0.038 0.134 321 Planarity : 0.004 0.023 303 Dihedral : 3.568 12.420 259 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 6.67 % Allowed : 23.08 % Favored : 70.26 % 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: 2.36 (0.56), residues: 229 helix: 1.96 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -2.86 (1.16), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP R 268 HIS 0.004 0.001 HIS R 272 PHE 0.033 0.002 PHE R 182 TYR 0.010 0.002 TYR R 318 ARG 0.002 0.000 ARG R 149 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 158) hydrogen bonds : angle 4.23138 ( 474) covalent geometry : bond 0.00336 ( 1874) covalent geometry : angle 0.69256 ( 2551) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 102 LEU cc_start: 0.8740 (tp) cc_final: 0.8526 (tt) REVERT: R 132 ASN cc_start: 0.8081 (m-40) cc_final: 0.7820 (m-40) REVERT: R 135 PHE cc_start: 0.8249 (t80) cc_final: 0.7511 (t80) REVERT: R 245 SER cc_start: 0.7740 (p) cc_final: 0.7199 (t) REVERT: R 254 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7314 (mpp) REVERT: R 268 TRP cc_start: 0.7269 (m100) cc_final: 0.6628 (m100) outliers start: 13 outliers final: 7 residues processed: 52 average time/residue: 0.0710 time to fit residues: 4.7472 Evaluate side-chains 51 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 282 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 11 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 237 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.121679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.101504 restraints weight = 4765.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.103956 restraints weight = 2858.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.105353 restraints weight = 2154.654| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1874 Z= 0.125 Angle : 0.702 9.920 2551 Z= 0.308 Chirality : 0.037 0.131 321 Planarity : 0.003 0.024 303 Dihedral : 3.480 12.693 259 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 5.13 % Allowed : 23.08 % Favored : 71.79 % 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: 2.67 (0.57), residues: 229 helix: 2.16 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -2.66 (1.22), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 268 HIS 0.004 0.001 HIS R 272 PHE 0.022 0.002 PHE R 182 TYR 0.009 0.001 TYR R 136 ARG 0.001 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 158) hydrogen bonds : angle 4.12373 ( 474) covalent geometry : bond 0.00245 ( 1874) covalent geometry : angle 0.70198 ( 2551) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.215 Fit side-chains REVERT: R 132 ASN cc_start: 0.8161 (m-40) cc_final: 0.7778 (m-40) REVERT: R 135 PHE cc_start: 0.8182 (t80) cc_final: 0.7606 (t80) REVERT: R 254 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7270 (mpp) REVERT: R 268 TRP cc_start: 0.7281 (m100) cc_final: 0.6594 (m100) REVERT: R 318 TYR cc_start: 0.8851 (m-80) cc_final: 0.8610 (m-80) outliers start: 10 outliers final: 5 residues processed: 50 average time/residue: 0.0771 time to fit residues: 4.9297 Evaluate side-chains 46 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 282 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 0.0970 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.121212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100820 restraints weight = 4930.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.103197 restraints weight = 3019.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.104675 restraints weight = 2302.039| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.6046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1874 Z= 0.131 Angle : 0.701 9.210 2551 Z= 0.313 Chirality : 0.037 0.132 321 Planarity : 0.003 0.024 303 Dihedral : 3.412 12.399 259 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 5.13 % Allowed : 24.62 % Favored : 70.26 % 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: 2.87 (0.58), residues: 229 helix: 2.28 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.48 (1.29), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 268 HIS 0.004 0.001 HIS R 272 PHE 0.029 0.002 PHE R 131 TYR 0.009 0.001 TYR R 318 ARG 0.001 0.000 ARG R 292 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 158) hydrogen bonds : angle 4.02221 ( 474) covalent geometry : bond 0.00264 ( 1874) covalent geometry : angle 0.70131 ( 2551) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: R 135 PHE cc_start: 0.8238 (t80) cc_final: 0.7614 (t80) REVERT: R 254 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7169 (mpp) REVERT: R 268 TRP cc_start: 0.7368 (m100) cc_final: 0.6749 (m100) REVERT: R 318 TYR cc_start: 0.8798 (m-80) cc_final: 0.8592 (m-80) outliers start: 10 outliers final: 7 residues processed: 48 average time/residue: 0.0767 time to fit residues: 4.7264 Evaluate side-chains 47 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 282 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.0270 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 5 optimal weight: 0.0040 overall best weight: 0.5050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.122432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.102667 restraints weight = 5090.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.104997 restraints weight = 3170.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.106292 restraints weight = 2431.978| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 1874 Z= 0.125 Angle : 0.704 9.748 2551 Z= 0.315 Chirality : 0.036 0.129 321 Planarity : 0.003 0.024 303 Dihedral : 3.386 12.349 259 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 6.15 % Allowed : 25.13 % Favored : 68.72 % 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: 2.94 (0.58), residues: 229 helix: 2.32 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.37 (1.30), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 268 HIS 0.004 0.001 HIS R 272 PHE 0.026 0.002 PHE R 131 TYR 0.031 0.002 TYR R 136 ARG 0.001 0.000 ARG R 292 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 158) hydrogen bonds : angle 3.96961 ( 474) covalent geometry : bond 0.00250 ( 1874) covalent geometry : angle 0.70388 ( 2551) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: R 135 PHE cc_start: 0.8173 (t80) cc_final: 0.7575 (t80) REVERT: R 254 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7149 (mpp) REVERT: R 268 TRP cc_start: 0.7306 (m100) cc_final: 0.6731 (m100) REVERT: R 318 TYR cc_start: 0.8787 (m-80) cc_final: 0.8556 (m-80) outliers start: 12 outliers final: 8 residues processed: 50 average time/residue: 0.0992 time to fit residues: 5.9758 Evaluate side-chains 49 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain R residue 306 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 0.0050 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.121625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.101260 restraints weight = 4955.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.103658 restraints weight = 3111.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.105086 restraints weight = 2374.775| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.6414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1874 Z= 0.129 Angle : 0.707 9.606 2551 Z= 0.318 Chirality : 0.037 0.119 321 Planarity : 0.003 0.023 303 Dihedral : 3.381 12.049 259 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 5.13 % Allowed : 24.62 % Favored : 70.26 % 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: 2.99 (0.58), residues: 229 helix: 2.35 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.35 (1.36), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP R 268 HIS 0.004 0.001 HIS R 272 PHE 0.025 0.002 PHE R 131 TYR 0.018 0.001 TYR R 136 ARG 0.001 0.000 ARG R 149 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 158) hydrogen bonds : angle 4.00917 ( 474) covalent geometry : bond 0.00268 ( 1874) covalent geometry : angle 0.70733 ( 2551) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: R 135 PHE cc_start: 0.8221 (t80) cc_final: 0.7617 (t80) REVERT: R 254 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7134 (mpp) REVERT: R 268 TRP cc_start: 0.7300 (m100) cc_final: 0.6743 (m100) outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 0.0966 time to fit residues: 5.5371 Evaluate side-chains 47 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain R residue 306 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.122185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101973 restraints weight = 4971.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.104530 restraints weight = 2977.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.106135 restraints weight = 2217.022| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.6520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1874 Z= 0.129 Angle : 0.703 9.886 2551 Z= 0.321 Chirality : 0.037 0.116 321 Planarity : 0.004 0.024 303 Dihedral : 3.439 12.026 259 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 5.64 % Allowed : 24.62 % Favored : 69.74 % 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: 2.85 (0.58), residues: 229 helix: 2.26 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.46 (1.31), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP R 330 HIS 0.004 0.001 HIS R 272 PHE 0.025 0.002 PHE R 131 TYR 0.019 0.001 TYR R 136 ARG 0.001 0.000 ARG R 149 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 158) hydrogen bonds : angle 4.04382 ( 474) covalent geometry : bond 0.00267 ( 1874) covalent geometry : angle 0.70277 ( 2551) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: R 135 PHE cc_start: 0.8182 (t80) cc_final: 0.7584 (t80) REVERT: R 254 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7149 (mpp) REVERT: R 268 TRP cc_start: 0.7357 (m100) cc_final: 0.6818 (m100) outliers start: 11 outliers final: 10 residues processed: 47 average time/residue: 0.0926 time to fit residues: 5.3648 Evaluate side-chains 51 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain R residue 306 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 237 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.121239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.101342 restraints weight = 4827.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.103630 restraints weight = 3092.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.104929 restraints weight = 2390.393| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.6544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1874 Z= 0.134 Angle : 0.702 9.632 2551 Z= 0.322 Chirality : 0.037 0.116 321 Planarity : 0.004 0.024 303 Dihedral : 3.417 11.616 259 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 5.64 % Allowed : 25.13 % Favored : 69.23 % 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: 2.79 (0.58), residues: 229 helix: 2.23 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.49 (1.28), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 330 HIS 0.004 0.001 HIS R 272 PHE 0.025 0.003 PHE R 131 TYR 0.022 0.002 TYR R 136 ARG 0.002 0.000 ARG R 149 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 158) hydrogen bonds : angle 4.08663 ( 474) covalent geometry : bond 0.00282 ( 1874) covalent geometry : angle 0.70178 ( 2551) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 994.82 seconds wall clock time: 18 minutes 12.45 seconds (1092.45 seconds total)