Starting phenix.real_space_refine on Sat Apr 26 15:28:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9as7_43807/04_2025/9as7_43807.cif Found real_map, /net/cci-nas-00/data/ceres_data/9as7_43807/04_2025/9as7_43807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9as7_43807/04_2025/9as7_43807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9as7_43807/04_2025/9as7_43807.map" model { file = "/net/cci-nas-00/data/ceres_data/9as7_43807/04_2025/9as7_43807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9as7_43807/04_2025/9as7_43807.cif" } resolution = 2.72 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= -0.003 sd= 0.140 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 1341 2.51 5 N 303 2.21 5 O 329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 1987 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1972 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'91Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.62, per 1000 atoms: 1.32 Number of scatterers: 1987 At special positions: 0 Unit cell: (60.72, 69.52, 66, 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 329 8.00 N 303 7.00 C 1341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " 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: 0.63 Conformation dependent library (CDL) restraints added in 236.5 milliseconds 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 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: 14 helices and 1 sheets defined 90.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 81 through 102 removed outlier: 3.548A pdb=" N GLU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.830A pdb=" N GLN A 106 " --> pdb=" O LYS A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 107 through 127 removed outlier: 3.634A pdb=" N PHE A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 146 through 179 removed outlier: 4.219A pdb=" N VAL A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 188 through 208 Processing helix chain 'A' and resid 208 through 215 removed outlier: 4.157A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 215 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 231 through 241 removed outlier: 3.698A pdb=" N SER A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 261 Processing helix chain 'A' and resid 314 through 349 removed outlier: 3.524A pdb=" N GLU A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.613A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 382 removed outlier: 3.611A pdb=" N VAL A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 384 through 392 Processing sheet with id=AA1, first strand: chain 'A' and resid 222 through 223 164 hydrogen bonds defined for protein. 486 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: 0.54 Time building geometry restraints manager: 0.65 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: 574 1.35 - 1.46: 531 1.46 - 1.58: 908 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 2035 Sorted by residual: bond pdb=" N ASN A 384 " pdb=" CA ASN A 384 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.33e-02 5.65e+03 6.45e+00 bond pdb=" C9 91Q A 501 " pdb=" O1 91Q A 501 " ideal model delta sigma weight residual 1.349 1.399 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" N ASN A 110 " pdb=" CA ASN A 110 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.28e-02 6.10e+03 6.07e+00 bond pdb=" N ASP A 172 " pdb=" CA ASP A 172 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.92e+00 bond pdb=" C6 91Q A 501 " pdb=" N2 91Q A 501 " ideal model delta sigma weight residual 1.368 1.323 0.045 2.00e-02 2.50e+03 5.01e+00 ... (remaining 2030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 2569 1.24 - 2.47: 160 2.47 - 3.71: 38 3.71 - 4.94: 13 4.94 - 6.18: 7 Bond angle restraints: 2787 Sorted by residual: angle pdb=" C ILE A 237 " pdb=" CA ILE A 237 " pdb=" CB ILE A 237 " ideal model delta sigma weight residual 112.22 108.09 4.13 1.38e+00 5.25e-01 8.95e+00 angle pdb=" CA THR A 381 " pdb=" CB THR A 381 " pdb=" OG1 THR A 381 " ideal model delta sigma weight residual 109.60 105.16 4.44 1.50e+00 4.44e-01 8.75e+00 angle pdb=" CA MET A 164 " pdb=" CB MET A 164 " pdb=" CG MET A 164 " ideal model delta sigma weight residual 114.10 119.83 -5.73 2.00e+00 2.50e-01 8.22e+00 angle pdb=" CA ASP A 172 " pdb=" CB ASP A 172 " pdb=" CG ASP A 172 " ideal model delta sigma weight residual 112.60 115.18 -2.58 1.00e+00 1.00e+00 6.68e+00 angle pdb=" CA TYR A 370 " pdb=" CB TYR A 370 " pdb=" CG TYR A 370 " ideal model delta sigma weight residual 113.90 118.26 -4.36 1.80e+00 3.09e-01 5.86e+00 ... (remaining 2782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.73: 1084 22.73 - 45.47: 78 45.47 - 68.20: 8 68.20 - 90.93: 0 90.93 - 113.66: 2 Dihedral angle restraints: 1172 sinusoidal: 400 harmonic: 772 Sorted by residual: dihedral pdb=" C2 91Q A 501 " pdb=" C3 91Q A 501 " pdb=" N1 91Q A 501 " pdb=" C4 91Q A 501 " ideal model delta sinusoidal sigma weight residual 73.77 -39.89 113.66 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" C1 91Q A 501 " pdb=" C3 91Q A 501 " pdb=" N1 91Q A 501 " pdb=" C4 91Q A 501 " ideal model delta sinusoidal sigma weight residual 198.00 87.95 110.05 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" CA PRO A 142 " pdb=" C PRO A 142 " pdb=" N LEU A 143 " pdb=" CA LEU A 143 " ideal model delta harmonic sigma weight residual -180.00 -164.23 -15.77 0 5.00e+00 4.00e-02 9.95e+00 ... (remaining 1169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 217 0.031 - 0.063: 92 0.063 - 0.094: 40 0.094 - 0.126: 4 0.126 - 0.157: 1 Chirality restraints: 354 Sorted by residual: chirality pdb=" CA MET A 164 " pdb=" N MET A 164 " pdb=" C MET A 164 " pdb=" CB MET A 164 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CA PRO A 209 " pdb=" N PRO A 209 " pdb=" C PRO A 209 " pdb=" CB PRO A 209 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.91e-01 chirality pdb=" CA PRO A 129 " pdb=" N PRO A 129 " pdb=" C PRO A 129 " pdb=" CB PRO A 129 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.77e-01 ... (remaining 351 not shown) Planarity restraints: 327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 141 " -0.066 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO A 142 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 336 " 0.012 2.00e-02 2.50e+03 1.05e-02 2.74e+00 pdb=" CG TRP A 336 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 336 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 336 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 336 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 336 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 336 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 336 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 336 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 336 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 383 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C PHE A 383 " 0.027 2.00e-02 2.50e+03 pdb=" O PHE A 383 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A 384 " -0.009 2.00e-02 2.50e+03 ... (remaining 324 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 121 2.74 - 3.28: 2092 3.28 - 3.82: 3361 3.82 - 4.36: 3819 4.36 - 4.90: 6669 Nonbonded interactions: 16062 Sorted by model distance: nonbonded pdb=" O SER A 392 " pdb=" OG SER A 392 " model vdw 2.198 3.040 nonbonded pdb=" O LEU A 382 " pdb=" NH1 ARG A 388 " model vdw 2.341 3.120 nonbonded pdb=" O ALA A 161 " pdb=" ND1 HIS A 165 " model vdw 2.477 3.120 nonbonded pdb=" O ILE A 249 " pdb=" OG1 THR A 253 " model vdw 2.521 3.040 nonbonded pdb=" O THR A 253 " pdb=" OG1 THR A 257 " model vdw 2.563 3.040 ... (remaining 16057 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 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: 1.250 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.350 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:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 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 : 0.005 0.050 2036 Z= 0.250 Angle : 0.792 6.177 2789 Z= 0.447 Chirality : 0.040 0.157 354 Planarity : 0.007 0.099 327 Dihedral : 16.113 113.662 665 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 21.15 % Favored : 78.85 % 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: 1.55 (0.53), residues: 256 helix: 1.25 (0.35), residues: 215 sheet: None (None), residues: 0 loop : 0.24 (1.11), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 336 HIS 0.003 0.001 HIS A 165 PHE 0.016 0.001 PHE A 332 TYR 0.009 0.001 TYR A 139 ARG 0.000 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.13892 ( 164) hydrogen bonds : angle 6.12270 ( 486) SS BOND : bond 0.00088 ( 1) SS BOND : angle 0.45270 ( 2) covalent geometry : bond 0.00498 ( 2035) covalent geometry : angle 0.79258 ( 2787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.224 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 30 average time/residue: 1.1342 time to fit residues: 34.9161 Evaluate side-chains 26 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 13 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.0170 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.192107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.178964 restraints weight = 2144.429| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 1.33 r_work: 0.4030 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2036 Z= 0.116 Angle : 0.551 5.928 2789 Z= 0.280 Chirality : 0.038 0.114 354 Planarity : 0.006 0.079 327 Dihedral : 8.530 86.269 278 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 3.37 % Allowed : 15.87 % Favored : 80.77 % 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: 1.55 (0.54), residues: 256 helix: 1.37 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -0.97 (1.13), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 367 HIS 0.003 0.001 HIS A 165 PHE 0.012 0.001 PHE A 332 TYR 0.011 0.001 TYR A 139 ARG 0.002 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 164) hydrogen bonds : angle 4.64223 ( 486) SS BOND : bond 0.00207 ( 1) SS BOND : angle 0.15129 ( 2) covalent geometry : bond 0.00237 ( 2035) covalent geometry : angle 0.55122 ( 2787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.220 Fit side-chains REVERT: A 132 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6926 (ttp) REVERT: A 153 TYR cc_start: 0.8140 (t80) cc_final: 0.7905 (t80) REVERT: A 318 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: A 392 SER cc_start: 0.6976 (t) cc_final: 0.6486 (m) outliers start: 7 outliers final: 0 residues processed: 32 average time/residue: 0.7372 time to fit residues: 24.4558 Evaluate side-chains 29 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 318 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.186495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.173370 restraints weight = 2189.495| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 1.33 r_work: 0.3976 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3882 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2036 Z= 0.154 Angle : 0.612 7.580 2789 Z= 0.306 Chirality : 0.041 0.118 354 Planarity : 0.005 0.072 327 Dihedral : 7.971 76.980 276 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 3.85 % Allowed : 18.27 % Favored : 77.88 % 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: 1.23 (0.53), residues: 256 helix: 1.17 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.19 (1.09), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 367 HIS 0.003 0.001 HIS A 165 PHE 0.012 0.002 PHE A 244 TYR 0.014 0.002 TYR A 139 ARG 0.001 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 164) hydrogen bonds : angle 4.64888 ( 486) SS BOND : bond 0.00228 ( 1) SS BOND : angle 0.09066 ( 2) covalent geometry : bond 0.00358 ( 2035) covalent geometry : angle 0.61203 ( 2787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.189 Fit side-chains REVERT: A 114 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.6193 (ttm) REVERT: A 193 PHE cc_start: 0.5981 (m-10) cc_final: 0.5780 (m-10) REVERT: A 318 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: A 392 SER cc_start: 0.7084 (t) cc_final: 0.6671 (m) outliers start: 8 outliers final: 2 residues processed: 30 average time/residue: 0.8678 time to fit residues: 26.8488 Evaluate side-chains 28 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.189718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.177216 restraints weight = 2169.784| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.27 r_work: 0.3991 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2036 Z= 0.131 Angle : 0.577 7.233 2789 Z= 0.289 Chirality : 0.040 0.122 354 Planarity : 0.005 0.069 327 Dihedral : 7.848 76.599 276 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 3.85 % Allowed : 19.23 % Favored : 76.92 % 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: 1.33 (0.53), residues: 256 helix: 1.23 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.12 (1.10), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 367 HIS 0.002 0.001 HIS A 165 PHE 0.010 0.001 PHE A 332 TYR 0.012 0.001 TYR A 139 ARG 0.005 0.001 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 164) hydrogen bonds : angle 4.50978 ( 486) SS BOND : bond 0.00225 ( 1) SS BOND : angle 0.03214 ( 2) covalent geometry : bond 0.00294 ( 2035) covalent geometry : angle 0.57676 ( 2787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.200 Fit side-chains REVERT: A 114 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.6243 (ttm) REVERT: A 194 LEU cc_start: 0.4854 (OUTLIER) cc_final: 0.4537 (tt) REVERT: A 318 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: A 392 SER cc_start: 0.7026 (t) cc_final: 0.6629 (m) outliers start: 8 outliers final: 5 residues processed: 33 average time/residue: 0.7071 time to fit residues: 24.2086 Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.185745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.172693 restraints weight = 2219.651| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 1.34 r_work: 0.3963 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3867 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2036 Z= 0.154 Angle : 0.616 7.879 2789 Z= 0.310 Chirality : 0.041 0.129 354 Planarity : 0.005 0.068 327 Dihedral : 7.798 74.523 276 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 4.81 % Allowed : 18.75 % Favored : 76.44 % 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: 0.98 (0.52), residues: 256 helix: 1.02 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -1.36 (1.05), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 367 HIS 0.002 0.001 HIS A 165 PHE 0.011 0.002 PHE A 332 TYR 0.015 0.002 TYR A 139 ARG 0.004 0.001 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.04544 ( 164) hydrogen bonds : angle 4.61574 ( 486) SS BOND : bond 0.00257 ( 1) SS BOND : angle 0.04783 ( 2) covalent geometry : bond 0.00360 ( 2035) covalent geometry : angle 0.61663 ( 2787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.233 Fit side-chains REVERT: A 194 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.4612 (tt) REVERT: A 318 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7230 (mt-10) REVERT: A 392 SER cc_start: 0.7037 (t) cc_final: 0.6612 (m) outliers start: 10 outliers final: 8 residues processed: 32 average time/residue: 0.7127 time to fit residues: 23.7721 Evaluate side-chains 34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.4160 r_free = 0.4160 target = 0.187124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.174249 restraints weight = 2188.088| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.32 r_work: 0.3982 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2036 Z= 0.131 Angle : 0.579 7.427 2789 Z= 0.291 Chirality : 0.040 0.138 354 Planarity : 0.005 0.066 327 Dihedral : 7.690 74.137 276 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 3.85 % Allowed : 19.23 % Favored : 76.92 % 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: 1.20 (0.52), residues: 256 helix: 1.15 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.19 (1.10), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 367 HIS 0.002 0.001 HIS A 165 PHE 0.010 0.001 PHE A 332 TYR 0.012 0.002 TYR A 139 ARG 0.005 0.001 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 164) hydrogen bonds : angle 4.50356 ( 486) SS BOND : bond 0.00214 ( 1) SS BOND : angle 0.05819 ( 2) covalent geometry : bond 0.00294 ( 2035) covalent geometry : angle 0.57945 ( 2787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.240 Fit side-chains REVERT: A 194 LEU cc_start: 0.4902 (OUTLIER) cc_final: 0.4587 (tt) REVERT: A 318 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7235 (mt-10) outliers start: 8 outliers final: 6 residues processed: 28 average time/residue: 0.8576 time to fit residues: 24.8918 Evaluate side-chains 31 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 0.0570 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.187060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.174198 restraints weight = 2190.908| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 1.30 r_work: 0.3978 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3885 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2036 Z= 0.147 Angle : 0.602 7.784 2789 Z= 0.303 Chirality : 0.041 0.146 354 Planarity : 0.005 0.066 327 Dihedral : 7.663 72.806 276 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 5.77 % Allowed : 17.31 % Favored : 76.92 % 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: 0.96 (0.52), residues: 256 helix: 1.01 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -1.34 (1.07), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 367 HIS 0.002 0.001 HIS A 165 PHE 0.012 0.002 PHE A 193 TYR 0.014 0.002 TYR A 139 ARG 0.005 0.001 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 164) hydrogen bonds : angle 4.55216 ( 486) SS BOND : bond 0.00249 ( 1) SS BOND : angle 0.06522 ( 2) covalent geometry : bond 0.00343 ( 2035) covalent geometry : angle 0.60231 ( 2787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.201 Fit side-chains REVERT: A 194 LEU cc_start: 0.4933 (OUTLIER) cc_final: 0.4614 (tt) REVERT: A 318 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7204 (mt-10) outliers start: 12 outliers final: 9 residues processed: 35 average time/residue: 0.6880 time to fit residues: 24.9684 Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 373 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.0020 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.188225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.175147 restraints weight = 2177.829| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.34 r_work: 0.4030 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2036 Z= 0.128 Angle : 0.573 7.237 2789 Z= 0.288 Chirality : 0.040 0.118 354 Planarity : 0.005 0.062 327 Dihedral : 7.557 72.545 276 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 5.29 % Allowed : 18.27 % Favored : 76.44 % 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: 1.22 (0.52), residues: 256 helix: 1.17 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.26 (1.11), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 367 HIS 0.002 0.001 HIS A 165 PHE 0.010 0.001 PHE A 332 TYR 0.012 0.002 TYR A 139 ARG 0.006 0.001 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 164) hydrogen bonds : angle 4.45165 ( 486) SS BOND : bond 0.00204 ( 1) SS BOND : angle 0.06909 ( 2) covalent geometry : bond 0.00288 ( 2035) covalent geometry : angle 0.57353 ( 2787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.231 Fit side-chains REVERT: A 194 LEU cc_start: 0.4859 (OUTLIER) cc_final: 0.4538 (tt) REVERT: A 318 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7198 (mt-10) outliers start: 11 outliers final: 8 residues processed: 35 average time/residue: 0.7065 time to fit residues: 25.6875 Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 373 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 0.0270 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.188526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.175368 restraints weight = 2225.390| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 1.35 r_work: 0.4005 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 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 0.027 2036 Z= 0.125 Angle : 0.578 7.007 2789 Z= 0.292 Chirality : 0.040 0.148 354 Planarity : 0.005 0.062 327 Dihedral : 7.460 71.437 276 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 4.33 % Allowed : 20.67 % Favored : 75.00 % 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: 1.34 (0.52), residues: 256 helix: 1.26 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.23 (1.12), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 367 HIS 0.002 0.001 HIS A 165 PHE 0.018 0.001 PHE A 193 TYR 0.012 0.002 TYR A 139 ARG 0.005 0.001 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 164) hydrogen bonds : angle 4.43058 ( 486) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.07661 ( 2) covalent geometry : bond 0.00278 ( 2035) covalent geometry : angle 0.57847 ( 2787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.231 Fit side-chains REVERT: A 194 LEU cc_start: 0.4913 (OUTLIER) cc_final: 0.4557 (tt) REVERT: A 318 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7230 (mt-10) outliers start: 9 outliers final: 7 residues processed: 31 average time/residue: 0.7547 time to fit residues: 24.3008 Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 373 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.0070 chunk 16 optimal weight: 0.0670 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.191584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.179052 restraints weight = 2156.450| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.27 r_work: 0.4028 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3936 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2036 Z= 0.111 Angle : 0.543 6.187 2789 Z= 0.273 Chirality : 0.039 0.118 354 Planarity : 0.005 0.060 327 Dihedral : 7.227 69.974 276 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 3.37 % Allowed : 21.63 % Favored : 75.00 % 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: 1.80 (0.53), residues: 256 helix: 1.56 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.07 (1.14), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 367 HIS 0.002 0.001 HIS A 165 PHE 0.010 0.001 PHE A 332 TYR 0.010 0.001 TYR A 139 ARG 0.006 0.001 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 164) hydrogen bonds : angle 4.25426 ( 486) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.10870 ( 2) covalent geometry : bond 0.00236 ( 2035) covalent geometry : angle 0.54272 ( 2787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.216 Fit side-chains REVERT: A 194 LEU cc_start: 0.4905 (OUTLIER) cc_final: 0.4524 (tt) REVERT: A 318 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7276 (mt-10) outliers start: 7 outliers final: 5 residues processed: 30 average time/residue: 0.7943 time to fit residues: 24.7029 Evaluate side-chains 32 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 373 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.186991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.174258 restraints weight = 2198.880| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.30 r_work: 0.3993 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2036 Z= 0.147 Angle : 0.610 7.234 2789 Z= 0.306 Chirality : 0.041 0.143 354 Planarity : 0.005 0.063 327 Dihedral : 7.443 70.542 276 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 4.33 % Allowed : 21.63 % Favored : 74.04 % 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: 1.38 (0.52), residues: 256 helix: 1.29 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.26 (1.11), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 367 HIS 0.002 0.001 HIS A 165 PHE 0.021 0.002 PHE A 193 TYR 0.016 0.002 TYR A 153 ARG 0.004 0.001 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 164) hydrogen bonds : angle 4.47350 ( 486) SS BOND : bond 0.00248 ( 1) SS BOND : angle 0.05745 ( 2) covalent geometry : bond 0.00341 ( 2035) covalent geometry : angle 0.61019 ( 2787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1888.66 seconds wall clock time: 33 minutes 31.97 seconds (2011.97 seconds total)