Starting phenix.real_space_refine on Sat Apr 26 16:04:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z66_39793/04_2025/8z66_39793.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z66_39793/04_2025/8z66_39793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z66_39793/04_2025/8z66_39793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z66_39793/04_2025/8z66_39793.map" model { file = "/net/cci-nas-00/data/ceres_data/8z66_39793/04_2025/8z66_39793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z66_39793/04_2025/8z66_39793.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 13 5.16 5 C 1468 2.51 5 N 377 2.21 5 O 362 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 2220 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2220 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 2.33, per 1000 atoms: 1.05 Number of scatterers: 2220 At special positions: 0 Unit cell: (60.68, 71.34, 70.52, 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 13 16.00 O 362 8.00 N 377 7.00 C 1468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " 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: 0.53 Conformation dependent library (CDL) restraints added in 263.1 milliseconds 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 562 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 80.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'R' and resid 13 through 48 removed outlier: 3.966A pdb=" N HIS R 17 " --> pdb=" O SER R 13 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU R 18 " --> pdb=" O ARG R 14 " (cutoff:3.500A) Proline residue: R 20 - end of helix Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 52 through 78 removed outlier: 3.686A pdb=" N TYR R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 120 removed outlier: 4.582A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 129 Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 151 through 155 Processing helix chain 'R' and resid 177 through 190 removed outlier: 3.578A pdb=" N PHE R 190 " --> pdb=" O VAL R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 210 removed outlier: 4.076A pdb=" N GLY R 210 " --> pdb=" O ARG R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 252 Proline residue: R 239 - end of helix removed outlier: 3.552A pdb=" N LEU R 252 " --> pdb=" O SER R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 276 Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 304 removed outlier: 3.667A pdb=" N LEU R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) 169 hydrogen bonds defined for protein. 498 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: 0.57 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 691 1.34 - 1.46: 620 1.46 - 1.58: 959 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 2286 Sorted by residual: bond pdb=" CB MET R 57 " pdb=" CG MET R 57 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.32e+00 bond pdb=" CA MET R 57 " pdb=" C MET R 57 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.34e-02 5.57e+03 3.01e+00 bond pdb=" SD MET R 57 " pdb=" CE MET R 57 " ideal model delta sigma weight residual 1.791 1.748 0.043 2.50e-02 1.60e+03 3.00e+00 bond pdb=" CB VAL R 54 " pdb=" CG2 VAL R 54 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.32e+00 bond pdb=" CB VAL R 141 " pdb=" CG1 VAL R 141 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 ... (remaining 2281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 3113 3.81 - 7.63: 15 7.63 - 11.44: 1 11.44 - 15.25: 2 15.25 - 19.06: 1 Bond angle restraints: 3132 Sorted by residual: angle pdb=" C MET R 57 " pdb=" CA MET R 57 " pdb=" CB MET R 57 " ideal model delta sigma weight residual 110.42 91.36 19.06 1.99e+00 2.53e-01 9.18e+01 angle pdb=" N MET R 57 " pdb=" CA MET R 57 " pdb=" C MET R 57 " ideal model delta sigma weight residual 110.80 126.03 -15.23 2.13e+00 2.20e-01 5.11e+01 angle pdb=" CB MET R 57 " pdb=" CG MET R 57 " pdb=" SD MET R 57 " ideal model delta sigma weight residual 112.70 97.50 15.20 3.00e+00 1.11e-01 2.57e+01 angle pdb=" N GLY R 253 " pdb=" CA GLY R 253 " pdb=" C GLY R 253 " ideal model delta sigma weight residual 112.13 105.99 6.14 1.34e+00 5.57e-01 2.10e+01 angle pdb=" CA MET R 57 " pdb=" CB MET R 57 " pdb=" CG MET R 57 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 ... (remaining 3127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 1145 14.94 - 29.88: 115 29.88 - 44.83: 37 44.83 - 59.77: 4 59.77 - 74.71: 2 Dihedral angle restraints: 1303 sinusoidal: 434 harmonic: 869 Sorted by residual: dihedral pdb=" C MET R 57 " pdb=" N MET R 57 " pdb=" CA MET R 57 " pdb=" CB MET R 57 " ideal model delta harmonic sigma weight residual -122.60 -109.05 -13.55 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" CA THR R 166 " pdb=" C THR R 166 " pdb=" N PHE R 167 " pdb=" CA PHE R 167 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sinusoidal sigma weight residual 93.00 127.07 -34.07 1 1.00e+01 1.00e-02 1.65e+01 ... (remaining 1300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 205 0.036 - 0.072: 115 0.072 - 0.109: 32 0.109 - 0.145: 9 0.145 - 0.181: 3 Chirality restraints: 364 Sorted by residual: chirality pdb=" CG LEU R 108 " pdb=" CB LEU R 108 " pdb=" CD1 LEU R 108 " pdb=" CD2 LEU R 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CG LEU R 272 " pdb=" CB LEU R 272 " pdb=" CD1 LEU R 272 " pdb=" CD2 LEU R 272 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA LEU R 70 " pdb=" N LEU R 70 " pdb=" C LEU R 70 " pdb=" CB LEU R 70 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 361 not shown) Planarity restraints: 389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 19 " -0.048 5.00e-02 4.00e+02 7.18e-02 8.26e+00 pdb=" N PRO R 20 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO R 20 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 20 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 20 " -0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO R 21 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO R 21 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 21 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 107 " -0.018 2.00e-02 2.50e+03 1.42e-02 3.55e+00 pdb=" CG PHE R 107 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE R 107 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE R 107 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 107 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 107 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE R 107 " -0.008 2.00e-02 2.50e+03 ... (remaining 386 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 473 2.77 - 3.31: 2238 3.31 - 3.84: 3713 3.84 - 4.37: 4131 4.37 - 4.90: 7228 Nonbonded interactions: 17783 Sorted by model distance: nonbonded pdb=" O ALA R 273 " pdb=" OG SER R 276 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR R 43 " pdb=" NE2 GLN R 47 " model vdw 2.355 3.120 nonbonded pdb=" O MET R 57 " pdb=" CG1 ILE R 61 " model vdw 2.390 3.440 nonbonded pdb=" O LEU R 225 " pdb=" OG SER R 228 " model vdw 2.400 3.040 nonbonded pdb=" O ALA R 136 " pdb=" OG SER R 139 " model vdw 2.485 3.040 ... (remaining 17778 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.570 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 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 : 0.006 0.069 2287 Z= 0.265 Angle : 0.942 19.064 3134 Z= 0.506 Chirality : 0.049 0.181 364 Planarity : 0.007 0.072 389 Dihedral : 13.496 74.712 738 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 8.33 % 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: -0.94 (0.47), residues: 292 helix: 0.46 (0.35), residues: 207 sheet: None (None), residues: 0 loop : -3.42 (0.51), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 142 HIS 0.008 0.002 HIS R 17 PHE 0.032 0.003 PHE R 107 TYR 0.023 0.002 TYR R 55 ARG 0.008 0.001 ARG R 202 Details of bonding type rmsd hydrogen bonds : bond 0.13951 ( 169) hydrogen bonds : angle 6.38803 ( 498) SS BOND : bond 0.00010 ( 1) SS BOND : angle 1.80582 ( 2) covalent geometry : bond 0.00626 ( 2286) covalent geometry : angle 0.94091 ( 3132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.210 Fit side-chains REVERT: R 102 TYR cc_start: 0.8025 (m-80) cc_final: 0.7292 (m-80) REVERT: R 168 CYS cc_start: 0.5941 (t) cc_final: 0.5719 (t) REVERT: R 184 TYR cc_start: 0.7455 (t80) cc_final: 0.7226 (t80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1940 time to fit residues: 9.6769 Evaluate side-chains 40 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 12 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 overall best weight: 0.1776 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.143225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.129831 restraints weight = 2971.656| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.35 r_work: 0.3564 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2287 Z= 0.151 Angle : 0.610 5.249 3134 Z= 0.322 Chirality : 0.042 0.130 364 Planarity : 0.006 0.049 389 Dihedral : 4.636 17.325 319 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.96 % Allowed : 11.00 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.23 (0.50), residues: 292 helix: 1.35 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.97 (0.60), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 194 HIS 0.004 0.001 HIS R 302 PHE 0.017 0.002 PHE R 265 TYR 0.016 0.002 TYR R 66 ARG 0.008 0.001 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 169) hydrogen bonds : angle 4.75624 ( 498) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.76915 ( 2) covalent geometry : bond 0.00333 ( 2286) covalent geometry : angle 0.60945 ( 3132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.233 Fit side-chains REVERT: R 102 TYR cc_start: 0.7922 (m-80) cc_final: 0.7361 (m-80) REVERT: R 168 CYS cc_start: 0.6166 (t) cc_final: 0.5930 (t) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.1379 time to fit residues: 8.3617 Evaluate side-chains 44 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 196 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 21 optimal weight: 0.0980 chunk 1 optimal weight: 0.0970 chunk 27 optimal weight: 0.2980 chunk 17 optimal weight: 0.4980 chunk 4 optimal weight: 0.0060 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 overall best weight: 0.0972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.145222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131979 restraints weight = 3027.389| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.31 r_work: 0.3594 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2287 Z= 0.125 Angle : 0.549 5.434 3134 Z= 0.288 Chirality : 0.039 0.125 364 Planarity : 0.005 0.050 389 Dihedral : 4.229 15.500 319 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.87 % Allowed : 13.88 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.80 (0.51), residues: 292 helix: 1.79 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -2.78 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 194 HIS 0.003 0.001 HIS R 269 PHE 0.012 0.002 PHE R 107 TYR 0.014 0.001 TYR R 66 ARG 0.006 0.001 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 169) hydrogen bonds : angle 4.46941 ( 498) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.71682 ( 2) covalent geometry : bond 0.00261 ( 2286) covalent geometry : angle 0.54891 ( 3132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.263 Fit side-chains REVERT: R 57 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5945 (mpp) REVERT: R 83 TRP cc_start: 0.7390 (t-100) cc_final: 0.7003 (t-100) REVERT: R 102 TYR cc_start: 0.7927 (m-80) cc_final: 0.7341 (m-80) REVERT: R 169 PHE cc_start: 0.6050 (OUTLIER) cc_final: 0.5661 (m-10) REVERT: R 244 LEU cc_start: 0.7608 (tp) cc_final: 0.7408 (tp) outliers start: 6 outliers final: 2 residues processed: 41 average time/residue: 0.1433 time to fit residues: 7.0663 Evaluate side-chains 44 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 228 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 8 optimal weight: 0.3980 chunk 3 optimal weight: 0.0970 chunk 5 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.0870 chunk 12 optimal weight: 0.0670 chunk 20 optimal weight: 0.0470 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 2 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 overall best weight: 0.0770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.147649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134818 restraints weight = 3006.347| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.31 r_work: 0.3632 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2287 Z= 0.119 Angle : 0.534 5.559 3134 Z= 0.280 Chirality : 0.039 0.129 364 Planarity : 0.005 0.053 389 Dihedral : 4.025 15.897 319 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.83 % Allowed : 14.83 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.15 (0.51), residues: 292 helix: 1.88 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -2.46 (0.64), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 194 HIS 0.005 0.001 HIS R 79 PHE 0.012 0.001 PHE R 107 TYR 0.012 0.001 TYR R 66 ARG 0.005 0.000 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 169) hydrogen bonds : angle 4.34315 ( 498) SS BOND : bond 0.00152 ( 1) SS BOND : angle 1.75186 ( 2) covalent geometry : bond 0.00245 ( 2286) covalent geometry : angle 0.53205 ( 3132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.365 Fit side-chains REVERT: R 83 TRP cc_start: 0.7408 (t-100) cc_final: 0.7131 (t-100) REVERT: R 102 TYR cc_start: 0.7895 (m-80) cc_final: 0.7288 (m-80) REVERT: R 116 TYR cc_start: 0.8219 (t80) cc_final: 0.7766 (t80) REVERT: R 121 HIS cc_start: 0.7724 (m170) cc_final: 0.7453 (m-70) REVERT: R 169 PHE cc_start: 0.5950 (OUTLIER) cc_final: 0.5561 (m-10) outliers start: 8 outliers final: 3 residues processed: 38 average time/residue: 0.2345 time to fit residues: 10.5511 Evaluate side-chains 35 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.0170 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 18 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 chunk 27 optimal weight: 0.3980 overall best weight: 0.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS R 149 ASN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.144680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.131796 restraints weight = 3048.787| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.33 r_work: 0.3588 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2287 Z= 0.157 Angle : 0.579 5.695 3134 Z= 0.308 Chirality : 0.041 0.123 364 Planarity : 0.005 0.051 389 Dihedral : 4.196 16.089 319 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.87 % Allowed : 15.31 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.08 (0.52), residues: 292 helix: 1.77 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -2.35 (0.69), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 83 HIS 0.006 0.002 HIS R 79 PHE 0.011 0.002 PHE R 107 TYR 0.014 0.002 TYR R 66 ARG 0.004 0.000 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 169) hydrogen bonds : angle 4.42661 ( 498) SS BOND : bond 0.00054 ( 1) SS BOND : angle 1.78438 ( 2) covalent geometry : bond 0.00355 ( 2286) covalent geometry : angle 0.57717 ( 3132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.241 Fit side-chains REVERT: R 57 MET cc_start: 0.6120 (OUTLIER) cc_final: 0.5900 (mtp) REVERT: R 102 TYR cc_start: 0.7928 (m-80) cc_final: 0.7306 (m-80) REVERT: R 121 HIS cc_start: 0.7712 (m170) cc_final: 0.7435 (m-70) REVERT: R 169 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.5704 (m-10) outliers start: 6 outliers final: 1 residues processed: 42 average time/residue: 0.1383 time to fit residues: 7.0346 Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 228 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 12 optimal weight: 0.1980 chunk 20 optimal weight: 0.0030 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 15 optimal weight: 0.0970 chunk 23 optimal weight: 0.0980 overall best weight: 0.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 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 = 0.146909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.134217 restraints weight = 3010.457| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.32 r_work: 0.3621 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2287 Z= 0.127 Angle : 0.557 6.451 3134 Z= 0.290 Chirality : 0.039 0.117 364 Planarity : 0.005 0.049 389 Dihedral : 4.054 15.077 319 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.39 % Allowed : 16.75 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.26 (0.51), residues: 292 helix: 1.91 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -2.26 (0.69), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 83 HIS 0.004 0.001 HIS R 269 PHE 0.011 0.001 PHE R 237 TYR 0.014 0.001 TYR R 66 ARG 0.003 0.000 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 169) hydrogen bonds : angle 4.29967 ( 498) SS BOND : bond 0.00074 ( 1) SS BOND : angle 1.19151 ( 2) covalent geometry : bond 0.00273 ( 2286) covalent geometry : angle 0.55614 ( 3132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.245 Fit side-chains REVERT: R 57 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5808 (mtp) REVERT: R 102 TYR cc_start: 0.7869 (m-80) cc_final: 0.7332 (m-80) REVERT: R 121 HIS cc_start: 0.7654 (m170) cc_final: 0.7367 (m-70) REVERT: R 169 PHE cc_start: 0.6005 (OUTLIER) cc_final: 0.5610 (m-10) outliers start: 5 outliers final: 2 residues processed: 39 average time/residue: 0.1214 time to fit residues: 5.9290 Evaluate side-chains 41 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 228 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 12 optimal weight: 0.1980 chunk 3 optimal weight: 0.0970 chunk 13 optimal weight: 0.0980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.144478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.132002 restraints weight = 3055.948| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.31 r_work: 0.3593 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2287 Z= 0.168 Angle : 0.590 6.125 3134 Z= 0.309 Chirality : 0.041 0.120 364 Planarity : 0.005 0.049 389 Dihedral : 4.177 15.639 319 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.35 % Allowed : 17.22 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.14 (0.51), residues: 292 helix: 1.85 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -2.34 (0.70), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 83 HIS 0.005 0.001 HIS R 269 PHE 0.013 0.002 PHE R 237 TYR 0.014 0.002 TYR R 66 ARG 0.003 0.000 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 169) hydrogen bonds : angle 4.35979 ( 498) SS BOND : bond 0.00073 ( 1) SS BOND : angle 1.41805 ( 2) covalent geometry : bond 0.00384 ( 2286) covalent geometry : angle 0.58886 ( 3132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.230 Fit side-chains REVERT: R 57 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5890 (mtp) REVERT: R 102 TYR cc_start: 0.7912 (m-80) cc_final: 0.7298 (m-80) REVERT: R 121 HIS cc_start: 0.7664 (m170) cc_final: 0.7365 (m-70) REVERT: R 169 PHE cc_start: 0.6086 (OUTLIER) cc_final: 0.5687 (m-10) outliers start: 7 outliers final: 2 residues processed: 43 average time/residue: 0.1526 time to fit residues: 7.7673 Evaluate side-chains 47 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 228 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 8 optimal weight: 0.3980 chunk 23 optimal weight: 0.0980 chunk 5 optimal weight: 0.1980 chunk 9 optimal weight: 0.2980 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 0.0870 overall best weight: 0.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.145784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.133258 restraints weight = 3129.386| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.36 r_work: 0.3610 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2287 Z= 0.148 Angle : 0.569 5.709 3134 Z= 0.301 Chirality : 0.040 0.117 364 Planarity : 0.005 0.049 389 Dihedral : 4.069 15.897 319 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.35 % Allowed : 17.70 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.31 (0.51), residues: 292 helix: 1.96 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -2.26 (0.69), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 83 HIS 0.005 0.001 HIS R 269 PHE 0.011 0.001 PHE R 107 TYR 0.014 0.002 TYR R 66 ARG 0.003 0.000 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 169) hydrogen bonds : angle 4.28275 ( 498) SS BOND : bond 0.00156 ( 1) SS BOND : angle 2.18116 ( 2) covalent geometry : bond 0.00330 ( 2286) covalent geometry : angle 0.56615 ( 3132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.215 Fit side-chains REVERT: R 27 VAL cc_start: 0.6651 (t) cc_final: 0.6217 (t) REVERT: R 57 MET cc_start: 0.6106 (OUTLIER) cc_final: 0.5880 (mtp) REVERT: R 102 TYR cc_start: 0.7864 (m-80) cc_final: 0.7253 (m-80) REVERT: R 121 HIS cc_start: 0.7661 (m170) cc_final: 0.7360 (m-70) REVERT: R 169 PHE cc_start: 0.6046 (OUTLIER) cc_final: 0.5679 (m-10) REVERT: R 272 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7749 (mp) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.1328 time to fit residues: 6.6349 Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 22 optimal weight: 0.0980 chunk 12 optimal weight: 0.0870 chunk 10 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 4 optimal weight: 0.0570 chunk 19 optimal weight: 0.1980 chunk 23 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 21 optimal weight: 0.2980 overall best weight: 0.1476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.147287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.134897 restraints weight = 3046.301| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.33 r_work: 0.3634 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2287 Z= 0.130 Angle : 0.555 5.666 3134 Z= 0.292 Chirality : 0.039 0.116 364 Planarity : 0.005 0.048 389 Dihedral : 3.992 15.600 319 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.35 % Allowed : 18.18 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.49 (0.51), residues: 292 helix: 2.09 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -2.21 (0.68), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 83 HIS 0.004 0.001 HIS R 269 PHE 0.011 0.001 PHE R 107 TYR 0.013 0.001 TYR R 66 ARG 0.003 0.000 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 169) hydrogen bonds : angle 4.18728 ( 498) SS BOND : bond 0.00069 ( 1) SS BOND : angle 1.85868 ( 2) covalent geometry : bond 0.00281 ( 2286) covalent geometry : angle 0.55342 ( 3132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.219 Fit side-chains REVERT: R 27 VAL cc_start: 0.6562 (t) cc_final: 0.6090 (t) REVERT: R 57 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.5781 (mtp) REVERT: R 102 TYR cc_start: 0.7839 (m-80) cc_final: 0.7220 (m-80) REVERT: R 121 HIS cc_start: 0.7646 (m170) cc_final: 0.7340 (m-70) REVERT: R 169 PHE cc_start: 0.6034 (OUTLIER) cc_final: 0.5661 (m-10) REVERT: R 272 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7744 (mp) outliers start: 7 outliers final: 3 residues processed: 38 average time/residue: 0.1324 time to fit residues: 6.0771 Evaluate side-chains 42 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 3 optimal weight: 0.0980 chunk 25 optimal weight: 0.0370 chunk 10 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 23 optimal weight: 0.0570 chunk 5 optimal weight: 0.0970 chunk 16 optimal weight: 0.2980 chunk 24 optimal weight: 0.0770 chunk 1 optimal weight: 0.0670 chunk 18 optimal weight: 0.7980 overall best weight: 0.0670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.151098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138892 restraints weight = 3013.940| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.32 r_work: 0.3688 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2287 Z= 0.114 Angle : 0.542 5.651 3134 Z= 0.283 Chirality : 0.038 0.112 364 Planarity : 0.005 0.048 389 Dihedral : 3.769 15.147 319 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.39 % Allowed : 19.62 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.89 (0.51), residues: 292 helix: 2.41 (0.35), residues: 213 sheet: None (None), residues: 0 loop : -2.20 (0.69), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 83 HIS 0.006 0.001 HIS R 79 PHE 0.012 0.001 PHE R 107 TYR 0.012 0.001 TYR R 66 ARG 0.009 0.001 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 169) hydrogen bonds : angle 4.06389 ( 498) SS BOND : bond 0.00115 ( 1) SS BOND : angle 1.23213 ( 2) covalent geometry : bond 0.00234 ( 2286) covalent geometry : angle 0.54141 ( 3132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.235 Fit side-chains REVERT: R 57 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.5668 (mtp) REVERT: R 102 TYR cc_start: 0.7791 (m-80) cc_final: 0.7236 (m-80) REVERT: R 116 TYR cc_start: 0.8057 (t80) cc_final: 0.7571 (t80) REVERT: R 169 PHE cc_start: 0.5958 (OUTLIER) cc_final: 0.5596 (m-10) REVERT: R 272 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7691 (mp) outliers start: 5 outliers final: 2 residues processed: 31 average time/residue: 0.1412 time to fit residues: 5.4704 Evaluate side-chains 32 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 0.0870 chunk 12 optimal weight: 0.0470 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.146774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.133886 restraints weight = 2989.734| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.35 r_work: 0.3621 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2287 Z= 0.165 Angle : 0.591 5.824 3134 Z= 0.312 Chirality : 0.041 0.120 364 Planarity : 0.005 0.049 389 Dihedral : 4.072 15.543 319 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.35 % Allowed : 18.66 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.65 (0.50), residues: 292 helix: 2.26 (0.35), residues: 210 sheet: None (None), residues: 0 loop : -2.20 (0.69), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 83 HIS 0.005 0.001 HIS R 302 PHE 0.010 0.002 PHE R 97 TYR 0.011 0.002 TYR R 66 ARG 0.009 0.001 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 169) hydrogen bonds : angle 4.22670 ( 498) SS BOND : bond 0.00043 ( 1) SS BOND : angle 1.97883 ( 2) covalent geometry : bond 0.00378 ( 2286) covalent geometry : angle 0.58858 ( 3132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1930.62 seconds wall clock time: 33 minutes 46.56 seconds (2026.56 seconds total)