Starting phenix.real_space_refine on Fri May 9 13:45:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z66_39793/05_2025/8z66_39793.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z66_39793/05_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_39793/05_2025/8z66_39793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z66_39793/05_2025/8z66_39793.map" model { file = "/net/cci-nas-00/data/ceres_data/8z66_39793/05_2025/8z66_39793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z66_39793/05_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-5687/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: 2.24, per 1000 atoms: 1.01 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: 0.51 Conformation dependent library (CDL) restraints added in 272.0 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: 0.19 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: 0.56 Time building geometry restraints manager: 0.60 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.040 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.410 ------------------------------------------------------------------------------- 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 : 0.233 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: 0.1923 time to fit residues: 9.6660 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 : 0.235 ------------------------------------------------------------------------------- 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: 0.1980 overall best weight: 0.1978 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.143078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.129674 restraints weight = 2964.375| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.36 r_work: 0.3561 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.1600 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= 0.155 Angle : 0.613 5.253 3134 Z= 0.325 Chirality : 0.042 0.133 364 Planarity : 0.006 0.049 389 Dihedral : 4.654 17.698 319 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.96 % Allowed : 11.48 % Favored : 87.56 % 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: 0.19 (0.50), residues: 292 helix: 1.32 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.96 (0.60), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.04508 ( 169) hydrogen bonds : angle 4.74344 ( 498) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.83365 ( 2) covalent geometry : bond 0.00345 ( 2286) covalent geometry : angle 0.61279 ( 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 47 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.217 Fit side-chains REVERT: R 83 TRP cc_start: 0.7362 (t-100) cc_final: 0.6952 (t-100) REVERT: R 102 TYR cc_start: 0.7919 (m-80) cc_final: 0.7355 (m-80) REVERT: R 116 TYR cc_start: 0.8369 (t80) cc_final: 0.7903 (t80) REVERT: R 168 CYS cc_start: 0.6156 (t) cc_final: 0.5919 (t) outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.1636 time to fit residues: 8.7058 Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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: 0.9990 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 10 optimal weight: 0.0980 chunk 21 optimal weight: 0.1980 chunk 1 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.0670 overall best weight: 0.1696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.144717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.130980 restraints weight = 2978.893| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.30 r_work: 0.3584 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2080 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= 0.141 Angle : 0.559 5.471 3134 Z= 0.296 Chirality : 0.040 0.130 364 Planarity : 0.005 0.049 389 Dihedral : 4.324 16.682 319 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.95 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: 0.70 (0.51), residues: 292 helix: 1.71 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -2.81 (0.61), 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 0.012 0.002 PHE R 237 TYR 0.015 0.001 TYR R 66 ARG 0.007 0.001 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 169) hydrogen bonds : angle 4.53303 ( 498) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.76118 ( 2) covalent geometry : bond 0.00311 ( 2286) covalent geometry : angle 0.55846 ( 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 49 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.226 Fit side-chains REVERT: R 102 TYR cc_start: 0.7951 (m-80) cc_final: 0.7363 (m-80) REVERT: R 169 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.5702 (m-10) REVERT: R 244 LEU cc_start: 0.7615 (tp) cc_final: 0.7403 (tp) outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 0.1028 time to fit residues: 5.9329 Evaluate side-chains 50 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 250 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 5 optimal weight: 0.1980 chunk 6 optimal weight: 0.2980 chunk 1 optimal weight: 0.0770 chunk 12 optimal weight: 0.0970 chunk 20 optimal weight: 0.0570 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 2 optimal weight: 0.0670 chunk 25 optimal weight: 0.7980 overall best weight: 0.0992 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.146837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133922 restraints weight = 3002.492| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.31 r_work: 0.3619 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2506 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= 0.122 Angle : 0.545 5.580 3134 Z= 0.284 Chirality : 0.040 0.125 364 Planarity : 0.005 0.055 389 Dihedral : 4.081 15.989 319 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.18 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: 1.01 (0.51), residues: 292 helix: 1.81 (0.37), residues: 212 sheet: None (None), residues: 0 loop : -2.62 (0.64), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 194 HIS 0.003 0.001 HIS R 269 PHE 0.011 0.002 PHE R 107 TYR 0.014 0.001 TYR R 66 ARG 0.006 0.000 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 169) hydrogen bonds : angle 4.35863 ( 498) SS BOND : bond 0.00156 ( 1) SS BOND : angle 1.69928 ( 2) covalent geometry : bond 0.00261 ( 2286) covalent geometry : angle 0.54381 ( 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 44 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.227 Fit side-chains REVERT: R 83 TRP cc_start: 0.7402 (t-100) cc_final: 0.7095 (t-100) REVERT: R 102 TYR cc_start: 0.7907 (m-80) cc_final: 0.7293 (m-80) REVERT: R 121 HIS cc_start: 0.7759 (m90) cc_final: 0.7484 (m-70) REVERT: R 169 PHE cc_start: 0.6023 (OUTLIER) cc_final: 0.5616 (m-10) outliers start: 6 outliers final: 2 residues processed: 42 average time/residue: 0.1355 time to fit residues: 6.8404 Evaluate side-chains 39 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 9 optimal weight: 0.1980 chunk 28 optimal weight: 0.0270 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.0870 chunk 8 optimal weight: 0.3980 chunk 5 optimal weight: 0.2980 chunk 27 optimal weight: 0.2980 overall best weight: 0.1394 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.146326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.133207 restraints weight = 3054.803| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.35 r_work: 0.3611 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2287 Z= 0.125 Angle : 0.540 5.717 3134 Z= 0.285 Chirality : 0.040 0.118 364 Planarity : 0.005 0.052 389 Dihedral : 3.983 15.150 319 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.83 % Allowed : 15.31 % 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: 1.46 (0.52), residues: 292 helix: 2.14 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -2.39 (0.65), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 194 HIS 0.005 0.001 HIS R 79 PHE 0.011 0.001 PHE R 107 TYR 0.013 0.001 TYR R 66 ARG 0.005 0.000 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 169) hydrogen bonds : angle 4.28773 ( 498) SS BOND : bond 0.00094 ( 1) SS BOND : angle 1.42730 ( 2) covalent geometry : bond 0.00271 ( 2286) covalent geometry : angle 0.53915 ( 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 52 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.229 Fit side-chains REVERT: R 102 TYR cc_start: 0.7930 (m-80) cc_final: 0.7308 (m-80) REVERT: R 169 PHE cc_start: 0.6032 (OUTLIER) cc_final: 0.5664 (m-10) outliers start: 8 outliers final: 5 residues processed: 45 average time/residue: 0.1231 time to fit residues: 6.7594 Evaluate side-chains 50 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 295 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 24 optimal weight: 0.0570 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 23 optimal weight: 0.0870 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.145288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131947 restraints weight = 2952.194| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.33 r_work: 0.3597 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2695 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= 0.155 Angle : 0.573 5.783 3134 Z= 0.302 Chirality : 0.041 0.119 364 Planarity : 0.005 0.050 389 Dihedral : 4.131 15.680 319 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.87 % Allowed : 19.14 % 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: 1.41 (0.52), residues: 292 helix: 2.10 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -2.39 (0.67), 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 0.011 0.002 PHE R 107 TYR 0.013 0.002 TYR R 66 ARG 0.009 0.001 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 169) hydrogen bonds : angle 4.33367 ( 498) SS BOND : bond 0.00045 ( 1) SS BOND : angle 1.42398 ( 2) covalent geometry : bond 0.00353 ( 2286) covalent geometry : angle 0.57186 ( 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 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.221 Fit side-chains REVERT: R 102 TYR cc_start: 0.7921 (m-80) cc_final: 0.7299 (m-80) REVERT: R 169 PHE cc_start: 0.6072 (OUTLIER) cc_final: 0.5704 (m-10) outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 0.1634 time to fit residues: 8.1027 Evaluate side-chains 44 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 280 VAL Chi-restraints excluded: chain R residue 295 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 9 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 14 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 3 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 overall best weight: 0.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.146443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133158 restraints weight = 2996.042| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.36 r_work: 0.3614 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2856 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= 0.138 Angle : 0.551 5.761 3134 Z= 0.291 Chirality : 0.040 0.117 364 Planarity : 0.005 0.049 389 Dihedral : 4.026 15.068 319 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % 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: 1.53 (0.51), residues: 292 helix: 2.20 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -2.40 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 83 HIS 0.004 0.001 HIS R 269 PHE 0.011 0.001 PHE R 107 TYR 0.013 0.002 TYR R 66 ARG 0.008 0.001 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 169) hydrogen bonds : angle 4.25203 ( 498) SS BOND : bond 0.00103 ( 1) SS BOND : angle 1.01127 ( 2) covalent geometry : bond 0.00307 ( 2286) covalent geometry : angle 0.55034 ( 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 54 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.228 Fit side-chains REVERT: R 102 TYR cc_start: 0.7873 (m-80) cc_final: 0.7212 (m-80) REVERT: R 169 PHE cc_start: 0.6071 (OUTLIER) cc_final: 0.5681 (m-10) REVERT: R 232 ILE cc_start: 0.7882 (tt) cc_final: 0.7668 (tt) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 0.1391 time to fit residues: 8.2443 Evaluate side-chains 53 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.0870 chunk 23 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 9 optimal weight: 0.0870 chunk 20 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.145635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.132602 restraints weight = 3092.077| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.37 r_work: 0.3605 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2287 Z= 0.150 Angle : 0.560 5.772 3134 Z= 0.298 Chirality : 0.040 0.118 364 Planarity : 0.005 0.049 389 Dihedral : 4.071 15.218 319 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.83 % Allowed : 17.22 % 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: 1.51 (0.51), residues: 292 helix: 2.13 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -2.21 (0.68), 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 0.014 0.002 PHE R 107 TYR 0.013 0.002 TYR R 66 ARG 0.008 0.001 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 169) hydrogen bonds : angle 4.27595 ( 498) SS BOND : bond 0.00090 ( 1) SS BOND : angle 1.07467 ( 2) covalent geometry : bond 0.00340 ( 2286) covalent geometry : angle 0.55991 ( 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 53 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.232 Fit side-chains REVERT: R 102 TYR cc_start: 0.7775 (m-80) cc_final: 0.7147 (m-80) REVERT: R 121 HIS cc_start: 0.7685 (m90) cc_final: 0.7436 (m-70) REVERT: R 169 PHE cc_start: 0.6090 (OUTLIER) cc_final: 0.5698 (m-10) REVERT: R 232 ILE cc_start: 0.7862 (tt) cc_final: 0.7654 (tt) REVERT: R 272 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7714 (mp) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.1399 time to fit residues: 7.9817 Evaluate side-chains 52 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 265 PHE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 22 optimal weight: 0.3980 chunk 12 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.0670 chunk 19 optimal weight: 0.0870 chunk 23 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 21 optimal weight: 0.0980 overall best weight: 0.1296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.147245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.134719 restraints weight = 3035.813| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.34 r_work: 0.3632 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2287 Z= 0.123 Angle : 0.541 5.700 3134 Z= 0.286 Chirality : 0.039 0.114 364 Planarity : 0.005 0.049 389 Dihedral : 3.880 15.552 319 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.83 % Allowed : 17.70 % 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: 1.81 (0.52), residues: 292 helix: 2.34 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -2.08 (0.68), residues: 81 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 0.014 0.001 PHE R 107 TYR 0.013 0.001 TYR R 66 ARG 0.008 0.001 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 169) hydrogen bonds : angle 4.18111 ( 498) SS BOND : bond 0.00165 ( 1) SS BOND : angle 1.88843 ( 2) covalent geometry : bond 0.00266 ( 2286) covalent geometry : angle 0.53865 ( 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 48 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.226 Fit side-chains REVERT: R 27 VAL cc_start: 0.6694 (t) cc_final: 0.6260 (t) REVERT: R 102 TYR cc_start: 0.7708 (m-80) cc_final: 0.7158 (m-80) REVERT: R 121 HIS cc_start: 0.7673 (m90) cc_final: 0.7362 (m-70) REVERT: R 169 PHE cc_start: 0.6028 (OUTLIER) cc_final: 0.5663 (m-10) REVERT: R 272 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7722 (mp) outliers start: 8 outliers final: 4 residues processed: 43 average time/residue: 0.1031 time to fit residues: 5.5872 Evaluate side-chains 45 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 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 196 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 3 optimal weight: 0.1980 chunk 25 optimal weight: 0.4980 chunk 10 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 0.0980 chunk 16 optimal weight: 0.0570 chunk 24 optimal weight: 0.0770 chunk 1 optimal weight: 0.0870 chunk 18 optimal weight: 0.0870 overall best weight: 0.0812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.150031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137748 restraints weight = 2988.285| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.31 r_work: 0.3672 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3364 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= 0.113 Angle : 0.529 5.689 3134 Z= 0.277 Chirality : 0.038 0.113 364 Planarity : 0.005 0.048 389 Dihedral : 3.718 15.239 319 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.35 % Allowed : 19.14 % Favored : 77.51 % 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: 1.97 (0.51), residues: 292 helix: 2.45 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -2.05 (0.68), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 83 HIS 0.004 0.001 HIS R 269 PHE 0.013 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 0.03293 ( 169) hydrogen bonds : angle 4.03674 ( 498) SS BOND : bond 0.00163 ( 1) SS BOND : angle 1.31239 ( 2) covalent geometry : bond 0.00235 ( 2286) covalent geometry : angle 0.52803 ( 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 40 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.228 Fit side-chains REVERT: R 27 VAL cc_start: 0.6546 (t) cc_final: 0.6050 (t) REVERT: R 102 TYR cc_start: 0.7674 (m-80) cc_final: 0.7104 (m-80) REVERT: R 121 HIS cc_start: 0.7672 (m90) cc_final: 0.7467 (m-70) REVERT: R 169 PHE cc_start: 0.5923 (OUTLIER) cc_final: 0.5563 (m-10) REVERT: R 272 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7718 (mp) outliers start: 7 outliers final: 5 residues processed: 36 average time/residue: 0.1189 time to fit residues: 5.3584 Evaluate side-chains 39 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 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 183 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 0.0030 chunk 12 optimal weight: 0.0970 chunk 7 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.2386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.147415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.134410 restraints weight = 2980.509| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.37 r_work: 0.3626 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2287 Z= 0.152 Angle : 0.572 5.782 3134 Z= 0.299 Chirality : 0.041 0.119 364 Planarity : 0.005 0.049 389 Dihedral : 3.944 15.702 319 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.87 % Allowed : 19.14 % 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: 1.70 (0.51), residues: 292 helix: 2.22 (0.35), residues: 213 sheet: None (None), residues: 0 loop : -2.09 (0.70), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 83 HIS 0.005 0.001 HIS R 302 PHE 0.012 0.002 PHE R 107 TYR 0.011 0.002 TYR R 66 ARG 0.008 0.001 ARG R 130 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 169) hydrogen bonds : angle 4.21632 ( 498) SS BOND : bond 0.00095 ( 1) SS BOND : angle 1.97045 ( 2) covalent geometry : bond 0.00344 ( 2286) covalent geometry : angle 0.56965 ( 3132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1777.92 seconds wall clock time: 31 minutes 42.73 seconds (1902.73 seconds total)