Starting phenix.real_space_refine on Tue Feb 3 17:49:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jl6_61579/02_2026/9jl6_61579.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jl6_61579/02_2026/9jl6_61579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jl6_61579/02_2026/9jl6_61579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jl6_61579/02_2026/9jl6_61579.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jl6_61579/02_2026/9jl6_61579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jl6_61579/02_2026/9jl6_61579.map" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 30 5.16 5 C 3694 2.51 5 N 1004 2.21 5 O 1062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5790 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2895 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 22, 'TRANS': 359} Chain: "B" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2895 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 22, 'TRANS': 359} Time building chain proxies: 1.43, per 1000 atoms: 0.25 Number of scatterers: 5790 At special positions: 0 Unit cell: (89.832, 71.708, 73.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1062 8.00 N 1004 7.00 C 3694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 322.5 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 46.2% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 41 through 50 removed outlier: 3.556A pdb=" N THR A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 68 Processing helix chain 'A' and resid 79 through 86 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 106 through 124 Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.512A pdb=" N LEU A 215 " --> pdb=" O HIS A 211 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 293 removed outlier: 4.871A pdb=" N GLU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LYS A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.616A pdb=" N LEU A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 329 Processing helix chain 'A' and resid 330 through 341 removed outlier: 3.612A pdb=" N ARG A 334 " --> pdb=" O MET A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 362 removed outlier: 4.239A pdb=" N VAL A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'B' and resid 41 through 50 removed outlier: 3.578A pdb=" N THR B 50 " --> pdb=" O PHE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 69 Processing helix chain 'B' and resid 80 through 86 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.536A pdb=" N THR B 91 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 124 Proline residue: B 109 - end of helix Processing helix chain 'B' and resid 126 through 130 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 171 through 187 Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 276 through 285 Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.666A pdb=" N LEU B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU B 291 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'B' and resid 312 through 324 removed outlier: 3.575A pdb=" N LEU B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 329 Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.518A pdb=" N ARG B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 363 removed outlier: 4.338A pdb=" N VAL B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 31 removed outlier: 6.218A pdb=" N VAL A 229 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE A 28 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 227 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR A 30 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA A 225 " --> pdb=" O THR A 30 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N HIS A 132 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL A 195 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL A 134 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE A 133 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N MET A 165 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE A 135 " --> pdb=" O MET A 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 265 Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 31 removed outlier: 6.203A pdb=" N VAL B 229 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE B 28 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 227 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR B 30 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA B 225 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N HIS B 132 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL B 195 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL B 134 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE B 133 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N MET B 165 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE B 135 " --> pdb=" O MET B 165 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA7, first strand: chain 'B' and resid 243 through 245 Processing sheet with id=AA8, first strand: chain 'B' and resid 260 through 265 removed outlier: 3.797A pdb=" N ASP B 261 " --> pdb=" O HIS B 272 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 744 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: 0.86 Time building geometry restraints manager: 0.62 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: 1916 1.34 - 1.46: 1125 1.46 - 1.58: 2825 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 5916 Sorted by residual: bond pdb=" N ASN A 302 " pdb=" CA ASN A 302 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.16e-02 7.43e+03 9.17e+00 bond pdb=" N ILE B 281 " pdb=" CA ILE B 281 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.49e+00 bond pdb=" N ILE A 281 " pdb=" CA ILE A 281 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.19e+00 bond pdb=" N VAL A 296 " pdb=" CA VAL A 296 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.17e-02 7.31e+03 6.59e+00 bond pdb=" N GLU A 303 " pdb=" CA GLU A 303 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.19e-02 7.06e+03 6.26e+00 ... (remaining 5911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 7815 1.88 - 3.75: 159 3.75 - 5.63: 21 5.63 - 7.50: 4 7.50 - 9.38: 3 Bond angle restraints: 8002 Sorted by residual: angle pdb=" N PRO A 299 " pdb=" CA PRO A 299 " pdb=" C PRO A 299 " ideal model delta sigma weight residual 112.47 103.09 9.38 2.06e+00 2.36e-01 2.07e+01 angle pdb=" N VAL A 238 " pdb=" CA VAL A 238 " pdb=" C VAL A 238 " ideal model delta sigma weight residual 111.62 108.60 3.02 7.90e-01 1.60e+00 1.46e+01 angle pdb=" N LEU B 273 " pdb=" CA LEU B 273 " pdb=" CB LEU B 273 " ideal model delta sigma weight residual 110.24 105.28 4.96 1.45e+00 4.76e-01 1.17e+01 angle pdb=" CA ILE B 281 " pdb=" C ILE B 281 " pdb=" O ILE B 281 " ideal model delta sigma weight residual 121.17 117.90 3.27 1.06e+00 8.90e-01 9.54e+00 angle pdb=" N GLU A 303 " pdb=" CA GLU A 303 " pdb=" C GLU A 303 " ideal model delta sigma weight residual 111.87 107.56 4.31 1.41e+00 5.03e-01 9.36e+00 ... (remaining 7997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 3025 17.59 - 35.17: 377 35.17 - 52.75: 118 52.75 - 70.34: 32 70.34 - 87.92: 4 Dihedral angle restraints: 3556 sinusoidal: 1408 harmonic: 2148 Sorted by residual: dihedral pdb=" CA ASP B 328 " pdb=" CB ASP B 328 " pdb=" CG ASP B 328 " pdb=" OD1 ASP B 328 " ideal model delta sinusoidal sigma weight residual -30.00 -89.86 59.86 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP A 328 " pdb=" CB ASP A 328 " pdb=" CG ASP A 328 " pdb=" OD1 ASP A 328 " ideal model delta sinusoidal sigma weight residual -30.00 -89.13 59.13 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CG ARG B 18 " pdb=" CD ARG B 18 " pdb=" NE ARG B 18 " pdb=" CZ ARG B 18 " ideal model delta sinusoidal sigma weight residual -180.00 -135.24 -44.76 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 3553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 720 0.056 - 0.111: 154 0.111 - 0.167: 15 0.167 - 0.223: 2 0.223 - 0.279: 1 Chirality restraints: 892 Sorted by residual: chirality pdb=" CA VAL A 296 " pdb=" N VAL A 296 " pdb=" C VAL A 296 " pdb=" CB VAL A 296 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA ILE B 281 " pdb=" N ILE B 281 " pdb=" C ILE B 281 " pdb=" CB ILE B 281 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA ILE A 281 " pdb=" N ILE A 281 " pdb=" C ILE A 281 " pdb=" CB ILE A 281 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 889 not shown) Planarity restraints: 1042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 143 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 144 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 143 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO B 144 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 144 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 144 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 298 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO B 299 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 299 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 299 " -0.018 5.00e-02 4.00e+02 ... (remaining 1039 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 69 2.57 - 3.16: 4744 3.16 - 3.74: 9930 3.74 - 4.32: 13891 4.32 - 4.90: 22929 Nonbonded interactions: 51563 Sorted by model distance: nonbonded pdb=" CG2 ILE B 130 " pdb=" CD2 LEU B 156 " model vdw 1.992 3.880 nonbonded pdb=" CB ILE B 130 " pdb=" CD2 LEU B 156 " model vdw 2.134 3.890 nonbonded pdb=" O PRO B 278 " pdb=" OG SER B 282 " model vdw 2.154 3.040 nonbonded pdb=" O LEU B 253 " pdb=" OG SER B 256 " model vdw 2.189 3.040 nonbonded pdb=" NH1 ARG A 162 " pdb=" CG2 THR B 384 " model vdw 2.195 3.540 ... (remaining 51558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.460 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.060 Find NCS groups from input model: 0.040 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:8.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 0.004 0.035 5916 Z= 0.199 Angle : 0.646 9.377 8002 Z= 0.349 Chirality : 0.046 0.279 892 Planarity : 0.004 0.038 1042 Dihedral : 17.744 87.923 2180 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 32.95 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.32), residues: 760 helix: 0.43 (0.32), residues: 298 sheet: -1.44 (0.51), residues: 106 loop : -0.98 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 18 TYR 0.007 0.001 TYR A 166 PHE 0.015 0.002 PHE B 271 TRP 0.008 0.001 TRP A 301 HIS 0.002 0.001 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5916) covalent geometry : angle 0.64637 ( 8002) hydrogen bonds : bond 0.14490 ( 262) hydrogen bonds : angle 7.27484 ( 744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.204 Fit side-chains REVERT: A 18 ARG cc_start: 0.7247 (ttt180) cc_final: 0.6787 (ttt-90) REVERT: A 40 SER cc_start: 0.8161 (m) cc_final: 0.7776 (p) REVERT: A 41 GLU cc_start: 0.7744 (tm-30) cc_final: 0.6993 (tm-30) REVERT: A 126 ARG cc_start: 0.7238 (tpp80) cc_final: 0.6276 (tmt170) REVERT: A 274 MET cc_start: 0.4417 (mmt) cc_final: 0.3887 (mmt) REVERT: A 303 GLU cc_start: 0.5410 (tm-30) cc_final: 0.4996 (tm-30) REVERT: B 40 SER cc_start: 0.8218 (m) cc_final: 0.7989 (p) REVERT: B 41 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7271 (tm-30) REVERT: B 93 MET cc_start: 0.5928 (mmm) cc_final: 0.5306 (mpp) REVERT: B 126 ARG cc_start: 0.7297 (ttm170) cc_final: 0.6301 (tmt170) REVERT: B 290 ASN cc_start: 0.6801 (m-40) cc_final: 0.5878 (p0) REVERT: B 327 LYS cc_start: 0.6591 (tptp) cc_final: 0.6295 (tptp) REVERT: B 344 SER cc_start: 0.8629 (m) cc_final: 0.8314 (t) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.5599 time to fit residues: 51.5369 Evaluate side-chains 77 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 86 ASN B 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.181643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.158747 restraints weight = 6855.512| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.25 r_work: 0.3921 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 5916 Z= 0.244 Angle : 0.688 6.803 8002 Z= 0.352 Chirality : 0.047 0.165 892 Planarity : 0.005 0.041 1042 Dihedral : 5.017 16.130 804 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 6.56 % Allowed : 26.72 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.31), residues: 760 helix: 0.11 (0.30), residues: 302 sheet: -1.16 (0.47), residues: 126 loop : -0.94 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 18 TYR 0.011 0.002 TYR A 166 PHE 0.024 0.003 PHE A 305 TRP 0.008 0.002 TRP B 306 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 5916) covalent geometry : angle 0.68798 ( 8002) hydrogen bonds : bond 0.05494 ( 262) hydrogen bonds : angle 6.15506 ( 744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 83 time to evaluate : 0.355 Fit side-chains REVERT: A 18 ARG cc_start: 0.7285 (ttt180) cc_final: 0.7026 (ttt180) REVERT: A 41 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6616 (tm-30) REVERT: A 94 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: A 126 ARG cc_start: 0.7319 (tpp80) cc_final: 0.6311 (tmt170) REVERT: A 188 LYS cc_start: 0.7372 (tppt) cc_final: 0.6751 (tptt) REVERT: A 274 MET cc_start: 0.4365 (mmt) cc_final: 0.3825 (mmt) REVERT: A 303 GLU cc_start: 0.5770 (OUTLIER) cc_final: 0.5188 (tm-30) REVERT: B 41 GLU cc_start: 0.7906 (mt-10) cc_final: 0.6777 (tm-30) REVERT: B 74 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.6411 (ttp80) REVERT: B 93 MET cc_start: 0.5955 (OUTLIER) cc_final: 0.5358 (mpp) REVERT: B 126 ARG cc_start: 0.7252 (ttm170) cc_final: 0.6095 (tmt170) REVERT: B 129 ASP cc_start: 0.5822 (t0) cc_final: 0.5582 (t0) REVERT: B 274 MET cc_start: 0.5423 (mpt) cc_final: 0.5123 (mpt) REVERT: B 290 ASN cc_start: 0.6849 (m-40) cc_final: 0.6051 (p0) REVERT: B 327 LYS cc_start: 0.6660 (tptp) cc_final: 0.6430 (tptp) REVERT: B 344 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8203 (t) outliers start: 40 outliers final: 20 residues processed: 110 average time/residue: 0.4697 time to fit residues: 54.4996 Evaluate side-chains 103 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 384 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 86 ASN ** B 167 GLN ** 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 = 0.4226 r_free = 0.4226 target = 0.179190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.156371 restraints weight = 6805.644| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.20 r_work: 0.3894 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 5916 Z= 0.268 Angle : 0.710 5.935 8002 Z= 0.365 Chirality : 0.049 0.166 892 Planarity : 0.006 0.039 1042 Dihedral : 5.307 18.286 804 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 6.39 % Allowed : 27.87 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.30), residues: 760 helix: -0.21 (0.29), residues: 304 sheet: -0.99 (0.51), residues: 106 loop : -1.12 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 18 TYR 0.013 0.002 TYR A 166 PHE 0.025 0.003 PHE A 305 TRP 0.011 0.002 TRP B 306 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 5916) covalent geometry : angle 0.70969 ( 8002) hydrogen bonds : bond 0.05389 ( 262) hydrogen bonds : angle 6.14374 ( 744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 0.174 Fit side-chains REVERT: A 18 ARG cc_start: 0.7380 (ttt180) cc_final: 0.7022 (ttt180) REVERT: A 41 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6519 (tm-30) REVERT: A 94 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: A 126 ARG cc_start: 0.7296 (tpp80) cc_final: 0.6280 (tmt170) REVERT: A 188 LYS cc_start: 0.7414 (tppt) cc_final: 0.6791 (tptt) REVERT: A 274 MET cc_start: 0.4379 (mmt) cc_final: 0.3817 (mmt) REVERT: B 41 GLU cc_start: 0.7887 (mt-10) cc_final: 0.6693 (tm-30) REVERT: B 74 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.6833 (mtp85) REVERT: B 126 ARG cc_start: 0.7191 (ttm170) cc_final: 0.6049 (tmt170) REVERT: B 129 ASP cc_start: 0.5788 (t0) cc_final: 0.5564 (t0) REVERT: B 274 MET cc_start: 0.5319 (mpt) cc_final: 0.4998 (mpt) outliers start: 39 outliers final: 19 residues processed: 109 average time/residue: 0.4275 time to fit residues: 48.9655 Evaluate side-chains 97 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 384 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 0.0070 chunk 64 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 86 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 HIS B 357 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.185230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.162405 restraints weight = 6793.089| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.23 r_work: 0.3960 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5916 Z= 0.140 Angle : 0.598 5.712 8002 Z= 0.303 Chirality : 0.044 0.151 892 Planarity : 0.005 0.036 1042 Dihedral : 4.800 16.384 804 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.57 % Allowed : 29.34 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.31), residues: 760 helix: 0.13 (0.30), residues: 302 sheet: -1.02 (0.52), residues: 106 loop : -0.99 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.007 0.001 TYR A 166 PHE 0.019 0.002 PHE A 271 TRP 0.009 0.001 TRP A 301 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5916) covalent geometry : angle 0.59766 ( 8002) hydrogen bonds : bond 0.04265 ( 262) hydrogen bonds : angle 5.77227 ( 744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 78 time to evaluate : 0.210 Fit side-chains REVERT: A 41 GLU cc_start: 0.7532 (tm-30) cc_final: 0.6663 (tm-30) REVERT: A 94 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: A 126 ARG cc_start: 0.7307 (tpp80) cc_final: 0.6274 (tmt170) REVERT: A 188 LYS cc_start: 0.7290 (tppt) cc_final: 0.6654 (tptt) REVERT: A 274 MET cc_start: 0.4305 (mmt) cc_final: 0.3762 (mmt) REVERT: A 303 GLU cc_start: 0.5649 (OUTLIER) cc_final: 0.5090 (tm-30) REVERT: A 323 LEU cc_start: 0.3824 (OUTLIER) cc_final: 0.3364 (tt) REVERT: A 327 LYS cc_start: 0.6509 (tptp) cc_final: 0.6294 (tptp) REVERT: B 41 GLU cc_start: 0.7843 (mt-10) cc_final: 0.6626 (tm-30) REVERT: B 74 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8139 (tpp80) REVERT: B 126 ARG cc_start: 0.7195 (ttm170) cc_final: 0.6086 (tmt170) REVERT: B 274 MET cc_start: 0.5280 (mpt) cc_final: 0.4980 (mpt) REVERT: B 290 ASN cc_start: 0.6813 (m-40) cc_final: 0.5992 (p0) outliers start: 34 outliers final: 18 residues processed: 106 average time/residue: 0.4347 time to fit residues: 48.5631 Evaluate side-chains 96 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 384 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 0.0010 chunk 73 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 272 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.186809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.163675 restraints weight = 6847.482| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.27 r_work: 0.3976 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5916 Z= 0.137 Angle : 0.578 5.796 8002 Z= 0.291 Chirality : 0.044 0.148 892 Planarity : 0.005 0.038 1042 Dihedral : 4.649 16.127 804 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.41 % Allowed : 29.18 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.31), residues: 760 helix: 0.21 (0.30), residues: 302 sheet: -1.28 (0.50), residues: 114 loop : -0.93 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 18 TYR 0.007 0.002 TYR B 204 PHE 0.017 0.002 PHE A 305 TRP 0.008 0.001 TRP A 301 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5916) covalent geometry : angle 0.57781 ( 8002) hydrogen bonds : bond 0.04083 ( 262) hydrogen bonds : angle 5.61784 ( 744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 0.213 Fit side-chains REVERT: A 41 GLU cc_start: 0.7491 (tm-30) cc_final: 0.6644 (tm-30) REVERT: A 94 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: A 121 LYS cc_start: 0.6239 (OUTLIER) cc_final: 0.5705 (mmpt) REVERT: A 126 ARG cc_start: 0.7245 (tpp80) cc_final: 0.6305 (tmt170) REVERT: A 274 MET cc_start: 0.4150 (mmt) cc_final: 0.3626 (mmt) REVERT: A 303 GLU cc_start: 0.5507 (OUTLIER) cc_final: 0.5012 (tm-30) REVERT: A 323 LEU cc_start: 0.3763 (OUTLIER) cc_final: 0.3300 (tt) REVERT: B 20 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7603 (pm20) REVERT: B 41 GLU cc_start: 0.7743 (mt-10) cc_final: 0.6608 (tm-30) REVERT: B 93 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5018 (ttm) REVERT: B 126 ARG cc_start: 0.7220 (ttm170) cc_final: 0.6258 (tmt170) REVERT: B 274 MET cc_start: 0.5225 (mpt) cc_final: 0.4959 (mpt) REVERT: B 290 ASN cc_start: 0.6763 (m-40) cc_final: 0.6018 (p0) outliers start: 33 outliers final: 17 residues processed: 103 average time/residue: 0.4126 time to fit residues: 44.7744 Evaluate side-chains 98 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 384 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.0270 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 86 ASN B 167 GLN B 272 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.185096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.162160 restraints weight = 6763.182| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.24 r_work: 0.3959 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3854 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5916 Z= 0.166 Angle : 0.612 5.701 8002 Z= 0.308 Chirality : 0.045 0.150 892 Planarity : 0.005 0.038 1042 Dihedral : 4.749 16.015 804 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 6.39 % Allowed : 29.02 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.31), residues: 760 helix: 0.12 (0.30), residues: 302 sheet: -0.96 (0.53), residues: 106 loop : -0.97 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 74 TYR 0.008 0.002 TYR A 166 PHE 0.019 0.002 PHE A 305 TRP 0.007 0.001 TRP A 306 HIS 0.002 0.001 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5916) covalent geometry : angle 0.61162 ( 8002) hydrogen bonds : bond 0.04265 ( 262) hydrogen bonds : angle 5.65218 ( 744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 0.165 Fit side-chains REVERT: A 41 GLU cc_start: 0.7516 (tm-30) cc_final: 0.6639 (tm-30) REVERT: A 94 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7506 (tt0) REVERT: A 126 ARG cc_start: 0.7302 (tpp80) cc_final: 0.6238 (tmt170) REVERT: A 188 LYS cc_start: 0.7320 (tppt) cc_final: 0.6701 (tptt) REVERT: A 274 MET cc_start: 0.4283 (mmt) cc_final: 0.3750 (mmt) REVERT: A 303 GLU cc_start: 0.5657 (OUTLIER) cc_final: 0.5101 (tm-30) REVERT: B 20 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7649 (pm20) REVERT: B 41 GLU cc_start: 0.7835 (mt-10) cc_final: 0.6586 (tm-30) REVERT: B 93 MET cc_start: 0.5998 (OUTLIER) cc_final: 0.5032 (ttm) REVERT: B 126 ARG cc_start: 0.7245 (ttm170) cc_final: 0.6168 (tmt170) REVERT: B 274 MET cc_start: 0.5263 (mpt) cc_final: 0.4967 (mpt) REVERT: B 290 ASN cc_start: 0.6814 (m-40) cc_final: 0.6020 (p0) REVERT: B 303 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5546 (tp30) outliers start: 39 outliers final: 24 residues processed: 103 average time/residue: 0.3773 time to fit residues: 41.0269 Evaluate side-chains 103 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 384 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.0030 chunk 63 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.185142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.162009 restraints weight = 6887.184| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.27 r_work: 0.3958 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5916 Z= 0.164 Angle : 0.618 6.394 8002 Z= 0.311 Chirality : 0.045 0.150 892 Planarity : 0.005 0.038 1042 Dihedral : 4.761 16.021 804 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.90 % Allowed : 29.18 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.31), residues: 760 helix: 0.12 (0.30), residues: 306 sheet: -1.28 (0.50), residues: 114 loop : -0.84 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 74 TYR 0.008 0.002 TYR A 166 PHE 0.019 0.002 PHE A 305 TRP 0.006 0.001 TRP A 301 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5916) covalent geometry : angle 0.61809 ( 8002) hydrogen bonds : bond 0.04257 ( 262) hydrogen bonds : angle 5.64636 ( 744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 71 time to evaluate : 0.204 Fit side-chains REVERT: A 41 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6605 (tm-30) REVERT: A 94 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: A 126 ARG cc_start: 0.7198 (tpp80) cc_final: 0.6295 (tmt170) REVERT: A 188 LYS cc_start: 0.7330 (tppt) cc_final: 0.6703 (tptt) REVERT: A 274 MET cc_start: 0.4111 (mmt) cc_final: 0.3593 (mmt) REVERT: A 303 GLU cc_start: 0.5533 (OUTLIER) cc_final: 0.5033 (tm-30) REVERT: B 20 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: B 41 GLU cc_start: 0.7745 (mt-10) cc_final: 0.6590 (tm-30) REVERT: B 93 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.4979 (ttm) REVERT: B 126 ARG cc_start: 0.7184 (ttm170) cc_final: 0.6214 (tmt170) REVERT: B 274 MET cc_start: 0.5233 (mpt) cc_final: 0.4955 (mpt) REVERT: B 290 ASN cc_start: 0.6753 (m-40) cc_final: 0.6022 (p0) REVERT: B 303 GLU cc_start: 0.5666 (OUTLIER) cc_final: 0.5444 (tp30) outliers start: 36 outliers final: 24 residues processed: 98 average time/residue: 0.3559 time to fit residues: 37.0014 Evaluate side-chains 100 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 384 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 5.9990 chunk 69 optimal weight: 0.0770 chunk 55 optimal weight: 0.0470 chunk 44 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN B 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.187018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.164335 restraints weight = 6720.602| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.23 r_work: 0.3987 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5916 Z= 0.134 Angle : 0.599 6.649 8002 Z= 0.299 Chirality : 0.044 0.146 892 Planarity : 0.005 0.037 1042 Dihedral : 4.615 15.766 804 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 6.23 % Allowed : 29.02 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.32), residues: 760 helix: 0.21 (0.30), residues: 306 sheet: -1.26 (0.50), residues: 114 loop : -0.77 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 74 TYR 0.007 0.001 TYR B 204 PHE 0.016 0.002 PHE A 305 TRP 0.009 0.001 TRP A 301 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5916) covalent geometry : angle 0.59945 ( 8002) hydrogen bonds : bond 0.03950 ( 262) hydrogen bonds : angle 5.54721 ( 744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 73 time to evaluate : 0.212 Fit side-chains REVERT: A 41 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6574 (tm-30) REVERT: A 94 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: A 121 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5675 (mmpt) REVERT: A 126 ARG cc_start: 0.7275 (tpp80) cc_final: 0.6277 (tmt170) REVERT: A 274 MET cc_start: 0.4261 (mmt) cc_final: 0.3752 (mmt) REVERT: A 303 GLU cc_start: 0.5697 (OUTLIER) cc_final: 0.5140 (tm-30) REVERT: A 323 LEU cc_start: 0.3786 (OUTLIER) cc_final: 0.3365 (tt) REVERT: B 20 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: B 41 GLU cc_start: 0.7798 (mt-10) cc_final: 0.6553 (tm-30) REVERT: B 93 MET cc_start: 0.5899 (OUTLIER) cc_final: 0.5002 (ttm) REVERT: B 126 ARG cc_start: 0.7223 (ttm170) cc_final: 0.6190 (tmt170) REVERT: B 274 MET cc_start: 0.5235 (mpt) cc_final: 0.4944 (mpt) REVERT: B 285 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7493 (tp) REVERT: B 290 ASN cc_start: 0.6776 (m-40) cc_final: 0.5963 (p0) REVERT: B 303 GLU cc_start: 0.5782 (OUTLIER) cc_final: 0.5464 (tp30) outliers start: 38 outliers final: 16 residues processed: 104 average time/residue: 0.4297 time to fit residues: 47.1078 Evaluate side-chains 96 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 384 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 86 ASN B 167 GLN B 272 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.186002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.162774 restraints weight = 6846.071| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.27 r_work: 0.3966 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5916 Z= 0.166 Angle : 0.638 8.282 8002 Z= 0.319 Chirality : 0.045 0.149 892 Planarity : 0.005 0.038 1042 Dihedral : 4.746 15.715 804 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.90 % Allowed : 29.51 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.31), residues: 760 helix: 0.10 (0.30), residues: 306 sheet: -1.25 (0.51), residues: 114 loop : -0.78 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.008 0.002 TYR A 166 PHE 0.018 0.002 PHE A 305 TRP 0.006 0.001 TRP A 301 HIS 0.002 0.001 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5916) covalent geometry : angle 0.63751 ( 8002) hydrogen bonds : bond 0.04162 ( 262) hydrogen bonds : angle 5.61762 ( 744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 0.161 Fit side-chains REVERT: A 41 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6574 (tm-30) REVERT: A 94 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: A 126 ARG cc_start: 0.7209 (tpp80) cc_final: 0.6290 (tmt170) REVERT: A 188 LYS cc_start: 0.7315 (tppt) cc_final: 0.6688 (tptt) REVERT: A 274 MET cc_start: 0.4160 (mmt) cc_final: 0.3637 (mmt) REVERT: A 303 GLU cc_start: 0.5575 (OUTLIER) cc_final: 0.5069 (tm-30) REVERT: B 41 GLU cc_start: 0.7741 (mt-10) cc_final: 0.6586 (tm-30) REVERT: B 93 MET cc_start: 0.5830 (OUTLIER) cc_final: 0.4969 (ttm) REVERT: B 126 ARG cc_start: 0.7220 (ttm170) cc_final: 0.6231 (tmt170) REVERT: B 274 MET cc_start: 0.5218 (mpt) cc_final: 0.4948 (mpt) REVERT: B 290 ASN cc_start: 0.6763 (m-40) cc_final: 0.6008 (p0) REVERT: B 303 GLU cc_start: 0.5639 (OUTLIER) cc_final: 0.5426 (tp30) outliers start: 36 outliers final: 24 residues processed: 99 average time/residue: 0.4443 time to fit residues: 46.4991 Evaluate side-chains 99 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 384 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 27 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 7 optimal weight: 0.0020 chunk 69 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN B 86 ASN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** 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 = 0.4321 r_free = 0.4321 target = 0.189069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.165944 restraints weight = 6851.170| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.28 r_work: 0.4002 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5916 Z= 0.130 Angle : 0.613 8.667 8002 Z= 0.305 Chirality : 0.044 0.143 892 Planarity : 0.005 0.036 1042 Dihedral : 4.575 15.453 804 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.08 % Allowed : 30.98 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.32), residues: 760 helix: 0.32 (0.31), residues: 306 sheet: -1.61 (0.49), residues: 126 loop : -0.57 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.006 0.001 TYR A 166 PHE 0.015 0.002 PHE B 271 TRP 0.011 0.001 TRP A 301 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5916) covalent geometry : angle 0.61293 ( 8002) hydrogen bonds : bond 0.03847 ( 262) hydrogen bonds : angle 5.49910 ( 744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.215 Fit side-chains REVERT: A 41 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6617 (tm-30) REVERT: A 94 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: A 126 ARG cc_start: 0.7148 (tpp80) cc_final: 0.6308 (tmt170) REVERT: A 274 MET cc_start: 0.3971 (mmt) cc_final: 0.3528 (mmt) REVERT: A 303 GLU cc_start: 0.5562 (OUTLIER) cc_final: 0.5090 (tm-30) REVERT: A 323 LEU cc_start: 0.3782 (OUTLIER) cc_final: 0.3379 (tt) REVERT: B 20 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: B 41 GLU cc_start: 0.7702 (mt-10) cc_final: 0.6542 (tm-30) REVERT: B 93 MET cc_start: 0.5720 (OUTLIER) cc_final: 0.4923 (ttm) REVERT: B 126 ARG cc_start: 0.7195 (ttm170) cc_final: 0.6290 (tmt170) REVERT: B 274 MET cc_start: 0.5130 (mpt) cc_final: 0.4866 (mpt) REVERT: B 285 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7406 (tp) REVERT: B 290 ASN cc_start: 0.6681 (m-40) cc_final: 0.5948 (p0) outliers start: 31 outliers final: 21 residues processed: 98 average time/residue: 0.4441 time to fit residues: 45.9098 Evaluate side-chains 98 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 384 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** 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 = 0.4311 r_free = 0.4311 target = 0.188024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.165351 restraints weight = 6733.484| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.22 r_work: 0.3998 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5916 Z= 0.145 Angle : 0.638 12.554 8002 Z= 0.322 Chirality : 0.045 0.146 892 Planarity : 0.005 0.043 1042 Dihedral : 4.590 15.732 804 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.59 % Allowed : 31.31 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.32), residues: 760 helix: 0.15 (0.30), residues: 306 sheet: -1.56 (0.49), residues: 126 loop : -0.64 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 74 TYR 0.007 0.001 TYR A 166 PHE 0.019 0.002 PHE B 305 TRP 0.009 0.001 TRP A 301 HIS 0.003 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5916) covalent geometry : angle 0.63766 ( 8002) hydrogen bonds : bond 0.03950 ( 262) hydrogen bonds : angle 5.49984 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2169.25 seconds wall clock time: 37 minutes 47.13 seconds (2267.13 seconds total)