Starting phenix.real_space_refine on Tue Feb 3 13:38:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lvw_63425/02_2026/9lvw_63425_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lvw_63425/02_2026/9lvw_63425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lvw_63425/02_2026/9lvw_63425_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lvw_63425/02_2026/9lvw_63425_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lvw_63425/02_2026/9lvw_63425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lvw_63425/02_2026/9lvw_63425.map" } resolution = 3.41 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= 0.034 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 19 5.16 5 C 2127 2.51 5 N 490 2.21 5 O 589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 3226 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3083 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 15, 'TRANS': 388} Chain breaks: 1 Chain: "A" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 143 Unusual residues: {'LMN': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 0.60, per 1000 atoms: 0.19 Number of scatterers: 3226 At special positions: 0 Unit cell: (76.5, 56.95, 73.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 1 15.00 O 589 8.00 N 490 7.00 C 2127 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: 0.21 Conformation dependent library (CDL) restraints added in 73.4 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 726 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 84.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 5 through 27 removed outlier: 4.166A pdb=" N TYR A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 36 through 39 removed outlier: 3.783A pdb=" N VAL A 39 " --> pdb=" O PRO A 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 39' Processing helix chain 'A' and resid 45 through 71 removed outlier: 3.525A pdb=" N LEU A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.695A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 4.188A pdb=" N CYS A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 161 removed outlier: 3.875A pdb=" N TRP A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N MET A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 165 through 187 removed outlier: 3.634A pdb=" N LEU A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.447A pdb=" N VAL A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 190 through 195' Processing helix chain 'A' and resid 216 through 222 removed outlier: 3.555A pdb=" N LEU A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 4.009A pdb=" N TRP A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLN A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 290 removed outlier: 4.303A pdb=" N SER A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 321 removed outlier: 3.544A pdb=" N LEU A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 356 removed outlier: 3.701A pdb=" N ILE A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Proline residue: A 345 - end of helix Processing helix chain 'A' and resid 361 through 372 removed outlier: 3.627A pdb=" N SER A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 392 through 414 removed outlier: 3.690A pdb=" N ALA A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) 226 hydrogen bonds defined for protein. 678 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: 0.28 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 562 1.33 - 1.45: 890 1.45 - 1.57: 1814 1.57 - 1.69: 21 1.69 - 1.81: 31 Bond restraints: 3318 Sorted by residual: bond pdb=" C5 LMN A 501 " pdb=" O5 LMN A 501 " ideal model delta sigma weight residual 1.413 1.548 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C5 LMN A 502 " pdb=" O5 LMN A 502 " ideal model delta sigma weight residual 1.413 1.543 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C5 LMN A 502 " pdb=" C6 LMN A 502 " ideal model delta sigma weight residual 1.513 1.402 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" CBL LMN A 502 " pdb=" CBR LMN A 502 " ideal model delta sigma weight residual 1.525 1.634 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" CBT LMN A 502 " pdb=" CCM LMN A 502 " ideal model delta sigma weight residual 1.533 1.640 -0.107 2.00e-02 2.50e+03 2.84e+01 ... (remaining 3313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 4404 2.75 - 5.50: 94 5.50 - 8.26: 13 8.26 - 11.01: 5 11.01 - 13.76: 1 Bond angle restraints: 4517 Sorted by residual: angle pdb=" CCQ LMN A 501 " pdb=" OCB LMN A 501 " pdb=" CCS LMN A 501 " ideal model delta sigma weight residual 119.65 105.89 13.76 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N LEU A 85 " pdb=" CA LEU A 85 " pdb=" C LEU A 85 " ideal model delta sigma weight residual 110.97 106.92 4.05 1.09e+00 8.42e-01 1.38e+01 angle pdb=" CA TYR A 24 " pdb=" C TYR A 24 " pdb=" O TYR A 24 " ideal model delta sigma weight residual 120.82 116.94 3.88 1.05e+00 9.07e-01 1.37e+01 angle pdb=" C4 LMN A 501 " pdb=" O4 LMN A 501 " pdb=" CCR LMN A 501 " ideal model delta sigma weight residual 120.22 109.39 10.83 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CA TYR A 24 " pdb=" CB TYR A 24 " pdb=" CG TYR A 24 " ideal model delta sigma weight residual 113.90 120.20 -6.30 1.80e+00 3.09e-01 1.23e+01 ... (remaining 4512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.90: 1813 26.90 - 53.81: 149 53.81 - 80.71: 38 80.71 - 107.61: 25 107.61 - 134.52: 20 Dihedral angle restraints: 2045 sinusoidal: 901 harmonic: 1144 Sorted by residual: dihedral pdb=" CCJ LMN A 501 " pdb=" CCH LMN A 501 " pdb=" CCL LMN A 501 " pdb=" OAN LMN A 501 " ideal model delta sinusoidal sigma weight residual -176.42 -41.90 -134.52 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" OAN LMN A 501 " pdb=" CCH LMN A 501 " pdb=" CCL LMN A 501 " pdb=" OAP LMN A 501 " ideal model delta sinusoidal sigma weight residual 55.06 -75.83 130.89 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CCJ LMN A 501 " pdb=" CCH LMN A 501 " pdb=" CCL LMN A 501 " pdb=" CCQ LMN A 501 " ideal model delta sinusoidal sigma weight residual -54.78 71.90 -126.68 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 2042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 418 0.055 - 0.110: 83 0.110 - 0.165: 22 0.165 - 0.220: 2 0.220 - 0.276: 3 Chirality restraints: 528 Sorted by residual: chirality pdb=" CCW LMN A 501 " pdb=" CCS LMN A 501 " pdb=" CCU LMN A 501 " pdb=" OAV LMN A 501 " both_signs ideal model delta sigma weight residual False 2.30 2.58 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA LEU A 38 " pdb=" N LEU A 38 " pdb=" C LEU A 38 " pdb=" CB LEU A 38 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C4 LMN A 502 " pdb=" C3 LMN A 502 " pdb=" C5 LMN A 502 " pdb=" O4 LMN A 502 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 525 not shown) Planarity restraints: 528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 100 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 101 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 118 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 119 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 24 " -0.018 2.00e-02 2.50e+03 1.15e-02 2.64e+00 pdb=" CG TYR A 24 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 24 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 24 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 24 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 24 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 24 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 24 " -0.003 2.00e-02 2.50e+03 ... (remaining 525 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 855 2.80 - 3.33: 3084 3.33 - 3.85: 5201 3.85 - 4.38: 5523 4.38 - 4.90: 10003 Nonbonded interactions: 24666 Sorted by model distance: nonbonded pdb=" O GLY A 297 " pdb=" OG1 THR A 419 " model vdw 2.276 3.040 nonbonded pdb=" O THR A 323 " pdb=" OG SER A 326 " model vdw 2.284 3.040 nonbonded pdb=" O TRP A 78 " pdb=" OG SER A 82 " model vdw 2.294 3.040 nonbonded pdb=" N THR A 136 " pdb=" OD2 ASP A 285 " model vdw 2.304 3.120 nonbonded pdb=" OD1 ASN A 27 " pdb=" ND2 ASN A 91 " model vdw 2.333 3.120 ... (remaining 24661 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.320 Find NCS groups from input model: 0.010 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:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.012 0.135 3318 Z= 0.599 Angle : 0.945 13.761 4517 Z= 0.472 Chirality : 0.052 0.276 528 Planarity : 0.005 0.046 528 Dihedral : 27.840 134.516 1319 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 23.08 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.03 (0.44), residues: 400 helix: 2.12 (0.31), residues: 310 sheet: None (None), residues: 0 loop : -1.50 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 300 TYR 0.026 0.001 TYR A 24 PHE 0.008 0.001 PHE A 338 TRP 0.014 0.001 TRP A 165 HIS 0.001 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.01155 ( 3318) covalent geometry : angle 0.94460 ( 4517) hydrogen bonds : bond 0.12060 ( 226) hydrogen bonds : angle 4.87849 ( 678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.082 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0374 time to fit residues: 2.9550 Evaluate side-chains 56 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.0970 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.146963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121475 restraints weight = 4446.730| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.10 r_work: 0.3218 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3318 Z= 0.149 Angle : 0.742 8.644 4517 Z= 0.325 Chirality : 0.047 0.344 528 Planarity : 0.005 0.044 528 Dihedral : 21.111 101.659 681 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.46 % Allowed : 20.92 % Favored : 76.62 % 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: 2.20 (0.44), residues: 400 helix: 2.14 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -1.39 (0.67), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.010 0.001 TYR A 25 PHE 0.016 0.001 PHE A 250 TRP 0.008 0.001 TRP A 107 HIS 0.001 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 3318) covalent geometry : angle 0.74245 ( 4517) hydrogen bonds : bond 0.04580 ( 226) hydrogen bonds : angle 3.83025 ( 678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.067 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 0.0656 time to fit residues: 5.4098 Evaluate side-chains 61 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 390 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.0270 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.145897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120674 restraints weight = 4428.108| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.06 r_work: 0.3176 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3318 Z= 0.132 Angle : 0.663 7.437 4517 Z= 0.300 Chirality : 0.044 0.278 528 Planarity : 0.005 0.040 528 Dihedral : 15.645 87.334 681 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.23 % Allowed : 21.23 % Favored : 77.54 % 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: 2.42 (0.44), residues: 400 helix: 2.40 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -1.50 (0.65), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 286 TYR 0.011 0.001 TYR A 24 PHE 0.010 0.001 PHE A 103 TRP 0.007 0.001 TRP A 138 HIS 0.001 0.000 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3318) covalent geometry : angle 0.66251 ( 4517) hydrogen bonds : bond 0.04460 ( 226) hydrogen bonds : angle 3.68643 ( 678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.109 Fit side-chains REVERT: A 166 ARG cc_start: 0.8241 (mtt-85) cc_final: 0.7852 (mtt-85) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 0.0477 time to fit residues: 3.8047 Evaluate side-chains 62 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 253 GLN A 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115758 restraints weight = 4452.619| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.07 r_work: 0.3083 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3318 Z= 0.145 Angle : 0.639 7.022 4517 Z= 0.295 Chirality : 0.045 0.352 528 Planarity : 0.005 0.040 528 Dihedral : 13.657 78.154 681 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.77 % Allowed : 21.54 % Favored : 75.69 % 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: 2.36 (0.44), residues: 400 helix: 2.28 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -1.46 (0.68), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 10 TYR 0.012 0.001 TYR A 24 PHE 0.010 0.001 PHE A 94 TRP 0.007 0.001 TRP A 138 HIS 0.001 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 3318) covalent geometry : angle 0.63894 ( 4517) hydrogen bonds : bond 0.04669 ( 226) hydrogen bonds : angle 3.73602 ( 678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.065 Fit side-chains REVERT: A 166 ARG cc_start: 0.8212 (mtt-85) cc_final: 0.7943 (mtt-85) outliers start: 9 outliers final: 8 residues processed: 63 average time/residue: 0.0332 time to fit residues: 2.7213 Evaluate side-chains 67 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 390 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 23 optimal weight: 0.0770 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.0000 chunk 30 optimal weight: 0.0030 overall best weight: 0.2552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 253 GLN A 257 GLN A 366 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.152823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.126124 restraints weight = 4323.234| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.22 r_work: 0.3154 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3318 Z= 0.109 Angle : 0.580 7.598 4517 Z= 0.268 Chirality : 0.040 0.276 528 Planarity : 0.004 0.039 528 Dihedral : 11.600 76.640 681 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.85 % Allowed : 22.46 % Favored : 75.69 % 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: 2.79 (0.45), residues: 400 helix: 2.70 (0.31), residues: 311 sheet: None (None), residues: 0 loop : -1.44 (0.65), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.007 0.001 TYR A 24 PHE 0.009 0.001 PHE A 94 TRP 0.006 0.001 TRP A 138 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 3318) covalent geometry : angle 0.57985 ( 4517) hydrogen bonds : bond 0.03641 ( 226) hydrogen bonds : angle 3.53319 ( 678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.066 Fit side-chains REVERT: A 166 ARG cc_start: 0.8095 (mtt-85) cc_final: 0.7689 (mtt-85) REVERT: A 419 THR cc_start: 0.8992 (m) cc_final: 0.8731 (p) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.0350 time to fit residues: 3.0463 Evaluate side-chains 60 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 390 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 253 GLN A 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.146442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120804 restraints weight = 4495.016| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.09 r_work: 0.3105 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3318 Z= 0.132 Angle : 0.592 6.251 4517 Z= 0.281 Chirality : 0.041 0.260 528 Planarity : 0.005 0.040 528 Dihedral : 11.074 74.341 681 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.77 % Allowed : 22.46 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.74 (0.44), residues: 400 helix: 2.65 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -1.48 (0.63), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 10 TYR 0.012 0.001 TYR A 24 PHE 0.009 0.001 PHE A 94 TRP 0.008 0.001 TRP A 138 HIS 0.001 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3318) covalent geometry : angle 0.59245 ( 4517) hydrogen bonds : bond 0.04355 ( 226) hydrogen bonds : angle 3.61911 ( 678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.090 Fit side-chains REVERT: A 166 ARG cc_start: 0.8265 (mtt-85) cc_final: 0.7846 (mtt-85) REVERT: A 307 MET cc_start: 0.7771 (mmm) cc_final: 0.7510 (mtp) REVERT: A 372 MET cc_start: 0.8445 (tpp) cc_final: 0.8214 (mmm) outliers start: 9 outliers final: 9 residues processed: 60 average time/residue: 0.0451 time to fit residues: 3.3635 Evaluate side-chains 62 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 390 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.0070 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 0.0010 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.142819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.115914 restraints weight = 4534.538| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.19 r_work: 0.3118 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3318 Z= 0.106 Angle : 0.553 6.128 4517 Z= 0.264 Chirality : 0.039 0.211 528 Planarity : 0.004 0.040 528 Dihedral : 10.497 71.776 681 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.15 % Allowed : 23.38 % Favored : 74.46 % 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: 2.89 (0.44), residues: 400 helix: 2.79 (0.30), residues: 310 sheet: None (None), residues: 0 loop : -1.44 (0.62), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.008 0.001 TYR A 24 PHE 0.008 0.001 PHE A 94 TRP 0.007 0.001 TRP A 138 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 3318) covalent geometry : angle 0.55258 ( 4517) hydrogen bonds : bond 0.03794 ( 226) hydrogen bonds : angle 3.53273 ( 678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.124 Fit side-chains REVERT: A 107 TRP cc_start: 0.9038 (OUTLIER) cc_final: 0.8673 (t-100) REVERT: A 307 MET cc_start: 0.7459 (mmm) cc_final: 0.7184 (mtp) REVERT: A 419 THR cc_start: 0.8985 (m) cc_final: 0.8659 (p) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.0455 time to fit residues: 3.6540 Evaluate side-chains 59 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 390 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 253 GLN A 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.146770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.121198 restraints weight = 4591.977| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.10 r_work: 0.3124 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3318 Z= 0.123 Angle : 0.561 6.138 4517 Z= 0.270 Chirality : 0.039 0.208 528 Planarity : 0.004 0.040 528 Dihedral : 10.316 70.027 681 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.38 % Allowed : 23.38 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.84 (0.44), residues: 400 helix: 2.75 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -1.52 (0.62), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.011 0.001 TYR A 24 PHE 0.008 0.001 PHE A 94 TRP 0.008 0.001 TRP A 138 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3318) covalent geometry : angle 0.56135 ( 4517) hydrogen bonds : bond 0.04240 ( 226) hydrogen bonds : angle 3.60701 ( 678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.067 Fit side-chains REVERT: A 107 TRP cc_start: 0.9128 (OUTLIER) cc_final: 0.8790 (t-100) REVERT: A 166 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.7847 (mtt-85) REVERT: A 307 MET cc_start: 0.7770 (mmm) cc_final: 0.7544 (mtp) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.0436 time to fit residues: 3.3802 Evaluate side-chains 64 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 390 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 38 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 0.0470 chunk 20 optimal weight: 0.8980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 253 GLN A 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.141666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.114266 restraints weight = 4498.523| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.27 r_work: 0.3103 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3318 Z= 0.111 Angle : 0.557 6.490 4517 Z= 0.265 Chirality : 0.038 0.200 528 Planarity : 0.004 0.040 528 Dihedral : 10.236 68.299 681 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.08 % Allowed : 23.08 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.87 (0.44), residues: 400 helix: 2.77 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -1.50 (0.62), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 286 TYR 0.009 0.001 TYR A 24 PHE 0.008 0.001 PHE A 94 TRP 0.007 0.001 TRP A 138 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 3318) covalent geometry : angle 0.55702 ( 4517) hydrogen bonds : bond 0.03980 ( 226) hydrogen bonds : angle 3.56119 ( 678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.068 Fit side-chains REVERT: A 107 TRP cc_start: 0.8993 (OUTLIER) cc_final: 0.8639 (t-100) REVERT: A 307 MET cc_start: 0.7361 (mmm) cc_final: 0.7095 (mtp) outliers start: 10 outliers final: 8 residues processed: 59 average time/residue: 0.0351 time to fit residues: 2.6697 Evaluate side-chains 62 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 390 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 0.0870 chunk 29 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 253 GLN A 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.146886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119595 restraints weight = 4392.170| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.29 r_work: 0.3097 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3318 Z= 0.119 Angle : 0.552 6.124 4517 Z= 0.266 Chirality : 0.038 0.194 528 Planarity : 0.004 0.041 528 Dihedral : 10.103 66.399 681 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.77 % Allowed : 23.38 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.70 (0.44), residues: 400 helix: 2.58 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -1.55 (0.65), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 28 TYR 0.011 0.001 TYR A 24 PHE 0.008 0.001 PHE A 94 TRP 0.008 0.001 TRP A 138 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3318) covalent geometry : angle 0.55201 ( 4517) hydrogen bonds : bond 0.04213 ( 226) hydrogen bonds : angle 3.60698 ( 678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: A 107 TRP cc_start: 0.9013 (OUTLIER) cc_final: 0.8660 (t-100) REVERT: A 307 MET cc_start: 0.7413 (mmm) cc_final: 0.7186 (mtp) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.0377 time to fit residues: 2.9388 Evaluate side-chains 62 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 390 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.149404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.122577 restraints weight = 4493.531| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.27 r_work: 0.3132 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3318 Z= 0.111 Angle : 0.543 6.247 4517 Z= 0.263 Chirality : 0.038 0.203 528 Planarity : 0.004 0.040 528 Dihedral : 10.167 64.890 681 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.77 % Allowed : 24.00 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.71 (0.44), residues: 400 helix: 2.59 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -1.54 (0.65), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 166 TYR 0.010 0.001 TYR A 24 PHE 0.008 0.001 PHE A 94 TRP 0.007 0.001 TRP A 138 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 3318) covalent geometry : angle 0.54254 ( 4517) hydrogen bonds : bond 0.04040 ( 226) hydrogen bonds : angle 3.57717 ( 678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 586.86 seconds wall clock time: 10 minutes 47.86 seconds (647.86 seconds total)