Starting phenix.real_space_refine on Tue Feb 3 13:05:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rsx_54236/02_2026/9rsx_54236.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rsx_54236/02_2026/9rsx_54236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rsx_54236/02_2026/9rsx_54236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rsx_54236/02_2026/9rsx_54236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rsx_54236/02_2026/9rsx_54236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rsx_54236/02_2026/9rsx_54236.map" } resolution = 2.91 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 1717 2.51 5 N 475 2.21 5 O 528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 2733 Number of models: 1 Model: "" Number of chains: 4 Chain: "N2" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 86 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "N3" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 112 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 12} Chain: "RD" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 2, 'TRANS': 6} Chain: "Rg" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 306} Time building chain proxies: 0.82, per 1000 atoms: 0.30 Number of scatterers: 2733 At special positions: 0 Unit cell: (62.522, 74.881, 62.522, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 13 16.00 O 528 8.00 N 475 7.00 C 1717 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 105.0 milliseconds 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 652 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 7 sheets defined 2.3% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'N2' and resid 610 through 617 Processing sheet with id=AA1, first strand: chain 'RD' and resid 223 through 225 removed outlier: 6.597A pdb=" N VALRg 176 " --> pdb=" O LYSRg 185 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASNRg 187 " --> pdb=" O VALRg 174 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VALRg 174 " --> pdb=" O ASNRg 187 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYSRg 153 " --> pdb=" O CYSRg 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Rg' and resid 2 through 11 removed outlier: 5.006A pdb=" N GLURg 3 " --> pdb=" O GLYRg 315 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLYRg 315 " --> pdb=" O GLURg 3 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N METRg 5 " --> pdb=" O THRRg 313 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THRRg 313 " --> pdb=" O METRg 5 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEURg 7 " --> pdb=" O GLNRg 311 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLNRg 311 " --> pdb=" O LEURg 7 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLYRg 9 " --> pdb=" O VALRg 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Rg' and resid 18 through 23 removed outlier: 3.913A pdb=" N GLNRg 20 " --> pdb=" O ALARg 34 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILERg 31 " --> pdb=" O TRPRg 43 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILERg 40 " --> pdb=" O ALARg 58 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALARg 58 " --> pdb=" O ILERg 40 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N METRg 42 " --> pdb=" O GLNRg 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Rg' and resid 66 through 71 removed outlier: 3.668A pdb=" N ASPRg 68 " --> pdb=" O GLYRg 81 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASPRg 91 " --> pdb=" O THRRg 97 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THRRg 97 " --> pdb=" O ASPRg 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Rg' and resid 108 through 113 removed outlier: 3.521A pdb=" N ILERg 129 " --> pdb=" O VALRg 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Rg' and resid 195 through 200 removed outlier: 7.034A pdb=" N GLYRg 210 " --> pdb=" O ASNRg 196 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VALRg 198 " --> pdb=" O ALARg 208 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALARg 208 " --> pdb=" O VALRg 198 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VALRg 200 " --> pdb=" O LEURg 206 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEURg 206 " --> pdb=" O VALRg 200 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLYRg 211 " --> pdb=" O GLNRg 215 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLNRg 215 " --> pdb=" O GLYRg 211 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYRRg 228 " --> pdb=" O LEURg 218 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ASPRg 220 " --> pdb=" O HISRg 226 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N HISRg 226 " --> pdb=" O ASPRg 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Rg' and resid 236 through 241 removed outlier: 4.040A pdb=" N ALARg 238 " --> pdb=" O ALARg 251 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASPRg 268 " --> pdb=" O ILERg 258 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASPRg 260 " --> pdb=" O ILERg 266 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILERg 266 " --> pdb=" O ASPRg 260 " (cutoff:3.500A) 80 hydrogen bonds defined for protein. 219 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: 0.38 Time building geometry restraints manager: 0.28 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: 896 1.34 - 1.46: 621 1.46 - 1.57: 1260 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 2795 Sorted by residual: bond pdb=" N GLYRg 81 " pdb=" CA GLYRg 81 " ideal model delta sigma weight residual 1.444 1.474 -0.030 1.02e-02 9.61e+03 8.49e+00 bond pdb=" N ASPRg 84 " pdb=" CA ASPRg 84 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.31e-02 5.83e+03 5.52e+00 bond pdb=" N SERRg 82 " pdb=" CA SERRg 82 " ideal model delta sigma weight residual 1.455 1.482 -0.028 1.25e-02 6.40e+03 4.87e+00 bond pdb=" CA SERRg 82 " pdb=" CB SERRg 82 " ideal model delta sigma weight residual 1.533 1.501 0.032 1.82e-02 3.02e+03 3.16e+00 bond pdb=" N TRPRg 83 " pdb=" CA TRPRg 83 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.32e-02 5.74e+03 3.13e+00 ... (remaining 2790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 3700 1.31 - 2.63: 86 2.63 - 3.94: 16 3.94 - 5.26: 2 5.26 - 6.57: 3 Bond angle restraints: 3807 Sorted by residual: angle pdb=" N ASPRg 84 " pdb=" CA ASPRg 84 " pdb=" C ASPRg 84 " ideal model delta sigma weight residual 113.18 107.94 5.24 1.21e+00 6.83e-01 1.87e+01 angle pdb=" CA ASPRg 84 " pdb=" CB ASPRg 84 " pdb=" CG ASPRg 84 " ideal model delta sigma weight residual 112.60 116.32 -3.72 1.00e+00 1.00e+00 1.38e+01 angle pdb=" CA GLYRg 81 " pdb=" C GLYRg 81 " pdb=" O GLYRg 81 " ideal model delta sigma weight residual 121.76 117.95 3.81 1.03e+00 9.43e-01 1.37e+01 angle pdb=" N TRPRg 83 " pdb=" CA TRPRg 83 " pdb=" C TRPRg 83 " ideal model delta sigma weight residual 113.20 109.24 3.96 1.21e+00 6.83e-01 1.07e+01 angle pdb=" C ASPRg 84 " pdb=" CA ASPRg 84 " pdb=" CB ASPRg 84 " ideal model delta sigma weight residual 109.95 115.75 -5.80 1.99e+00 2.53e-01 8.49e+00 ... (remaining 3802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 1463 17.99 - 35.98: 128 35.98 - 53.96: 41 53.96 - 71.95: 10 71.95 - 89.94: 4 Dihedral angle restraints: 1646 sinusoidal: 638 harmonic: 1008 Sorted by residual: dihedral pdb=" CA ASNRg 117 " pdb=" CB ASNRg 117 " pdb=" CG ASNRg 117 " pdb=" OD1 ASNRg 117 " ideal model delta sinusoidal sigma weight residual 120.00 -167.91 -72.09 2 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CG ARGRg 100 " pdb=" CD ARGRg 100 " pdb=" NE ARGRg 100 " pdb=" CZ ARGRg 100 " ideal model delta sinusoidal sigma weight residual 90.00 134.82 -44.82 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA LYSRg 106 " pdb=" CB LYSRg 106 " pdb=" CG LYSRg 106 " pdb=" CD LYSRg 106 " ideal model delta sinusoidal sigma weight residual -60.00 -119.78 59.78 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 236 0.026 - 0.051: 101 0.051 - 0.077: 44 0.077 - 0.103: 27 0.103 - 0.128: 25 Chirality restraints: 433 Sorted by residual: chirality pdb=" CA ILERg 129 " pdb=" N ILERg 129 " pdb=" C ILERg 129 " pdb=" CB ILERg 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILERg 120 " pdb=" N ILERg 120 " pdb=" C ILERg 120 " pdb=" CB ILERg 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILERg 40 " pdb=" N ILERg 40 " pdb=" C ILERg 40 " pdb=" CB ILERg 40 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 430 not shown) Planarity restraints: 484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THRRD 221 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRORD 222 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRORD 222 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRORD 222 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLUN3 402 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" CD GLUN3 402 " 0.022 2.00e-02 2.50e+03 pdb=" OE1 GLUN3 402 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLUN3 402 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SERRg 80 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.57e+00 pdb=" C SERRg 80 " 0.022 2.00e-02 2.50e+03 pdb=" O SERRg 80 " -0.008 2.00e-02 2.50e+03 pdb=" N GLYRg 81 " -0.007 2.00e-02 2.50e+03 ... (remaining 481 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 1281 2.96 - 3.45: 2435 3.45 - 3.93: 4758 3.93 - 4.42: 5735 4.42 - 4.90: 9433 Nonbonded interactions: 23642 Sorted by model distance: nonbonded pdb=" OD1 ASPRg 84 " pdb=" OG1 THRRg 86 " model vdw 2.478 3.040 nonbonded pdb=" O VALRg 18 " pdb=" OG1 THRRg 287 " model vdw 2.612 3.040 nonbonded pdb=" N ASPRg 84 " pdb=" N GLYRg 85 " model vdw 2.632 2.560 nonbonded pdb=" N ASPRg 234 " pdb=" O ASPRg 234 " model vdw 2.633 2.496 nonbonded pdb=" N TRPRg 83 " pdb=" N ASPRg 84 " model vdw 2.633 2.560 ... (remaining 23637 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: 0.00 ========== 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: 21.860 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.950 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:7.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 0.003 0.032 2795 Z= 0.175 Angle : 0.544 6.571 3807 Z= 0.314 Chirality : 0.046 0.128 433 Planarity : 0.004 0.033 484 Dihedral : 16.342 89.939 994 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.98 % Allowed : 17.16 % Favored : 80.86 % 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: -0.07 (0.42), residues: 345 helix: -0.27 (1.65), residues: 8 sheet: 0.30 (0.46), residues: 128 loop : -0.19 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGRg 118 TYR 0.012 0.001 TYRRg 194 PHE 0.010 0.001 PHERg 156 TRP 0.011 0.001 TRPRg 132 HIS 0.004 0.001 HISRg 62 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 2795) covalent geometry : angle 0.54385 ( 3807) hydrogen bonds : bond 0.18765 ( 80) hydrogen bonds : angle 8.71814 ( 219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: Rg 113 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7341 (t80) outliers start: 6 outliers final: 3 residues processed: 45 average time/residue: 0.6568 time to fit residues: 30.2995 Evaluate side-chains 42 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Rg residue 10 THR Chi-restraints excluded: chain Rg residue 113 PHE Chi-restraints excluded: chain Rg residue 148 SER Chi-restraints excluded: chain Rg residue 288 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.0570 chunk 26 optimal weight: 0.0670 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 overall best weight: 0.1836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.134102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.104338 restraints weight = 2937.990| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.92 r_work: 0.2831 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2795 Z= 0.104 Angle : 0.471 6.470 3807 Z= 0.253 Chirality : 0.045 0.139 433 Planarity : 0.003 0.032 484 Dihedral : 5.033 52.417 379 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.31 % Allowed : 17.16 % Favored : 80.53 % 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: 0.21 (0.43), residues: 345 helix: 0.88 (1.92), residues: 8 sheet: 0.40 (0.44), residues: 134 loop : 0.02 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGRg 118 TYR 0.010 0.001 TYRRg 194 PHE 0.007 0.001 PHERg 156 TRP 0.016 0.001 TRPRg 90 HIS 0.003 0.001 HISRg 62 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 2795) covalent geometry : angle 0.47079 ( 3807) hydrogen bonds : bond 0.03736 ( 80) hydrogen bonds : angle 5.89944 ( 219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: N3 404 PHE cc_start: 0.8321 (m-80) cc_final: 0.8026 (m-80) REVERT: Rg 113 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7695 (t80) outliers start: 7 outliers final: 3 residues processed: 47 average time/residue: 0.5045 time to fit residues: 24.5205 Evaluate side-chains 41 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain RD residue 223 ILE Chi-restraints excluded: chain Rg residue 113 PHE Chi-restraints excluded: chain Rg residue 132 TRP Chi-restraints excluded: chain Rg residue 189 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 3 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.0060 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.132521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.100222 restraints weight = 2944.510| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.82 r_work: 0.2808 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2795 Z= 0.129 Angle : 0.486 6.327 3807 Z= 0.259 Chirality : 0.046 0.136 433 Planarity : 0.004 0.033 484 Dihedral : 4.945 50.489 376 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.97 % Allowed : 17.82 % Favored : 79.21 % 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: 0.20 (0.42), residues: 345 helix: 1.39 (1.97), residues: 8 sheet: 0.32 (0.44), residues: 134 loop : 0.05 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGRg 118 TYR 0.012 0.001 TYRRg 194 PHE 0.008 0.001 PHERg 156 TRP 0.016 0.001 TRPRg 132 HIS 0.003 0.001 HISRg 62 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2795) covalent geometry : angle 0.48568 ( 3807) hydrogen bonds : bond 0.03521 ( 80) hydrogen bonds : angle 5.59556 ( 219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: Rg 113 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7650 (t80) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.5722 time to fit residues: 25.2903 Evaluate side-chains 44 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain RD residue 223 ILE Chi-restraints excluded: chain Rg residue 12 LYS Chi-restraints excluded: chain Rg residue 113 PHE Chi-restraints excluded: chain Rg residue 132 TRP Chi-restraints excluded: chain Rg residue 148 SER Chi-restraints excluded: chain Rg residue 189 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.131414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.100583 restraints weight = 2901.154| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.89 r_work: 0.2796 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2795 Z= 0.156 Angle : 0.503 6.479 3807 Z= 0.268 Chirality : 0.046 0.133 433 Planarity : 0.004 0.032 484 Dihedral : 5.001 47.475 376 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.30 % Allowed : 17.16 % Favored : 79.54 % 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: 0.09 (0.42), residues: 345 helix: 1.66 (1.94), residues: 8 sheet: 0.21 (0.44), residues: 128 loop : -0.01 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGRg 118 TYR 0.013 0.001 TYRRg 194 PHE 0.008 0.001 PHERg 156 TRP 0.016 0.001 TRPRg 132 HIS 0.003 0.001 HISRg 64 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 2795) covalent geometry : angle 0.50326 ( 3807) hydrogen bonds : bond 0.03560 ( 80) hydrogen bonds : angle 5.56585 ( 219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: Rg 113 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7607 (t80) outliers start: 10 outliers final: 6 residues processed: 46 average time/residue: 0.5118 time to fit residues: 24.2457 Evaluate side-chains 45 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain RD residue 223 ILE Chi-restraints excluded: chain Rg residue 12 LYS Chi-restraints excluded: chain Rg residue 113 PHE Chi-restraints excluded: chain Rg residue 132 TRP Chi-restraints excluded: chain Rg residue 148 SER Chi-restraints excluded: chain Rg residue 189 ILE Chi-restraints excluded: chain Rg residue 240 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 19 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.0270 chunk 3 optimal weight: 0.0770 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.133979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.102925 restraints weight = 2846.737| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.71 r_work: 0.2848 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2795 Z= 0.100 Angle : 0.454 6.206 3807 Z= 0.241 Chirality : 0.045 0.130 433 Planarity : 0.003 0.030 484 Dihedral : 4.698 47.457 376 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.96 % Allowed : 16.83 % Favored : 79.21 % 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: 0.22 (0.43), residues: 345 helix: 1.97 (2.05), residues: 8 sheet: 0.20 (0.43), residues: 135 loop : 0.16 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGRg 118 TYR 0.010 0.001 TYRRg 194 PHE 0.006 0.001 PHERg 241 TRP 0.015 0.001 TRPRg 132 HIS 0.002 0.001 HISRg 62 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 2795) covalent geometry : angle 0.45379 ( 3807) hydrogen bonds : bond 0.03076 ( 80) hydrogen bonds : angle 5.12241 ( 219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: Rg 113 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7638 (t80) outliers start: 12 outliers final: 5 residues processed: 47 average time/residue: 0.3583 time to fit residues: 17.3471 Evaluate side-chains 43 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain RD residue 223 ILE Chi-restraints excluded: chain Rg residue 113 PHE Chi-restraints excluded: chain Rg residue 115 SER Chi-restraints excluded: chain Rg residue 132 TRP Chi-restraints excluded: chain Rg residue 148 SER Chi-restraints excluded: chain Rg residue 189 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 0.4980 chunk 14 optimal weight: 0.0270 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 9 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 overall best weight: 0.2638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.132772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.101618 restraints weight = 2966.278| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.74 r_work: 0.2841 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 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 : 0.003 0.023 2795 Z= 0.123 Angle : 0.481 6.210 3807 Z= 0.257 Chirality : 0.045 0.131 433 Planarity : 0.003 0.030 484 Dihedral : 4.880 46.064 376 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.63 % Allowed : 16.50 % Favored : 79.87 % 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: 0.19 (0.43), residues: 345 helix: 2.03 (2.02), residues: 8 sheet: 0.21 (0.43), residues: 135 loop : 0.09 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGRg 118 TYR 0.012 0.001 TYRRg 194 PHE 0.007 0.001 PHERg 156 TRP 0.016 0.001 TRPRg 132 HIS 0.002 0.001 HISRg 64 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 2795) covalent geometry : angle 0.48055 ( 3807) hydrogen bonds : bond 0.03199 ( 80) hydrogen bonds : angle 5.18134 ( 219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: Rg 1 MET cc_start: 0.6508 (mtt) cc_final: 0.6257 (mtt) outliers start: 11 outliers final: 7 residues processed: 46 average time/residue: 0.4583 time to fit residues: 21.6950 Evaluate side-chains 41 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain RD residue 223 ILE Chi-restraints excluded: chain Rg residue 113 PHE Chi-restraints excluded: chain Rg residue 115 SER Chi-restraints excluded: chain Rg residue 132 TRP Chi-restraints excluded: chain Rg residue 148 SER Chi-restraints excluded: chain Rg residue 189 ILE Chi-restraints excluded: chain Rg residue 240 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 0.0770 chunk 10 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.131449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.100028 restraints weight = 2927.105| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.76 r_work: 0.2808 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2795 Z= 0.144 Angle : 0.494 6.299 3807 Z= 0.263 Chirality : 0.046 0.132 433 Planarity : 0.003 0.030 484 Dihedral : 4.968 43.756 376 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.30 % Allowed : 17.16 % Favored : 79.54 % 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: 0.07 (0.42), residues: 345 helix: 1.94 (1.96), residues: 8 sheet: 0.15 (0.44), residues: 129 loop : -0.00 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGRg 118 TYR 0.013 0.001 TYRRg 194 PHE 0.008 0.001 PHERg 156 TRP 0.016 0.001 TRPRg 132 HIS 0.003 0.001 HISRg 64 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 2795) covalent geometry : angle 0.49417 ( 3807) hydrogen bonds : bond 0.03370 ( 80) hydrogen bonds : angle 5.33067 ( 219) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.070 Fit side-chains revert: symmetry clash REVERT: Rg 1 MET cc_start: 0.6625 (mtt) cc_final: 0.6330 (mtt) outliers start: 10 outliers final: 8 residues processed: 41 average time/residue: 0.3589 time to fit residues: 15.1855 Evaluate side-chains 41 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain RD residue 223 ILE Chi-restraints excluded: chain Rg residue 12 LYS Chi-restraints excluded: chain Rg residue 113 PHE Chi-restraints excluded: chain Rg residue 115 SER Chi-restraints excluded: chain Rg residue 132 TRP Chi-restraints excluded: chain Rg residue 148 SER Chi-restraints excluded: chain Rg residue 189 ILE Chi-restraints excluded: chain Rg residue 240 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 9 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 0.0970 chunk 20 optimal weight: 0.0470 chunk 25 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 overall best weight: 0.2076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.102392 restraints weight = 2981.688| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.78 r_work: 0.2849 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2795 Z= 0.105 Angle : 0.463 6.119 3807 Z= 0.246 Chirality : 0.045 0.130 433 Planarity : 0.003 0.030 484 Dihedral : 4.720 43.647 376 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.30 % Allowed : 17.49 % Favored : 79.21 % 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: 0.20 (0.43), residues: 345 helix: 1.82 (1.94), residues: 8 sheet: 0.22 (0.43), residues: 135 loop : 0.11 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGRg 118 TYR 0.011 0.001 TYRRg 194 PHE 0.006 0.001 PHERg 156 TRP 0.016 0.001 TRPRg 132 HIS 0.002 0.001 HISRg 62 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 2795) covalent geometry : angle 0.46252 ( 3807) hydrogen bonds : bond 0.03068 ( 80) hydrogen bonds : angle 5.00425 ( 219) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: Rg 1 MET cc_start: 0.6556 (mtt) cc_final: 0.6274 (mtt) outliers start: 10 outliers final: 8 residues processed: 44 average time/residue: 0.5296 time to fit residues: 23.9881 Evaluate side-chains 43 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain RD residue 223 ILE Chi-restraints excluded: chain Rg residue 12 LYS Chi-restraints excluded: chain Rg residue 113 PHE Chi-restraints excluded: chain Rg residue 115 SER Chi-restraints excluded: chain Rg residue 132 TRP Chi-restraints excluded: chain Rg residue 148 SER Chi-restraints excluded: chain Rg residue 189 ILE Chi-restraints excluded: chain Rg residue 240 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 7 optimal weight: 0.0070 chunk 23 optimal weight: 0.0970 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 0.0370 chunk 12 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 overall best weight: 0.1072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Rg 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.136723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.106532 restraints weight = 2988.190| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.72 r_work: 0.2902 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2795 Z= 0.078 Angle : 0.434 6.028 3807 Z= 0.232 Chirality : 0.044 0.128 433 Planarity : 0.003 0.029 484 Dihedral : 4.459 44.486 376 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.64 % Allowed : 18.15 % Favored : 79.21 % 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: 0.33 (0.43), residues: 345 helix: 1.80 (1.92), residues: 8 sheet: 0.37 (0.42), residues: 133 loop : 0.16 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGRg 118 TYR 0.008 0.001 TYRRg 194 PHE 0.005 0.001 PHERg 241 TRP 0.015 0.001 TRPRg 132 HIS 0.001 0.001 HISRg 62 Details of bonding type rmsd covalent geometry : bond 0.00166 ( 2795) covalent geometry : angle 0.43401 ( 3807) hydrogen bonds : bond 0.02787 ( 80) hydrogen bonds : angle 4.67598 ( 219) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: Rg 1 MET cc_start: 0.6528 (mtt) cc_final: 0.6257 (mtt) REVERT: Rg 30 MET cc_start: 0.8484 (tmm) cc_final: 0.8144 (tmm) REVERT: Rg 113 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7559 (t80) REVERT: Rg 116 ASP cc_start: 0.8550 (p0) cc_final: 0.8014 (p0) REVERT: Rg 118 ARG cc_start: 0.8236 (mtt-85) cc_final: 0.8022 (mtm110) REVERT: Rg 148 SER cc_start: 0.8632 (p) cc_final: 0.8421 (m) outliers start: 8 outliers final: 4 residues processed: 47 average time/residue: 0.3989 time to fit residues: 19.3651 Evaluate side-chains 44 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Rg residue 113 PHE Chi-restraints excluded: chain Rg residue 115 SER Chi-restraints excluded: chain Rg residue 132 TRP Chi-restraints excluded: chain Rg residue 189 ILE Chi-restraints excluded: chain Rg residue 240 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 26 optimal weight: 0.3980 chunk 0 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.130175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.098341 restraints weight = 2985.487| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.78 r_work: 0.2781 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2795 Z= 0.191 Angle : 0.535 6.493 3807 Z= 0.284 Chirality : 0.047 0.135 433 Planarity : 0.004 0.031 484 Dihedral : 5.064 41.557 376 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.98 % Allowed : 18.48 % Favored : 79.54 % 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: 0.15 (0.42), residues: 345 helix: 2.06 (2.00), residues: 8 sheet: 0.26 (0.44), residues: 129 loop : 0.01 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGRg 118 TYR 0.015 0.002 TYRRg 194 PHE 0.008 0.002 PHERg 156 TRP 0.016 0.002 TRPRg 132 HIS 0.004 0.001 HISRg 64 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 2795) covalent geometry : angle 0.53471 ( 3807) hydrogen bonds : bond 0.03578 ( 80) hydrogen bonds : angle 5.38954 ( 219) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: Rg 1 MET cc_start: 0.6626 (mtt) cc_final: 0.6373 (mtt) outliers start: 6 outliers final: 4 residues processed: 38 average time/residue: 0.5963 time to fit residues: 23.2819 Evaluate side-chains 37 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Rg residue 132 TRP Chi-restraints excluded: chain Rg residue 189 ILE Chi-restraints excluded: chain Rg residue 240 CYS Chi-restraints excluded: chain Rg residue 282 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.130061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.098014 restraints weight = 2919.751| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.78 r_work: 0.2776 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2795 Z= 0.191 Angle : 0.539 6.391 3807 Z= 0.286 Chirality : 0.047 0.134 433 Planarity : 0.004 0.032 484 Dihedral : 4.472 15.606 374 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.31 % Allowed : 18.81 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.04 (0.42), residues: 345 helix: 2.02 (2.00), residues: 8 sheet: 0.20 (0.43), residues: 129 loop : -0.08 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGRg 118 TYR 0.016 0.002 TYRRg 194 PHE 0.008 0.002 PHERg 156 TRP 0.016 0.002 TRPRg 132 HIS 0.003 0.001 HISRg 64 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 2795) covalent geometry : angle 0.53895 ( 3807) hydrogen bonds : bond 0.03624 ( 80) hydrogen bonds : angle 5.43776 ( 219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1598.17 seconds wall clock time: 28 minutes 11.38 seconds (1691.38 seconds total)