Starting phenix.real_space_refine on Tue Mar 3 11:33:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m7d_30129/03_2026/6m7d_30129.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m7d_30129/03_2026/6m7d_30129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m7d_30129/03_2026/6m7d_30129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m7d_30129/03_2026/6m7d_30129.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m7d_30129/03_2026/6m7d_30129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m7d_30129/03_2026/6m7d_30129.map" } resolution = 2.9 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= 0.006 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 6 5.49 5 S 14 5.16 5 C 2054 2.51 5 N 552 2.21 5 O 654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3280 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3160 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 0.75, per 1000 atoms: 0.23 Number of scatterers: 3280 At special positions: 0 Unit cell: (78.52, 81.64, 88.4, 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 14 16.00 P 6 15.00 O 654 8.00 N 552 7.00 C 2054 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: 0.25 Conformation dependent library (CDL) restraints added in 106.9 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 67.5% alpha, 5.3% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 46 through 63 Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 162 through 182 removed outlier: 4.144A pdb=" N LYS A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 203 removed outlier: 4.224A pdb=" N ALA A 198 " --> pdb=" O ASN A 194 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.763A pdb=" N VAL A 210 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 226 through 240 Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 307 through 313 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 318 through 328 removed outlier: 4.001A pdb=" N GLY A 322 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 329 through 344 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 387 through 402 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 40 removed outlier: 6.533A pdb=" N SER A 33 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 102 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 35 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A 104 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL A 37 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE A 106 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 39 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N LYS A 108 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 105 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 120 " --> pdb=" O TYR A 127 " (cutoff:3.500A) 185 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 0.41 Time building geometry restraints manager: 0.34 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: 683 1.33 - 1.45: 765 1.45 - 1.57: 1863 1.57 - 1.69: 11 1.69 - 1.81: 26 Bond restraints: 3348 Sorted by residual: bond pdb=" N SER A 142 " pdb=" CA SER A 142 " ideal model delta sigma weight residual 1.453 1.488 -0.034 9.20e-03 1.18e+04 1.39e+01 bond pdb=" N VAL A 277 " pdb=" CA VAL A 277 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.18e-02 7.18e+03 1.37e+01 bond pdb=" N VAL A 99 " pdb=" CA VAL A 99 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.08e-02 8.57e+03 1.24e+01 bond pdb=" N VAL A 95 " pdb=" CA VAL A 95 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.85e+00 bond pdb=" N MET A 125 " pdb=" CA MET A 125 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.22e-02 6.72e+03 8.47e+00 ... (remaining 3343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 3587 1.07 - 2.14: 622 2.14 - 3.22: 299 3.22 - 4.29: 40 4.29 - 5.36: 8 Bond angle restraints: 4556 Sorted by residual: angle pdb=" CA ASP A 405 " pdb=" C ASP A 405 " pdb=" O ASP A 405 " ideal model delta sigma weight residual 122.63 118.22 4.41 1.29e+00 6.01e-01 1.17e+01 angle pdb=" N THR A 272 " pdb=" CA THR A 272 " pdb=" C THR A 272 " ideal model delta sigma weight residual 111.28 107.63 3.65 1.09e+00 8.42e-01 1.12e+01 angle pdb=" C ASN A 241 " pdb=" N THR A 242 " pdb=" CA THR A 242 " ideal model delta sigma weight residual 120.28 124.74 -4.46 1.34e+00 5.57e-01 1.11e+01 angle pdb=" C SER A 402 " pdb=" N GLY A 403 " pdb=" CA GLY A 403 " ideal model delta sigma weight residual 120.00 123.63 -3.63 1.10e+00 8.26e-01 1.09e+01 angle pdb=" CA ARG A 149 " pdb=" C ARG A 149 " pdb=" O ARG A 149 " ideal model delta sigma weight residual 121.56 118.10 3.46 1.09e+00 8.42e-01 1.01e+01 ... (remaining 4551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 1813 17.82 - 35.64: 159 35.64 - 53.46: 35 53.46 - 71.28: 15 71.28 - 89.10: 3 Dihedral angle restraints: 2025 sinusoidal: 847 harmonic: 1178 Sorted by residual: dihedral pdb=" C GLU A 278 " pdb=" N GLU A 278 " pdb=" CA GLU A 278 " pdb=" CB GLU A 278 " ideal model delta harmonic sigma weight residual -122.60 -130.72 8.12 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CA ASN A 140 " pdb=" CB ASN A 140 " pdb=" CG ASN A 140 " pdb=" OD1 ASN A 140 " ideal model delta sinusoidal sigma weight residual -90.00 -159.31 69.31 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU A 214 " pdb=" CG GLU A 214 " pdb=" CD GLU A 214 " pdb=" OE1 GLU A 214 " ideal model delta sinusoidal sigma weight residual 0.00 89.10 -89.10 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 2022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 286 0.046 - 0.092: 152 0.092 - 0.139: 69 0.139 - 0.185: 17 0.185 - 0.231: 9 Chirality restraints: 533 Sorted by residual: chirality pdb=" CA GLU A 278 " pdb=" N GLU A 278 " pdb=" C GLU A 278 " pdb=" CB GLU A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA VAL A 120 " pdb=" N VAL A 120 " pdb=" C VAL A 120 " pdb=" CB VAL A 120 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 273 " pdb=" N ILE A 273 " pdb=" C ILE A 273 " pdb=" CB ILE A 273 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 530 not shown) Planarity restraints: 564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 2 " 0.031 2.00e-02 2.50e+03 1.53e-02 5.25e+00 pdb=" N1 U B 2 " -0.031 2.00e-02 2.50e+03 pdb=" C2 U B 2 " -0.007 2.00e-02 2.50e+03 pdb=" O2 U B 2 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U B 2 " 0.005 2.00e-02 2.50e+03 pdb=" C4 U B 2 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 2 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U B 2 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 2 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 240 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C MET A 240 " 0.033 2.00e-02 2.50e+03 pdb=" O MET A 240 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN A 241 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 44 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C VAL A 44 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL A 44 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 45 " 0.010 2.00e-02 2.50e+03 ... (remaining 561 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 115 2.71 - 3.25: 3405 3.25 - 3.80: 5504 3.80 - 4.35: 7360 4.35 - 4.90: 11397 Nonbonded interactions: 27781 Sorted by model distance: nonbonded pdb=" O ALA A 346 " pdb=" O2' U B 4 " model vdw 2.157 3.040 nonbonded pdb=" O THR A 183 " pdb=" O2' U B 2 " model vdw 2.198 3.040 nonbonded pdb=" O ALA A 325 " pdb=" ND2 ASN A 328 " model vdw 2.211 3.120 nonbonded pdb=" NE2 GLN A 173 " pdb=" O LEU A 209 " model vdw 2.220 3.120 nonbonded pdb=" OD2 ASP A 202 " pdb=" OG1 THR A 204 " model vdw 2.262 3.040 ... (remaining 27776 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: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.000 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:5.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.010 0.056 3348 Z= 0.632 Angle : 1.033 5.361 4556 Z= 0.761 Chirality : 0.069 0.231 533 Planarity : 0.005 0.041 564 Dihedral : 14.955 89.104 1273 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.58 % Allowed : 13.12 % Favored : 86.30 % 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: -0.46 (0.38), residues: 410 helix: -0.14 (0.32), residues: 244 sheet: -0.49 (1.15), residues: 23 loop : -0.28 (0.41), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 195 TYR 0.011 0.002 TYR A 275 PHE 0.016 0.002 PHE A 193 TRP 0.006 0.001 TRP A 333 HIS 0.004 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.01002 ( 3348) covalent geometry : angle 1.03254 ( 4556) hydrogen bonds : bond 0.15669 ( 185) hydrogen bonds : angle 7.53487 ( 516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.081 Fit side-chains REVERT: A 290 ARG cc_start: 0.8141 (ttt180) cc_final: 0.7519 (ttp-110) REVERT: A 400 ASN cc_start: 0.8217 (m-40) cc_final: 0.7949 (m-40) outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 0.6478 time to fit residues: 45.0089 Evaluate side-chains 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.0070 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 93 ASN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN A 241 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 288 ASN A 366 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.148616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.125304 restraints weight = 3498.256| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.01 r_work: 0.2972 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3348 Z= 0.117 Angle : 0.478 4.764 4556 Z= 0.258 Chirality : 0.040 0.144 533 Planarity : 0.004 0.031 564 Dihedral : 9.641 60.009 541 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.33 % Allowed : 14.29 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.39), residues: 410 helix: 0.82 (0.33), residues: 248 sheet: -0.15 (1.03), residues: 23 loop : 0.38 (0.43), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 395 TYR 0.008 0.001 TYR A 275 PHE 0.013 0.001 PHE A 269 TRP 0.003 0.001 TRP A 175 HIS 0.003 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3348) covalent geometry : angle 0.47753 ( 4556) hydrogen bonds : bond 0.04606 ( 185) hydrogen bonds : angle 5.41968 ( 516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.076 Fit side-chains REVERT: A 56 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8460 (p) REVERT: A 62 LEU cc_start: 0.9080 (mt) cc_final: 0.8832 (mm) REVERT: A 290 ARG cc_start: 0.8704 (ttt180) cc_final: 0.7576 (ttp-110) REVERT: A 345 LYS cc_start: 0.8302 (tppt) cc_final: 0.8033 (mmpt) REVERT: A 377 SER cc_start: 0.8846 (p) cc_final: 0.8591 (p) REVERT: A 400 ASN cc_start: 0.8217 (m-40) cc_final: 0.8016 (m-40) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 0.5674 time to fit residues: 34.4243 Evaluate side-chains 52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.146774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.122152 restraints weight = 3402.372| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.06 r_work: 0.2916 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3348 Z= 0.127 Angle : 0.459 4.902 4556 Z= 0.245 Chirality : 0.039 0.117 533 Planarity : 0.003 0.030 564 Dihedral : 9.669 59.923 541 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.92 % Allowed : 14.58 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.40), residues: 410 helix: 1.28 (0.34), residues: 242 sheet: -0.39 (0.94), residues: 25 loop : 1.08 (0.48), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.006 0.001 TYR A 275 PHE 0.012 0.001 PHE A 269 TRP 0.005 0.001 TRP A 333 HIS 0.003 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3348) covalent geometry : angle 0.45878 ( 4556) hydrogen bonds : bond 0.04621 ( 185) hydrogen bonds : angle 5.17151 ( 516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.129 Fit side-chains REVERT: A 290 ARG cc_start: 0.8730 (ttt180) cc_final: 0.7616 (ttp-110) REVERT: A 345 LYS cc_start: 0.8270 (tppt) cc_final: 0.8039 (mmpt) REVERT: A 377 SER cc_start: 0.8875 (p) cc_final: 0.8606 (p) REVERT: A 400 ASN cc_start: 0.8213 (m-40) cc_final: 0.7955 (m-40) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.5674 time to fit residues: 31.5461 Evaluate side-chains 50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.145382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.121490 restraints weight = 3405.003| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.07 r_work: 0.2847 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3348 Z= 0.147 Angle : 0.472 5.609 4556 Z= 0.250 Chirality : 0.040 0.118 533 Planarity : 0.003 0.030 564 Dihedral : 9.643 59.899 541 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.92 % Allowed : 15.45 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.41), residues: 410 helix: 1.33 (0.34), residues: 240 sheet: -0.41 (0.88), residues: 25 loop : 1.11 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.006 0.001 TYR A 303 PHE 0.010 0.002 PHE A 269 TRP 0.005 0.001 TRP A 333 HIS 0.003 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3348) covalent geometry : angle 0.47188 ( 4556) hydrogen bonds : bond 0.04762 ( 185) hydrogen bonds : angle 5.13433 ( 516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.124 Fit side-chains REVERT: A 56 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8438 (p) REVERT: A 201 GLN cc_start: 0.6501 (OUTLIER) cc_final: 0.5943 (tt0) REVERT: A 290 ARG cc_start: 0.8636 (ttt180) cc_final: 0.7605 (ttp-110) REVERT: A 400 ASN cc_start: 0.8181 (m-40) cc_final: 0.7919 (m-40) outliers start: 10 outliers final: 4 residues processed: 50 average time/residue: 0.5727 time to fit residues: 29.4288 Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.149013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.125017 restraints weight = 3435.845| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.11 r_work: 0.2909 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3348 Z= 0.105 Angle : 0.432 5.582 4556 Z= 0.230 Chirality : 0.038 0.120 533 Planarity : 0.003 0.030 564 Dihedral : 9.536 59.641 541 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.62 % Allowed : 14.87 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.41), residues: 410 helix: 1.54 (0.34), residues: 242 sheet: -0.26 (0.89), residues: 25 loop : 1.26 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.007 0.001 TYR A 275 PHE 0.012 0.001 PHE A 269 TRP 0.004 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 3348) covalent geometry : angle 0.43224 ( 4556) hydrogen bonds : bond 0.04132 ( 185) hydrogen bonds : angle 4.85648 ( 516) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.163 Fit side-chains REVERT: A 201 GLN cc_start: 0.6398 (OUTLIER) cc_final: 0.5756 (tt0) REVERT: A 290 ARG cc_start: 0.8593 (ttt180) cc_final: 0.7580 (ttp-110) REVERT: A 400 ASN cc_start: 0.8100 (m-40) cc_final: 0.7873 (m-40) outliers start: 9 outliers final: 4 residues processed: 55 average time/residue: 0.5620 time to fit residues: 31.8142 Evaluate side-chains 48 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.146157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.121904 restraints weight = 3376.694| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.04 r_work: 0.2848 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3348 Z= 0.142 Angle : 0.486 8.269 4556 Z= 0.251 Chirality : 0.041 0.152 533 Planarity : 0.003 0.029 564 Dihedral : 9.559 59.823 541 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 2.62 % Allowed : 15.16 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.41), residues: 410 helix: 1.51 (0.34), residues: 240 sheet: 0.05 (0.92), residues: 25 loop : 1.23 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.007 0.001 TYR A 260 PHE 0.009 0.001 PHE A 269 TRP 0.005 0.001 TRP A 333 HIS 0.002 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3348) covalent geometry : angle 0.48604 ( 4556) hydrogen bonds : bond 0.04662 ( 185) hydrogen bonds : angle 5.00202 ( 516) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.135 Fit side-chains REVERT: A 201 GLN cc_start: 0.6484 (OUTLIER) cc_final: 0.5896 (tt0) REVERT: A 290 ARG cc_start: 0.8600 (ttt180) cc_final: 0.7612 (ttp-110) REVERT: A 400 ASN cc_start: 0.8182 (m-40) cc_final: 0.7927 (m-40) outliers start: 9 outliers final: 5 residues processed: 48 average time/residue: 0.5150 time to fit residues: 25.5015 Evaluate side-chains 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.144731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.120847 restraints weight = 3449.329| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.06 r_work: 0.2819 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3348 Z= 0.158 Angle : 0.495 7.035 4556 Z= 0.256 Chirality : 0.041 0.142 533 Planarity : 0.003 0.029 564 Dihedral : 9.633 59.955 541 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.62 % Allowed : 15.74 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.41), residues: 410 helix: 1.39 (0.34), residues: 240 sheet: 0.26 (0.93), residues: 25 loop : 1.26 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 395 TYR 0.008 0.001 TYR A 127 PHE 0.010 0.002 PHE A 269 TRP 0.005 0.001 TRP A 333 HIS 0.002 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 3348) covalent geometry : angle 0.49535 ( 4556) hydrogen bonds : bond 0.04826 ( 185) hydrogen bonds : angle 5.08788 ( 516) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.132 Fit side-chains REVERT: A 201 GLN cc_start: 0.6369 (OUTLIER) cc_final: 0.5799 (tt0) REVERT: A 290 ARG cc_start: 0.8650 (ttt180) cc_final: 0.7609 (ttp-110) REVERT: A 400 ASN cc_start: 0.8228 (m-40) cc_final: 0.7957 (m-40) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.5393 time to fit residues: 26.6307 Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.149030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.123879 restraints weight = 3495.327| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.06 r_work: 0.2894 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3348 Z= 0.104 Angle : 0.457 7.134 4556 Z= 0.235 Chirality : 0.039 0.130 533 Planarity : 0.003 0.030 564 Dihedral : 9.525 59.692 541 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.33 % Allowed : 15.45 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.41), residues: 410 helix: 1.59 (0.34), residues: 242 sheet: 0.33 (0.95), residues: 25 loop : 1.27 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 395 TYR 0.006 0.001 TYR A 275 PHE 0.012 0.001 PHE A 269 TRP 0.004 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 3348) covalent geometry : angle 0.45683 ( 4556) hydrogen bonds : bond 0.04082 ( 185) hydrogen bonds : angle 4.80193 ( 516) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.125 Fit side-chains REVERT: A 201 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.5807 (tt0) REVERT: A 290 ARG cc_start: 0.8631 (ttt180) cc_final: 0.7619 (ttp-110) REVERT: A 400 ASN cc_start: 0.8151 (m-40) cc_final: 0.7907 (m-40) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.4672 time to fit residues: 23.6405 Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 0.0170 overall best weight: 1.8036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.146295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.122354 restraints weight = 3442.272| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 0.99 r_work: 0.2860 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3348 Z= 0.138 Angle : 0.486 7.554 4556 Z= 0.250 Chirality : 0.040 0.127 533 Planarity : 0.003 0.029 564 Dihedral : 9.522 59.830 541 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.62 % Allowed : 15.45 % Favored : 81.92 % 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: 1.97 (0.41), residues: 410 helix: 1.54 (0.34), residues: 240 sheet: 0.44 (0.96), residues: 25 loop : 1.33 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 395 TYR 0.009 0.001 TYR A 127 PHE 0.010 0.001 PHE A 269 TRP 0.005 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3348) covalent geometry : angle 0.48599 ( 4556) hydrogen bonds : bond 0.04591 ( 185) hydrogen bonds : angle 4.91296 ( 516) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.132 Fit side-chains REVERT: A 201 GLN cc_start: 0.6413 (OUTLIER) cc_final: 0.5821 (tt0) REVERT: A 290 ARG cc_start: 0.8614 (ttt180) cc_final: 0.7607 (ttp-110) REVERT: A 400 ASN cc_start: 0.8192 (m-40) cc_final: 0.7921 (m-40) outliers start: 9 outliers final: 6 residues processed: 49 average time/residue: 0.5885 time to fit residues: 29.6980 Evaluate side-chains 48 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.148041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.123774 restraints weight = 3383.679| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 0.92 r_work: 0.2939 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3348 Z= 0.114 Angle : 0.476 7.759 4556 Z= 0.245 Chirality : 0.039 0.124 533 Planarity : 0.003 0.030 564 Dihedral : 9.484 59.745 541 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.75 % Allowed : 16.62 % Favored : 81.63 % 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: 2.05 (0.41), residues: 410 helix: 1.59 (0.34), residues: 242 sheet: 0.57 (0.97), residues: 25 loop : 1.38 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 395 TYR 0.006 0.001 TYR A 303 PHE 0.011 0.001 PHE A 269 TRP 0.004 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3348) covalent geometry : angle 0.47558 ( 4556) hydrogen bonds : bond 0.04280 ( 185) hydrogen bonds : angle 4.80055 ( 516) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.077 Fit side-chains REVERT: A 201 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.5821 (tt0) REVERT: A 290 ARG cc_start: 0.8540 (ttt180) cc_final: 0.7605 (ttp-110) REVERT: A 400 ASN cc_start: 0.8128 (m-40) cc_final: 0.7874 (m-40) outliers start: 6 outliers final: 5 residues processed: 46 average time/residue: 0.5482 time to fit residues: 25.9494 Evaluate side-chains 46 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.146373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.122340 restraints weight = 3433.544| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.16 r_work: 0.2850 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3348 Z= 0.135 Angle : 0.487 7.718 4556 Z= 0.251 Chirality : 0.040 0.126 533 Planarity : 0.003 0.029 564 Dihedral : 9.496 59.830 541 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.04 % Allowed : 16.62 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.41), residues: 410 helix: 1.50 (0.34), residues: 242 sheet: 0.51 (0.94), residues: 25 loop : 1.37 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 395 TYR 0.008 0.001 TYR A 127 PHE 0.010 0.001 PHE A 269 TRP 0.005 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3348) covalent geometry : angle 0.48687 ( 4556) hydrogen bonds : bond 0.04559 ( 185) hydrogen bonds : angle 4.88323 ( 516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1557.01 seconds wall clock time: 27 minutes 10.46 seconds (1630.46 seconds total)