Starting phenix.real_space_refine on Fri Dec 27 18:17:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8erp_28557/12_2024/8erp_28557_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8erp_28557/12_2024/8erp_28557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8erp_28557/12_2024/8erp_28557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8erp_28557/12_2024/8erp_28557.map" model { file = "/net/cci-nas-00/data/ceres_data/8erp_28557/12_2024/8erp_28557_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8erp_28557/12_2024/8erp_28557_neut.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.023 sd= 0.179 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 4 5.21 5 S 50 5.16 5 C 4074 2.51 5 N 894 2.21 5 O 1028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6056 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2836 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "A" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2836 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "B" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 192 Unusual residues: {' MG': 2, 'CDC': 1, 'LBN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 334 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'LBN:plan-2': 9, 'LBN:plan-3': 9, 'LBN:plan-1': 9} Unresolved non-hydrogen planarities: 93 Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 192 Unusual residues: {' MG': 2, 'CDC': 1, 'LBN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 334 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'LBN:plan-2': 9, 'LBN:plan-3': 9, 'LBN:plan-1': 9} Unresolved non-hydrogen planarities: 93 Time building chain proxies: 4.13, per 1000 atoms: 0.68 Number of scatterers: 6056 At special positions: 0 Unit cell: (73.7, 115.5, 70.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 6 15.00 Mg 4 11.99 O 1028 8.00 N 894 7.00 C 4074 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: 1.48 Conformation dependent library (CDL) restraints added in 765.5 milliseconds 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 76.4% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'B' and resid 22 through 30 removed outlier: 4.011A pdb=" N GLU B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.592A pdb=" N MET B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 85 removed outlier: 3.524A pdb=" N ILE B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 89 removed outlier: 4.113A pdb=" N THR B 89 " --> pdb=" O PRO B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 93 through 120 removed outlier: 3.696A pdb=" N TYR B 97 " --> pdb=" O PRO B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 152 removed outlier: 3.979A pdb=" N GLU B 129 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 159 Processing helix chain 'B' and resid 160 through 180 removed outlier: 4.234A pdb=" N CYS B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 209 Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.948A pdb=" N TRP B 213 " --> pdb=" O PRO B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 249 removed outlier: 3.657A pdb=" N GLY B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 284 removed outlier: 3.816A pdb=" N HIS B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 removed outlier: 3.680A pdb=" N GLN B 292 " --> pdb=" O ASN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 318 removed outlier: 3.686A pdb=" N LEU B 312 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.718A pdb=" N PHE B 341 " --> pdb=" O PHE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 378 removed outlier: 3.878A pdb=" N TRP B 352 " --> pdb=" O TYR B 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 30 removed outlier: 4.011A pdb=" N GLU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.592A pdb=" N MET A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 85 removed outlier: 3.524A pdb=" N ILE A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 89 removed outlier: 4.113A pdb=" N THR A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 93 through 120 removed outlier: 3.696A pdb=" N TYR A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 152 removed outlier: 3.979A pdb=" N GLU A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'A' and resid 160 through 180 removed outlier: 4.234A pdb=" N CYS A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 209 Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.948A pdb=" N TRP A 213 " --> pdb=" O PRO A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 249 removed outlier: 3.657A pdb=" N GLY A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 284 removed outlier: 3.816A pdb=" N HIS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 removed outlier: 3.680A pdb=" N GLN A 292 " --> pdb=" O ASN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 318 removed outlier: 3.686A pdb=" N LEU A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.718A pdb=" N PHE A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 378 removed outlier: 3.878A pdb=" N TRP A 352 " --> pdb=" O TYR A 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 38 406 hydrogen bonds defined for protein. 1200 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: 1.52 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 900 1.32 - 1.44: 1620 1.44 - 1.57: 3576 1.57 - 1.69: 12 1.69 - 1.81: 74 Bond restraints: 6182 Sorted by residual: bond pdb=" O3A CDC A 507 " pdb=" PA CDC A 507 " ideal model delta sigma weight residual 1.653 1.592 0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" O3A CDC B 505 " pdb=" PA CDC B 505 " ideal model delta sigma weight residual 1.653 1.592 0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" O1B CDC B 505 " pdb=" PB CDC B 505 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" O1B CDC A 507 " pdb=" PB CDC A 507 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" O2 LBN B 506 " pdb=" P1 LBN B 506 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.27e+00 ... (remaining 6177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 8092 2.29 - 4.59: 192 4.59 - 6.88: 30 6.88 - 9.17: 4 9.17 - 11.46: 6 Bond angle restraints: 8324 Sorted by residual: angle pdb=" O3A CDC A 507 " pdb=" PA CDC A 507 " pdb=" O5' CDC A 507 " ideal model delta sigma weight residual 94.32 105.78 -11.46 3.00e+00 1.11e-01 1.46e+01 angle pdb=" O3A CDC B 505 " pdb=" PA CDC B 505 " pdb=" O5' CDC B 505 " ideal model delta sigma weight residual 94.32 105.78 -11.46 3.00e+00 1.11e-01 1.46e+01 angle pdb=" C TYR A 215 " pdb=" N GLU A 216 " pdb=" CA GLU A 216 " ideal model delta sigma weight residual 121.31 126.84 -5.53 1.49e+00 4.50e-01 1.38e+01 angle pdb=" C TYR B 215 " pdb=" N GLU B 216 " pdb=" CA GLU B 216 " ideal model delta sigma weight residual 121.31 126.84 -5.53 1.49e+00 4.50e-01 1.38e+01 angle pdb=" O1 LBN A 508 " pdb=" P1 LBN A 508 " pdb=" O2 LBN A 508 " ideal model delta sigma weight residual 93.45 104.32 -10.87 3.00e+00 1.11e-01 1.31e+01 ... (remaining 8319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.95: 3456 28.95 - 57.91: 184 57.91 - 86.86: 36 86.86 - 115.82: 4 115.82 - 144.77: 12 Dihedral angle restraints: 3692 sinusoidal: 1590 harmonic: 2102 Sorted by residual: dihedral pdb=" C32 LBN A 513 " pdb=" C33 LBN A 513 " pdb=" C4 LBN A 513 " pdb=" C7 LBN A 513 " ideal model delta sinusoidal sigma weight residual 179.89 -35.34 -144.77 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C32 LBN B 511 " pdb=" C33 LBN B 511 " pdb=" C4 LBN B 511 " pdb=" C7 LBN B 511 " ideal model delta sinusoidal sigma weight residual 179.89 -35.34 -144.77 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" O5 LBN B 506 " pdb=" C2 LBN B 506 " pdb=" C3 LBN B 506 " pdb=" O7 LBN B 506 " ideal model delta sinusoidal sigma weight residual 62.67 -66.11 128.78 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 3689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 716 0.046 - 0.091: 196 0.091 - 0.137: 28 0.137 - 0.183: 2 0.183 - 0.228: 6 Chirality restraints: 948 Sorted by residual: chirality pdb=" CB ILE B 189 " pdb=" CA ILE B 189 " pdb=" CG1 ILE B 189 " pdb=" CG2 ILE B 189 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE A 189 " pdb=" CA ILE A 189 " pdb=" CG1 ILE A 189 " pdb=" CG2 ILE A 189 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1' CDC B 505 " pdb=" C2' CDC B 505 " pdb=" N1 CDC B 505 " pdb=" O4' CDC B 505 " both_signs ideal model delta sigma weight residual False 2.20 2.42 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 945 not shown) Planarity restraints: 968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN A 508 " 0.249 2.00e-02 2.50e+03 2.47e-01 6.08e+02 pdb=" C42 LBN A 508 " -0.255 2.00e-02 2.50e+03 pdb=" C5 LBN A 508 " -0.238 2.00e-02 2.50e+03 pdb=" C8 LBN A 508 " 0.244 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN B 506 " -0.249 2.00e-02 2.50e+03 2.47e-01 6.08e+02 pdb=" C42 LBN B 506 " 0.255 2.00e-02 2.50e+03 pdb=" C5 LBN B 506 " 0.238 2.00e-02 2.50e+03 pdb=" C8 LBN B 506 " -0.244 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 176 " 0.022 2.00e-02 2.50e+03 1.72e-02 7.44e+00 pdb=" CG TRP A 176 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A 176 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 176 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 176 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 176 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 176 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 176 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 176 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 176 " 0.003 2.00e-02 2.50e+03 ... (remaining 965 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 54 2.59 - 3.17: 5196 3.17 - 3.75: 8712 3.75 - 4.32: 11424 4.32 - 4.90: 19471 Nonbonded interactions: 44857 Sorted by model distance: nonbonded pdb=" OD1 ASP A 136 " pdb="MG MG A 503 " model vdw 2.016 2.170 nonbonded pdb=" OD1 ASP B 136 " pdb="MG MG B 501 " model vdw 2.016 2.170 nonbonded pdb=" OD1 ASP B 111 " pdb="MG MG B 501 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP A 111 " pdb="MG MG A 503 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP B 132 " pdb="MG MG B 501 " model vdw 2.067 2.170 ... (remaining 44852 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 383 or (resid 506 and (name C29 or name C30 or \ name C31 or name C32)) or (resid 508 and (name C25 or name C26 or name C27 or na \ me C28 or name C29 or name C30 or name C31 or name C32)) or (resid 509 and (name \ C10 or name C13 or name C26 or name C27 or name C28 or name C29 or name C30 or \ name C31 or name C32 or name C33 or name C4 or name C7 )) or resid 510 through 5 \ 12 or (resid 513 and (name C10 or name C13 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C30 or name C31 or name C32 or name C33 or name C \ 4 or name C7 )))) selection = (chain 'B' and (resid 20 through 383 or (resid 506 and (name C29 or name C30 or \ name C31 or name C32)) or (resid 508 and (name C25 or name C26 or name C27 or na \ me C28 or name C29 or name C30 or name C31 or name C32)) or resid 509 through 51 \ 0 or (resid 511 and (name C10 or name C13 or name C26 or name C27 or name C28 or \ name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name C7 \ )) or resid 512 through 513)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.960 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6182 Z= 0.276 Angle : 0.855 11.462 8324 Z= 0.452 Chirality : 0.044 0.228 948 Planarity : 0.013 0.247 968 Dihedral : 19.420 144.771 2348 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.32), residues: 724 helix: 1.54 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -3.07 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 176 HIS 0.004 0.001 HIS B 270 PHE 0.015 0.002 PHE A 171 TYR 0.007 0.001 TYR A 282 ARG 0.002 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.646 Fit side-chains REVERT: B 201 MET cc_start: 0.8097 (ttp) cc_final: 0.7738 (ttm) REVERT: A 201 MET cc_start: 0.8083 (ttp) cc_final: 0.7733 (ttm) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1447 time to fit residues: 23.4159 Evaluate side-chains 100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN B 177 GLN B 293 ASN A 74 ASN A 177 GLN A 293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6182 Z= 0.326 Angle : 0.747 7.080 8324 Z= 0.396 Chirality : 0.045 0.188 948 Planarity : 0.005 0.043 968 Dihedral : 16.564 116.103 1090 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.22 % Allowed : 12.70 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.32), residues: 724 helix: 1.72 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.71 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 176 HIS 0.005 0.002 HIS A 270 PHE 0.018 0.002 PHE B 171 TYR 0.022 0.002 TYR A 282 ARG 0.003 0.001 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.644 Fit side-chains REVERT: B 201 MET cc_start: 0.8152 (ttp) cc_final: 0.7733 (ttm) REVERT: A 201 MET cc_start: 0.8138 (ttp) cc_final: 0.7723 (ttm) outliers start: 14 outliers final: 14 residues processed: 110 average time/residue: 0.1665 time to fit residues: 24.9081 Evaluate side-chains 102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 316 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 0.0020 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6182 Z= 0.189 Angle : 0.634 7.781 8324 Z= 0.337 Chirality : 0.040 0.177 948 Planarity : 0.005 0.040 968 Dihedral : 14.636 98.801 1090 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.17 % Allowed : 15.24 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.33), residues: 724 helix: 2.32 (0.23), residues: 494 sheet: None (None), residues: 0 loop : -2.86 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 95 HIS 0.004 0.001 HIS B 270 PHE 0.013 0.001 PHE B 171 TYR 0.009 0.001 TYR A 243 ARG 0.002 0.000 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.634 Fit side-chains REVERT: B 201 MET cc_start: 0.7988 (ttp) cc_final: 0.7414 (ttm) REVERT: A 201 MET cc_start: 0.7978 (ttp) cc_final: 0.7404 (ttm) outliers start: 20 outliers final: 14 residues processed: 112 average time/residue: 0.1792 time to fit residues: 26.4800 Evaluate side-chains 104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 316 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6182 Z= 0.227 Angle : 0.632 6.235 8324 Z= 0.339 Chirality : 0.041 0.152 948 Planarity : 0.004 0.039 968 Dihedral : 13.766 95.591 1090 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.17 % Allowed : 16.83 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.33), residues: 724 helix: 2.40 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -2.79 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 176 HIS 0.004 0.001 HIS B 270 PHE 0.016 0.002 PHE B 171 TYR 0.013 0.001 TYR A 282 ARG 0.001 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.583 Fit side-chains REVERT: B 201 MET cc_start: 0.8027 (ttp) cc_final: 0.7501 (ttm) REVERT: A 201 MET cc_start: 0.8014 (ttp) cc_final: 0.7488 (ttm) outliers start: 20 outliers final: 14 residues processed: 106 average time/residue: 0.1802 time to fit residues: 25.3117 Evaluate side-chains 102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 316 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN A 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6182 Z= 0.286 Angle : 0.685 8.627 8324 Z= 0.361 Chirality : 0.043 0.217 948 Planarity : 0.004 0.039 968 Dihedral : 13.773 91.441 1090 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.17 % Allowed : 19.37 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.33), residues: 724 helix: 2.24 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -2.80 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 95 HIS 0.004 0.001 HIS B 270 PHE 0.032 0.002 PHE B 94 TYR 0.015 0.001 TYR A 282 ARG 0.001 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.607 Fit side-chains REVERT: B 55 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 201 MET cc_start: 0.8126 (ttp) cc_final: 0.7581 (ttm) REVERT: A 55 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7847 (tm-30) REVERT: A 201 MET cc_start: 0.8114 (ttp) cc_final: 0.7567 (ttm) outliers start: 20 outliers final: 20 residues processed: 102 average time/residue: 0.1653 time to fit residues: 22.8238 Evaluate side-chains 110 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 316 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.0010 chunk 69 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN A 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6182 Z= 0.184 Angle : 0.618 7.211 8324 Z= 0.329 Chirality : 0.041 0.210 948 Planarity : 0.004 0.038 968 Dihedral : 13.105 88.130 1090 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.49 % Allowed : 20.00 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.33), residues: 724 helix: 2.59 (0.23), residues: 494 sheet: None (None), residues: 0 loop : -2.89 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 95 HIS 0.004 0.001 HIS B 270 PHE 0.027 0.002 PHE A 94 TYR 0.007 0.001 TYR B 297 ARG 0.001 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.618 Fit side-chains REVERT: B 55 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7793 (tm-30) REVERT: B 201 MET cc_start: 0.7979 (ttp) cc_final: 0.7500 (ttm) REVERT: A 55 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7790 (tm-30) REVERT: A 201 MET cc_start: 0.7967 (ttp) cc_final: 0.7490 (ttm) outliers start: 22 outliers final: 20 residues processed: 110 average time/residue: 0.1626 time to fit residues: 24.2819 Evaluate side-chains 110 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 316 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6182 Z= 0.191 Angle : 0.615 6.259 8324 Z= 0.325 Chirality : 0.041 0.188 948 Planarity : 0.004 0.039 968 Dihedral : 12.786 85.391 1090 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.65 % Allowed : 21.11 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.33), residues: 724 helix: 2.58 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -2.75 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 176 HIS 0.004 0.001 HIS B 270 PHE 0.023 0.002 PHE A 94 TYR 0.008 0.001 TYR A 282 ARG 0.001 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.552 Fit side-chains REVERT: B 55 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 201 MET cc_start: 0.7978 (ttp) cc_final: 0.7545 (ttm) REVERT: A 55 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7769 (tm-30) REVERT: A 201 MET cc_start: 0.7969 (ttp) cc_final: 0.7535 (ttm) outliers start: 23 outliers final: 14 residues processed: 114 average time/residue: 0.1626 time to fit residues: 25.1590 Evaluate side-chains 102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 316 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.0970 chunk 13 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.0050 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN A 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6182 Z= 0.167 Angle : 0.595 6.203 8324 Z= 0.313 Chirality : 0.040 0.171 948 Planarity : 0.004 0.039 968 Dihedral : 11.918 79.595 1090 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.17 % Allowed : 22.22 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.33), residues: 724 helix: 2.91 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -3.06 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 95 HIS 0.004 0.001 HIS B 270 PHE 0.020 0.002 PHE A 94 TYR 0.006 0.001 TYR B 297 ARG 0.001 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.772 Fit side-chains REVERT: B 201 MET cc_start: 0.7901 (ttp) cc_final: 0.7427 (ttm) REVERT: A 201 MET cc_start: 0.7887 (ttp) cc_final: 0.7416 (ttm) outliers start: 20 outliers final: 14 residues processed: 110 average time/residue: 0.1794 time to fit residues: 26.0751 Evaluate side-chains 106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 316 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.0370 chunk 38 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN A 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6182 Z= 0.184 Angle : 0.608 6.192 8324 Z= 0.321 Chirality : 0.040 0.171 948 Planarity : 0.004 0.038 968 Dihedral : 11.484 75.239 1090 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.17 % Allowed : 22.22 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.33), residues: 724 helix: 2.76 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -2.85 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 176 HIS 0.004 0.001 HIS B 270 PHE 0.020 0.001 PHE B 94 TYR 0.008 0.001 TYR A 282 ARG 0.000 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.630 Fit side-chains REVERT: B 201 MET cc_start: 0.7919 (ttp) cc_final: 0.7413 (ttm) REVERT: A 201 MET cc_start: 0.7905 (ttp) cc_final: 0.7400 (ttm) outliers start: 20 outliers final: 18 residues processed: 100 average time/residue: 0.1899 time to fit residues: 25.0737 Evaluate side-chains 106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 326 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 57 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 0.0770 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN A 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6182 Z= 0.174 Angle : 0.604 7.076 8324 Z= 0.317 Chirality : 0.040 0.174 948 Planarity : 0.004 0.038 968 Dihedral : 11.005 71.281 1090 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.49 % Allowed : 21.90 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.33), residues: 724 helix: 2.76 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -2.85 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 176 HIS 0.004 0.001 HIS B 270 PHE 0.021 0.001 PHE B 94 TYR 0.007 0.001 TYR A 282 ARG 0.001 0.000 ARG B 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.714 Fit side-chains REVERT: B 201 MET cc_start: 0.7886 (ttp) cc_final: 0.7411 (ttm) REVERT: A 201 MET cc_start: 0.7872 (ttp) cc_final: 0.7398 (ttm) outliers start: 22 outliers final: 20 residues processed: 110 average time/residue: 0.1840 time to fit residues: 26.7482 Evaluate side-chains 106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 326 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN A 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.166807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.146020 restraints weight = 6700.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.143717 restraints weight = 11189.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.143146 restraints weight = 11040.753| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6182 Z= 0.260 Angle : 0.934 38.231 8324 Z= 0.552 Chirality : 0.042 0.256 948 Planarity : 0.008 0.160 968 Dihedral : 10.985 70.931 1090 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.49 % Allowed : 21.90 % Favored : 74.60 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.33), residues: 724 helix: 2.72 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -2.82 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 176 HIS 0.004 0.001 HIS A 270 PHE 0.016 0.001 PHE A 142 TYR 0.007 0.001 TYR B 282 ARG 0.006 0.000 ARG A 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1323.81 seconds wall clock time: 25 minutes 9.97 seconds (1509.97 seconds total)