Starting phenix.real_space_refine on Wed Feb 14 02:53:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2e_14463/02_2024/7z2e_14463_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2e_14463/02_2024/7z2e_14463.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2e_14463/02_2024/7z2e_14463_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2e_14463/02_2024/7z2e_14463_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2e_14463/02_2024/7z2e_14463_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2e_14463/02_2024/7z2e_14463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2e_14463/02_2024/7z2e_14463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2e_14463/02_2024/7z2e_14463_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2e_14463/02_2024/7z2e_14463_updated.pdb" } resolution = 3.45 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= 0.000 sd= 0.026 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 35 5.49 5 S 12 5.16 5 C 5380 2.51 5 N 1418 2.21 5 O 1634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8479 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4331 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 496} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3399 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 381} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 721 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'T27': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.87, per 1000 atoms: 0.57 Number of scatterers: 8479 At special positions: 0 Unit cell: (97.97, 112.52, 101.85, 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 12 16.00 P 35 15.00 O 1634 8.00 N 1418 7.00 C 5380 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 - 3.50 Amino acid : False - 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: 3.25 Conformation dependent library (CDL) restraints added in 1.4 seconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 8 sheets defined 32.9% alpha, 12.3% beta 13 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 78 through 81 No H-bonds generated for 'chain 'A' and resid 78 through 81' Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.834A pdb=" N PHE A 116 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 127 Processing helix chain 'A' and resid 154 through 174 removed outlier: 4.846A pdb=" N ALA A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 195 through 210 removed outlier: 4.006A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 269 removed outlier: 4.297A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.704A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 364 through 382 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.555A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.062A pdb=" N GLU A 546 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.854A pdb=" N LEU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 removed outlier: 3.574A pdb=" N LYS B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.804A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 155 through 174 removed outlier: 4.913A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.580A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.627A pdb=" N LYS B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 277 through 283' Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 365 through 382 Processing helix chain 'B' and resid 395 through 401 Processing sheet with id= A, first strand: chain 'A' and resid 105 through 110 Processing sheet with id= B, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.511A pdb=" N PHE A 227 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 414 through 416 removed outlier: 6.340A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 464 through 468 removed outlier: 3.887A pdb=" N VAL A 467 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 455 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS A 530 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE A 495 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A 532 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR A 497 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA A 534 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 47 through 49 Processing sheet with id= F, first strand: chain 'B' and resid 60 through 63 Processing sheet with id= G, first strand: chain 'B' and resid 105 through 110 Processing sheet with id= H, first strand: chain 'B' and resid 413 through 416 removed outlier: 3.925A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1319 1.27 - 1.40: 2160 1.40 - 1.54: 5031 1.54 - 1.67: 240 1.67 - 1.81: 22 Bond restraints: 8772 Sorted by residual: bond pdb=" C2 OMC E 2 " pdb=" N3 OMC E 2 " ideal model delta sigma weight residual 1.491 1.347 0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C2 OMC E 4 " pdb=" N3 OMC E 4 " ideal model delta sigma weight residual 1.491 1.349 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" CG PRO B 345 " pdb=" CD PRO B 345 " ideal model delta sigma weight residual 1.503 1.299 0.204 3.40e-02 8.65e+02 3.60e+01 bond pdb=" N1 OMC E 2 " pdb=" C6 OMC E 2 " ideal model delta sigma weight residual 1.455 1.335 0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" N1 OMC E 4 " pdb=" C6 OMC E 4 " ideal model delta sigma weight residual 1.455 1.340 0.115 2.00e-02 2.50e+03 3.32e+01 ... (remaining 8767 not shown) Histogram of bond angle deviations from ideal: 90.82 - 108.63: 925 108.63 - 126.44: 10845 126.44 - 144.25: 291 144.25 - 162.06: 0 162.06 - 179.87: 2 Bond angle restraints: 12063 Sorted by residual: angle pdb=" CA PRO B 345 " pdb=" N PRO B 345 " pdb=" CD PRO B 345 " ideal model delta sigma weight residual 112.00 94.85 17.15 1.40e+00 5.10e-01 1.50e+02 angle pdb=" N ASN B 418 " pdb=" CA ASN B 418 " pdb=" C ASN B 418 " ideal model delta sigma weight residual 107.75 90.82 16.93 1.86e+00 2.89e-01 8.28e+01 angle pdb=" N PRO B 345 " pdb=" CD PRO B 345 " pdb=" CG PRO B 345 " ideal model delta sigma weight residual 103.20 91.18 12.02 1.50e+00 4.44e-01 6.42e+01 angle pdb=" C2 T27 A 601 " pdb=" C1 T27 A 601 " pdb=" C7 T27 A 601 " ideal model delta sigma weight residual 120.40 104.25 16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" C PRO B 140 " pdb=" CA PRO B 140 " pdb=" CB PRO B 140 " ideal model delta sigma weight residual 111.56 102.70 8.86 1.65e+00 3.67e-01 2.88e+01 ... (remaining 12058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4375 17.79 - 35.57: 569 35.57 - 53.36: 163 53.36 - 71.14: 40 71.14 - 88.93: 15 Dihedral angle restraints: 5162 sinusoidal: 2408 harmonic: 2754 Sorted by residual: dihedral pdb=" C ILE A 184 " pdb=" N ILE A 184 " pdb=" CA ILE A 184 " pdb=" CB ILE A 184 " ideal model delta harmonic sigma weight residual -122.00 -137.20 15.20 0 2.50e+00 1.60e-01 3.70e+01 dihedral pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CA ILE A 184 " pdb=" CB ILE A 184 " ideal model delta harmonic sigma weight residual 123.40 136.42 -13.02 0 2.50e+00 1.60e-01 2.71e+01 dihedral pdb=" CD ARG B 143 " pdb=" NE ARG B 143 " pdb=" CZ ARG B 143 " pdb=" NH1 ARG B 143 " ideal model delta sinusoidal sigma weight residual 0.00 44.11 -44.11 1 1.00e+01 1.00e-02 2.71e+01 ... (remaining 5159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1200 0.085 - 0.171: 100 0.171 - 0.256: 1 0.256 - 0.341: 1 0.341 - 0.427: 2 Chirality restraints: 1304 Sorted by residual: chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.01 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA THR B 419 " pdb=" N THR B 419 " pdb=" C THR B 419 " pdb=" CB THR B 419 " both_signs ideal model delta sigma weight residual False 2.53 2.87 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA ASN B 418 " pdb=" N ASN B 418 " pdb=" C ASN B 418 " pdb=" CB ASN B 418 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 1301 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC E 4 " -0.023 2.00e-02 2.50e+03 5.96e-01 7.99e+03 pdb=" C4' OMC E 4 " 0.431 2.00e-02 2.50e+03 pdb=" O4' OMC E 4 " 0.656 2.00e-02 2.50e+03 pdb=" C3' OMC E 4 " -0.613 2.00e-02 2.50e+03 pdb=" O3' OMC E 4 " -0.601 2.00e-02 2.50e+03 pdb=" C2' OMC E 4 " -0.168 2.00e-02 2.50e+03 pdb=" O2' OMC E 4 " 0.967 2.00e-02 2.50e+03 pdb=" C1' OMC E 4 " 0.252 2.00e-02 2.50e+03 pdb=" N1 OMC E 4 " -0.901 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC E 2 " 0.155 2.00e-02 2.50e+03 5.07e-01 5.79e+03 pdb=" C4' OMC E 2 " -0.440 2.00e-02 2.50e+03 pdb=" O4' OMC E 2 " -0.772 2.00e-02 2.50e+03 pdb=" C3' OMC E 2 " 0.552 2.00e-02 2.50e+03 pdb=" O3' OMC E 2 " 0.285 2.00e-02 2.50e+03 pdb=" C2' OMC E 2 " 0.340 2.00e-02 2.50e+03 pdb=" O2' OMC E 2 " -0.607 2.00e-02 2.50e+03 pdb=" C1' OMC E 2 " -0.262 2.00e-02 2.50e+03 pdb=" N1 OMC E 2 " 0.750 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 143 " 0.761 9.50e-02 1.11e+02 3.41e-01 7.08e+01 pdb=" NE ARG B 143 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG B 143 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 143 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 143 " 0.023 2.00e-02 2.50e+03 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1216 2.76 - 3.30: 7583 3.30 - 3.83: 14041 3.83 - 4.37: 16422 4.37 - 4.90: 27373 Nonbonded interactions: 66635 Sorted by model distance: nonbonded pdb=" OH TYR A 354 " pdb=" OE1 GLU A 370 " model vdw 2.227 2.440 nonbonded pdb=" NZ LYS B 73 " pdb=" OH TYR B 146 " model vdw 2.249 2.520 nonbonded pdb=" OG1 THR A 27 " pdb=" O LYS A 30 " model vdw 2.253 2.440 nonbonded pdb=" OG1 THR A 253 " pdb=" OD2 ASP A 256 " model vdw 2.284 2.440 nonbonded pdb=" OD1 ASP A 443 " pdb=" N GLY A 444 " model vdw 2.291 2.520 ... (remaining 66630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 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: 0.980 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 27.250 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 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 : 0.007 0.204 8772 Z= 0.418 Angle : 0.748 17.151 12063 Z= 0.414 Chirality : 0.047 0.427 1304 Planarity : 0.024 0.596 1398 Dihedral : 17.759 88.931 3386 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.11 % Favored : 96.78 % Rotamer: Outliers : 0.24 % Allowed : 0.83 % Favored : 98.94 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.03 % 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: -0.47 (0.28), residues: 933 helix: 1.33 (0.31), residues: 311 sheet: -0.70 (0.40), residues: 161 loop : -1.34 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 266 HIS 0.003 0.000 HIS B 208 PHE 0.017 0.001 PHE B 87 TYR 0.014 0.001 TYR A 501 ARG 0.003 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.927 Fit side-chains REVERT: A 115 TYR cc_start: 0.6802 (t80) cc_final: 0.6540 (t80) REVERT: A 233 GLU cc_start: 0.7266 (mp0) cc_final: 0.6986 (mp0) outliers start: 2 outliers final: 0 residues processed: 117 average time/residue: 0.2108 time to fit residues: 34.3141 Evaluate side-chains 86 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN A 428 GLN A 547 GLN B 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8772 Z= 0.321 Angle : 0.768 14.981 12063 Z= 0.434 Chirality : 0.044 0.151 1304 Planarity : 0.007 0.112 1398 Dihedral : 16.571 81.551 1385 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.04 % Favored : 94.86 % Rotamer: Outliers : 1.30 % Allowed : 9.46 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.86 (0.27), residues: 933 helix: 0.88 (0.30), residues: 310 sheet: -0.71 (0.40), residues: 150 loop : -1.53 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 406 HIS 0.004 0.001 HIS B 208 PHE 0.014 0.002 PHE B 87 TYR 0.020 0.002 TYR B 181 ARG 0.005 0.001 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.869 Fit side-chains REVERT: A 83 ARG cc_start: 0.4852 (mpt180) cc_final: 0.4498 (mmp80) REVERT: A 503 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7687 (mp) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.2169 time to fit residues: 30.7472 Evaluate side-chains 93 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 531 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 87 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN A 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8772 Z= 0.192 Angle : 0.666 13.716 12063 Z= 0.385 Chirality : 0.041 0.235 1304 Planarity : 0.006 0.117 1398 Dihedral : 16.100 78.185 1385 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.79 % Favored : 97.11 % Rotamer: Outliers : 1.65 % Allowed : 12.17 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.61 (0.27), residues: 933 helix: 1.19 (0.31), residues: 307 sheet: -0.74 (0.40), residues: 146 loop : -1.38 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.007 0.001 PHE B 130 TYR 0.014 0.001 TYR A 144 ARG 0.002 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 1.095 Fit side-chains REVERT: A 83 ARG cc_start: 0.4704 (mpt180) cc_final: 0.4386 (mmp80) REVERT: B 342 TYR cc_start: 0.7671 (p90) cc_final: 0.7325 (p90) outliers start: 14 outliers final: 7 residues processed: 106 average time/residue: 0.2163 time to fit residues: 32.0093 Evaluate side-chains 94 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 142 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.5980 chunk 66 optimal weight: 0.3980 chunk 45 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 30.0000 chunk 25 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN B 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8772 Z= 0.148 Angle : 0.642 13.022 12063 Z= 0.373 Chirality : 0.040 0.140 1304 Planarity : 0.006 0.115 1398 Dihedral : 15.933 91.113 1385 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.25 % Favored : 97.64 % Rotamer: Outliers : 1.18 % Allowed : 13.83 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.15 (0.27), residues: 933 helix: 1.59 (0.32), residues: 305 sheet: -0.15 (0.40), residues: 151 loop : -1.24 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 406 HIS 0.004 0.001 HIS A 198 PHE 0.004 0.001 PHE A 124 TYR 0.012 0.001 TYR A 144 ARG 0.002 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.963 Fit side-chains REVERT: A 83 ARG cc_start: 0.4717 (mpt180) cc_final: 0.4449 (mmp80) REVERT: A 480 GLN cc_start: 0.6467 (pt0) cc_final: 0.6082 (pt0) outliers start: 10 outliers final: 2 residues processed: 99 average time/residue: 0.2164 time to fit residues: 29.6564 Evaluate side-chains 86 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 531 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.4980 chunk 53 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 overall best weight: 6.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 8772 Z= 0.362 Angle : 0.766 12.340 12063 Z= 0.431 Chirality : 0.045 0.214 1304 Planarity : 0.007 0.120 1398 Dihedral : 16.280 96.907 1385 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.14 % Favored : 94.75 % Rotamer: Outliers : 2.48 % Allowed : 14.66 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.90 (0.27), residues: 933 helix: 0.79 (0.30), residues: 308 sheet: -0.79 (0.39), residues: 143 loop : -1.48 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 406 HIS 0.005 0.001 HIS A 198 PHE 0.015 0.002 PHE B 130 TYR 0.024 0.002 TYR A 501 ARG 0.003 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.044 Fit side-chains REVERT: A 83 ARG cc_start: 0.4740 (mpt180) cc_final: 0.4416 (mmp80) REVERT: A 255 ASN cc_start: 0.7210 (m110) cc_final: 0.6998 (m-40) REVERT: A 310 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7589 (mp) outliers start: 21 outliers final: 14 residues processed: 104 average time/residue: 0.2051 time to fit residues: 29.8728 Evaluate side-chains 98 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 403 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8772 Z= 0.212 Angle : 0.688 12.801 12063 Z= 0.392 Chirality : 0.042 0.324 1304 Planarity : 0.006 0.117 1398 Dihedral : 15.873 94.395 1385 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.89 % Favored : 97.00 % Rotamer: Outliers : 2.13 % Allowed : 16.43 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.80 (0.27), residues: 933 helix: 0.89 (0.31), residues: 312 sheet: -0.78 (0.39), residues: 144 loop : -1.44 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 406 HIS 0.004 0.001 HIS A 198 PHE 0.009 0.001 PHE B 130 TYR 0.016 0.001 TYR A 501 ARG 0.002 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 1.465 Fit side-chains REVERT: A 83 ARG cc_start: 0.4662 (mpt180) cc_final: 0.4379 (mmp80) outliers start: 18 outliers final: 12 residues processed: 101 average time/residue: 0.2241 time to fit residues: 31.7727 Evaluate side-chains 94 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 93 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8772 Z= 0.273 Angle : 0.714 12.702 12063 Z= 0.404 Chirality : 0.043 0.253 1304 Planarity : 0.007 0.118 1398 Dihedral : 15.822 94.053 1385 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.82 % Favored : 95.07 % Rotamer: Outliers : 2.60 % Allowed : 17.14 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.93 (0.27), residues: 933 helix: 0.81 (0.30), residues: 308 sheet: -0.88 (0.38), residues: 144 loop : -1.51 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 406 HIS 0.004 0.001 HIS A 198 PHE 0.012 0.002 PHE B 130 TYR 0.016 0.002 TYR A 457 ARG 0.002 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 1.007 Fit side-chains REVERT: A 83 ARG cc_start: 0.4729 (mpt180) cc_final: 0.4415 (mmp80) REVERT: A 107 THR cc_start: 0.7560 (OUTLIER) cc_final: 0.7318 (m) REVERT: A 310 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7513 (mp) REVERT: A 480 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6336 (pt0) outliers start: 22 outliers final: 17 residues processed: 103 average time/residue: 0.2039 time to fit residues: 29.5338 Evaluate side-chains 104 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 30.0000 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 73 optimal weight: 0.0020 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8772 Z= 0.189 Angle : 0.667 12.939 12063 Z= 0.384 Chirality : 0.041 0.210 1304 Planarity : 0.006 0.116 1398 Dihedral : 15.599 92.645 1385 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.32 % Rotamer: Outliers : 2.25 % Allowed : 17.73 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.75 (0.27), residues: 933 helix: 0.91 (0.31), residues: 312 sheet: -0.72 (0.38), residues: 144 loop : -1.40 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 406 HIS 0.004 0.001 HIS A 198 PHE 0.007 0.001 PHE B 130 TYR 0.013 0.001 TYR A 144 ARG 0.002 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.958 Fit side-chains REVERT: A 83 ARG cc_start: 0.4739 (mpt180) cc_final: 0.4428 (mmp80) REVERT: A 107 THR cc_start: 0.7613 (OUTLIER) cc_final: 0.7365 (m) REVERT: A 202 ILE cc_start: 0.5836 (OUTLIER) cc_final: 0.5605 (mm) REVERT: A 310 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7545 (mp) REVERT: A 480 GLN cc_start: 0.6563 (OUTLIER) cc_final: 0.6177 (pt0) REVERT: B 137 ASN cc_start: 0.7574 (m-40) cc_final: 0.7283 (m-40) outliers start: 19 outliers final: 12 residues processed: 107 average time/residue: 0.2347 time to fit residues: 35.1993 Evaluate side-chains 104 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8772 Z= 0.170 Angle : 0.663 13.474 12063 Z= 0.378 Chirality : 0.041 0.393 1304 Planarity : 0.006 0.116 1398 Dihedral : 15.405 91.329 1385 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 2.01 % Allowed : 18.32 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.42 (0.27), residues: 933 helix: 1.16 (0.31), residues: 312 sheet: -0.23 (0.39), residues: 151 loop : -1.31 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 406 HIS 0.004 0.001 HIS A 198 PHE 0.005 0.001 PHE B 416 TYR 0.014 0.001 TYR A 457 ARG 0.002 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.929 Fit side-chains REVERT: A 107 THR cc_start: 0.7552 (OUTLIER) cc_final: 0.7292 (m) REVERT: A 202 ILE cc_start: 0.5828 (OUTLIER) cc_final: 0.5619 (mm) REVERT: A 310 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7495 (mp) REVERT: A 480 GLN cc_start: 0.6563 (OUTLIER) cc_final: 0.6156 (pt0) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 0.2150 time to fit residues: 32.0535 Evaluate side-chains 102 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 0.1980 chunk 47 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 chunk 81 optimal weight: 30.0000 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8772 Z= 0.261 Angle : 0.727 14.333 12063 Z= 0.406 Chirality : 0.043 0.339 1304 Planarity : 0.006 0.117 1398 Dihedral : 15.584 90.911 1385 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 1.89 % Allowed : 19.03 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.75 (0.27), residues: 933 helix: 0.92 (0.31), residues: 308 sheet: -0.69 (0.38), residues: 144 loop : -1.40 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.012 0.002 PHE B 130 TYR 0.019 0.002 TYR A 457 ARG 0.007 0.000 ARG A 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.967 Fit side-chains REVERT: A 107 THR cc_start: 0.7593 (OUTLIER) cc_final: 0.7352 (m) REVERT: A 202 ILE cc_start: 0.5972 (OUTLIER) cc_final: 0.5728 (mm) REVERT: A 310 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7537 (mp) REVERT: A 480 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6360 (pt0) REVERT: B 137 ASN cc_start: 0.7569 (m-40) cc_final: 0.7285 (m-40) outliers start: 16 outliers final: 11 residues processed: 105 average time/residue: 0.2289 time to fit residues: 33.2125 Evaluate side-chains 104 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.205482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.173150 restraints weight = 9280.937| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.55 r_work: 0.3663 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 8772 Z= 0.389 Angle : 0.805 14.866 12063 Z= 0.446 Chirality : 0.047 0.317 1304 Planarity : 0.007 0.120 1398 Dihedral : 15.670 89.609 1385 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.14 % Favored : 94.75 % Rotamer: Outliers : 2.36 % Allowed : 18.68 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.30 (0.26), residues: 933 helix: 0.39 (0.30), residues: 308 sheet: -1.09 (0.38), residues: 144 loop : -1.65 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 406 HIS 0.004 0.001 HIS A 208 PHE 0.017 0.002 PHE B 130 TYR 0.022 0.003 TYR A 457 ARG 0.007 0.001 ARG A 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1774.51 seconds wall clock time: 33 minutes 17.30 seconds (1997.30 seconds total)