Starting phenix.real_space_refine on Tue Feb 13 20:07:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uag_26425/02_2024/7uag_26425.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uag_26425/02_2024/7uag_26425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uag_26425/02_2024/7uag_26425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uag_26425/02_2024/7uag_26425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uag_26425/02_2024/7uag_26425.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uag_26425/02_2024/7uag_26425.pdb" } resolution = 3.5 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= 0.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4838 2.51 5 N 1318 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 313": "OD1" <-> "OD2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 443": "OD1" <-> "OD2" Residue "B PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "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: 7588 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3794 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3794 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLU A 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU A 504 " occ=0.50 residue: pdb=" N GLU B 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU B 504 " occ=0.50 Time building chain proxies: 4.54, per 1000 atoms: 0.60 Number of scatterers: 7588 At special positions: 0 Unit cell: (107.07, 125.33, 73.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1392 8.00 N 1318 7.00 C 4838 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: 3.06 Conformation dependent library (CDL) restraints added in 1.4 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 42.3% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 41 through 58 removed outlier: 5.272A pdb=" N TYR A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix removed outlier: 3.758A pdb=" N ASP A 58 " --> pdb=" O TRP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.958A pdb=" N MET A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 454 through 465 removed outlier: 3.617A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 489 through 500 removed outlier: 4.070A pdb=" N ASP A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 5.388A pdb=" N TYR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix removed outlier: 3.787A pdb=" N ASP B 58 " --> pdb=" O TRP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 86 through 89 removed outlier: 3.645A pdb=" N LYS 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 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.719A pdb=" N ARG B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.727A pdb=" N ILE B 196 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 removed outlier: 3.639A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.249A pdb=" N PHE B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 251' Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 299 through 303 removed outlier: 3.663A pdb=" N ASN B 302 " --> pdb=" O GLN B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.529A pdb=" N THR B 319 " --> pdb=" O GLY B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.835A pdb=" N ASP B 350 " --> pdb=" O GLU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 454 through 476 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 489 through 500 removed outlier: 4.117A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 106 removed outlier: 3.828A pdb=" N VAL A 68 " --> pdb=" O PHE A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 106 removed outlier: 3.828A pdb=" N VAL A 68 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TYR A 139 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 35 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 373 removed outlier: 3.571A pdb=" N LYS A 366 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA A 231 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE A 355 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL A 233 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ILE A 480 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 305 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TYR A 482 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN A 307 " --> pdb=" O TYR A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 393 Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 407 Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.341A pdb=" N ILE B 33 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TYR B 139 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE B 35 " --> pdb=" O TYR B 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 356 removed outlier: 8.410A pdb=" N ILE B 355 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 233 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.645A pdb=" N LEU B 305 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR B 482 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLN B 307 " --> pdb=" O TYR B 482 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 391 through 393 Processing sheet with id=AB1, first strand: chain 'B' and resid 405 through 407 285 hydrogen bonds defined for protein. 813 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: 2.16 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2296 1.33 - 1.45: 1200 1.45 - 1.57: 4203 1.57 - 1.69: 1 1.69 - 1.81: 66 Bond restraints: 7766 Sorted by residual: bond pdb=" CB PRO A 172 " pdb=" CG PRO A 172 " ideal model delta sigma weight residual 1.506 1.600 -0.094 3.90e-02 6.57e+02 5.76e+00 bond pdb=" C VAL A 68 " pdb=" N GLY A 69 " ideal model delta sigma weight residual 1.328 1.305 0.023 1.13e-02 7.83e+03 4.29e+00 bond pdb=" C VAL B 68 " pdb=" N GLY B 69 " ideal model delta sigma weight residual 1.328 1.305 0.023 1.13e-02 7.83e+03 4.23e+00 bond pdb=" CA GLY B 69 " pdb=" C GLY B 69 " ideal model delta sigma weight residual 1.519 1.495 0.024 1.47e-02 4.63e+03 2.77e+00 bond pdb=" C TYR A 70 " pdb=" O TYR A 70 " ideal model delta sigma weight residual 1.235 1.215 0.021 1.26e-02 6.30e+03 2.65e+00 ... (remaining 7761 not shown) Histogram of bond angle deviations from ideal: 97.46 - 104.81: 145 104.81 - 112.15: 3678 112.15 - 119.50: 2750 119.50 - 126.84: 3830 126.84 - 134.19: 99 Bond angle restraints: 10502 Sorted by residual: angle pdb=" CA PRO A 172 " pdb=" N PRO A 172 " pdb=" CD PRO A 172 " ideal model delta sigma weight residual 111.50 105.35 6.15 1.40e+00 5.10e-01 1.93e+01 angle pdb=" N PRO A 172 " pdb=" CD PRO A 172 " pdb=" CG PRO A 172 " ideal model delta sigma weight residual 103.80 98.57 5.23 1.20e+00 6.94e-01 1.90e+01 angle pdb=" C PRO A 276 " pdb=" N ALA A 277 " pdb=" CA ALA A 277 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" N PRO B 172 " pdb=" CD PRO B 172 " pdb=" CG PRO B 172 " ideal model delta sigma weight residual 103.80 99.84 3.96 1.20e+00 6.94e-01 1.09e+01 angle pdb=" CA GLY A 69 " pdb=" C GLY A 69 " pdb=" O GLY A 69 " ideal model delta sigma weight residual 122.76 119.25 3.51 1.12e+00 7.97e-01 9.81e+00 ... (remaining 10497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4262 17.98 - 35.97: 345 35.97 - 53.95: 57 53.95 - 71.93: 7 71.93 - 89.91: 3 Dihedral angle restraints: 4674 sinusoidal: 1944 harmonic: 2730 Sorted by residual: dihedral pdb=" CA MET A 207 " pdb=" C MET A 207 " pdb=" N VAL A 208 " pdb=" CA VAL A 208 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ASN B 218 " pdb=" C ASN B 218 " pdb=" N ARG B 219 " pdb=" CA ARG B 219 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ASN A 218 " pdb=" C ASN A 218 " pdb=" N ARG A 219 " pdb=" CA ARG A 219 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 4671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 593 0.028 - 0.056: 298 0.056 - 0.084: 144 0.084 - 0.111: 64 0.111 - 0.139: 25 Chirality restraints: 1124 Sorted by residual: chirality pdb=" CA ILE A 392 " pdb=" N ILE A 392 " pdb=" C ILE A 392 " pdb=" CB ILE A 392 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE B 196 " pdb=" N ILE B 196 " pdb=" C ILE B 196 " pdb=" CB ILE B 196 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA THR A 279 " pdb=" N THR A 279 " pdb=" C THR A 279 " pdb=" CB THR A 279 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 1121 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 433 " 0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A 434 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 434 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 434 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 352 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO A 353 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 239 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.17e+00 pdb=" N PRO A 240 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " -0.031 5.00e-02 4.00e+02 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1594 2.78 - 3.31: 7608 3.31 - 3.84: 12940 3.84 - 4.37: 14984 4.37 - 4.90: 26110 Nonbonded interactions: 63236 Sorted by model distance: nonbonded pdb=" O ILE A 80 " pdb=" OG SER A 84 " model vdw 2.247 2.440 nonbonded pdb=" OE2 GLU A 274 " pdb=" ND2 ASN A 346 " model vdw 2.247 2.520 nonbonded pdb=" OE1 GLN A 209 " pdb=" NZ LYS B 407 " model vdw 2.259 2.520 nonbonded pdb=" OE2 GLU B 274 " pdb=" ND2 ASN B 346 " model vdw 2.261 2.520 nonbonded pdb=" NH2 ARG B 215 " pdb=" O MET B 273 " model vdw 2.278 2.520 ... (remaining 63231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.50 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: 0.250 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: 1.700 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.120 Find NCS groups from input model: 0.410 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 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 0.094 7766 Z= 0.277 Angle : 0.663 8.837 10502 Z= 0.355 Chirality : 0.045 0.139 1124 Planarity : 0.006 0.081 1374 Dihedral : 13.108 89.913 2914 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.45 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.43 (0.27), residues: 930 helix: 0.02 (0.28), residues: 330 sheet: -2.33 (0.41), residues: 142 loop : -1.13 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 225 HIS 0.004 0.001 HIS A 263 PHE 0.027 0.002 PHE A 173 TYR 0.013 0.002 TYR B 118 ARG 0.008 0.000 ARG B 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.913 Fit side-chains REVERT: A 70 TYR cc_start: 0.7609 (t80) cc_final: 0.7267 (t80) REVERT: A 111 GLN cc_start: 0.6906 (mm110) cc_final: 0.6329 (mm-40) REVERT: A 137 LEU cc_start: 0.8189 (tt) cc_final: 0.7691 (tt) REVERT: B 70 TYR cc_start: 0.7377 (t80) cc_final: 0.7040 (t80) REVERT: B 111 GLN cc_start: 0.6751 (mm-40) cc_final: 0.6394 (mm-40) REVERT: B 207 MET cc_start: 0.7476 (mmm) cc_final: 0.7265 (mmm) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1910 time to fit residues: 29.8342 Evaluate side-chains 95 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7766 Z= 0.180 Angle : 0.576 8.874 10502 Z= 0.294 Chirality : 0.044 0.178 1124 Planarity : 0.005 0.056 1374 Dihedral : 4.461 22.721 1032 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.85 % Allowed : 7.20 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.27), residues: 930 helix: 0.19 (0.29), residues: 330 sheet: -2.09 (0.41), residues: 136 loop : -1.08 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 225 HIS 0.003 0.001 HIS A 263 PHE 0.020 0.002 PHE A 173 TYR 0.016 0.002 TYR B 484 ARG 0.005 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.879 Fit side-chains REVERT: A 70 TYR cc_start: 0.7519 (t80) cc_final: 0.7236 (t80) REVERT: A 95 LYS cc_start: 0.6828 (mmtt) cc_final: 0.6370 (mmtm) REVERT: A 111 GLN cc_start: 0.6676 (mm110) cc_final: 0.6393 (mm-40) REVERT: B 70 TYR cc_start: 0.7102 (t80) cc_final: 0.6762 (t80) REVERT: B 465 PHE cc_start: 0.6306 (t80) cc_final: 0.6087 (t80) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.1811 time to fit residues: 26.9946 Evaluate side-chains 100 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 456 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7766 Z= 0.353 Angle : 0.662 8.409 10502 Z= 0.339 Chirality : 0.047 0.184 1124 Planarity : 0.005 0.050 1374 Dihedral : 4.848 22.622 1032 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.46 % Allowed : 10.61 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.54 (0.26), residues: 930 helix: -0.16 (0.28), residues: 330 sheet: -2.29 (0.43), residues: 126 loop : -1.21 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 225 HIS 0.003 0.001 HIS B 382 PHE 0.028 0.002 PHE A 173 TYR 0.026 0.002 TYR B 484 ARG 0.007 0.001 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 95 LYS cc_start: 0.6954 (mmtt) cc_final: 0.6496 (mmtm) REVERT: A 111 GLN cc_start: 0.6557 (mm110) cc_final: 0.6277 (mm-40) REVERT: A 114 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6949 (p0) REVERT: A 244 GLU cc_start: 0.6099 (pm20) cc_final: 0.5512 (pm20) REVERT: B 70 TYR cc_start: 0.7369 (t80) cc_final: 0.7110 (t80) REVERT: B 111 GLN cc_start: 0.6695 (mm110) cc_final: 0.6205 (mm-40) outliers start: 12 outliers final: 7 residues processed: 110 average time/residue: 0.2126 time to fit residues: 31.8614 Evaluate side-chains 107 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7766 Z= 0.179 Angle : 0.569 8.740 10502 Z= 0.288 Chirality : 0.043 0.162 1124 Planarity : 0.005 0.072 1374 Dihedral : 4.532 25.744 1032 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.22 % Allowed : 12.20 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.22 (0.27), residues: 930 helix: 0.20 (0.29), residues: 330 sheet: -2.00 (0.38), residues: 154 loop : -1.05 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 225 HIS 0.004 0.001 HIS A 201 PHE 0.019 0.002 PHE A 253 TYR 0.016 0.002 TYR B 484 ARG 0.004 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 95 LYS cc_start: 0.6948 (mmtt) cc_final: 0.6506 (mmtm) REVERT: A 137 LEU cc_start: 0.8238 (tt) cc_final: 0.7885 (tt) REVERT: B 70 TYR cc_start: 0.7127 (t80) cc_final: 0.6803 (t80) REVERT: B 111 GLN cc_start: 0.6669 (mm110) cc_final: 0.5995 (mm-40) outliers start: 10 outliers final: 5 residues processed: 107 average time/residue: 0.1986 time to fit residues: 29.3785 Evaluate side-chains 104 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 456 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 75 optimal weight: 0.0980 chunk 61 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 29 optimal weight: 0.1980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7766 Z= 0.236 Angle : 0.594 8.768 10502 Z= 0.302 Chirality : 0.044 0.202 1124 Planarity : 0.005 0.072 1374 Dihedral : 4.585 28.259 1032 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.83 % Allowed : 13.05 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.45 (0.27), residues: 930 helix: 0.09 (0.29), residues: 334 sheet: -2.55 (0.34), residues: 190 loop : -0.88 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 225 HIS 0.003 0.001 HIS A 201 PHE 0.024 0.002 PHE A 173 TYR 0.019 0.002 TYR B 484 ARG 0.005 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: B 70 TYR cc_start: 0.7161 (t80) cc_final: 0.6945 (t80) REVERT: B 111 GLN cc_start: 0.6687 (mm110) cc_final: 0.6222 (mm-40) REVERT: B 450 MET cc_start: 0.8084 (tmm) cc_final: 0.7732 (tmm) outliers start: 15 outliers final: 9 residues processed: 109 average time/residue: 0.1952 time to fit residues: 29.3860 Evaluate side-chains 107 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 52 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7766 Z= 0.177 Angle : 0.567 9.345 10502 Z= 0.287 Chirality : 0.043 0.197 1124 Planarity : 0.005 0.069 1374 Dihedral : 4.474 30.087 1032 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.95 % Allowed : 14.15 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.29 (0.27), residues: 930 helix: 0.26 (0.29), residues: 334 sheet: -2.32 (0.35), residues: 182 loop : -0.94 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 225 HIS 0.003 0.001 HIS A 201 PHE 0.024 0.002 PHE A 173 TYR 0.015 0.001 TYR B 484 ARG 0.004 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 95 LYS cc_start: 0.6947 (mmtt) cc_final: 0.6554 (mmtm) REVERT: A 137 LEU cc_start: 0.8195 (tt) cc_final: 0.7917 (tt) REVERT: B 111 GLN cc_start: 0.6742 (mm110) cc_final: 0.6241 (mm-40) REVERT: B 450 MET cc_start: 0.8035 (tmm) cc_final: 0.7707 (tmm) outliers start: 16 outliers final: 8 residues processed: 106 average time/residue: 0.1919 time to fit residues: 28.2895 Evaluate side-chains 101 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 456 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 overall best weight: 2.8984 ------------------------------------------------------------------------------- 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: 0.6569 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7766 Z= 0.299 Angle : 0.644 9.623 10502 Z= 0.327 Chirality : 0.045 0.197 1124 Planarity : 0.005 0.048 1374 Dihedral : 4.703 29.940 1032 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.83 % Allowed : 14.76 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.44 (0.27), residues: 930 helix: -0.00 (0.29), residues: 334 sheet: -2.43 (0.36), residues: 178 loop : -0.91 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 349 HIS 0.003 0.001 HIS A 201 PHE 0.027 0.002 PHE A 173 TYR 0.022 0.002 TYR B 484 ARG 0.005 0.000 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 95 LYS cc_start: 0.6982 (mmtt) cc_final: 0.6596 (mmtm) REVERT: A 137 LEU cc_start: 0.8293 (tt) cc_final: 0.7981 (tt) REVERT: B 70 TYR cc_start: 0.7325 (t80) cc_final: 0.7087 (t80) outliers start: 15 outliers final: 9 residues processed: 108 average time/residue: 0.1892 time to fit residues: 28.3780 Evaluate side-chains 105 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 456 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.0270 chunk 8 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 0.0060 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 0.5454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7766 Z= 0.176 Angle : 0.599 9.669 10502 Z= 0.297 Chirality : 0.043 0.157 1124 Planarity : 0.005 0.072 1374 Dihedral : 4.439 26.991 1032 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.59 % Allowed : 16.22 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.27), residues: 930 helix: 0.33 (0.29), residues: 330 sheet: -2.31 (0.35), residues: 182 loop : -0.91 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 53 HIS 0.006 0.001 HIS B 451 PHE 0.023 0.002 PHE A 173 TYR 0.018 0.002 TYR B 70 ARG 0.005 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 137 LEU cc_start: 0.8224 (tt) cc_final: 0.7762 (tt) REVERT: A 495 LEU cc_start: 0.5010 (OUTLIER) cc_final: 0.4094 (tp) REVERT: B 70 TYR cc_start: 0.7141 (t80) cc_final: 0.6830 (t80) REVERT: B 111 GLN cc_start: 0.6644 (mm110) cc_final: 0.6399 (mm-40) outliers start: 13 outliers final: 9 residues processed: 104 average time/residue: 0.1911 time to fit residues: 27.3842 Evaluate side-chains 104 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 456 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 78 optimal weight: 0.0070 chunk 82 optimal weight: 0.0030 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7766 Z= 0.199 Angle : 0.609 9.662 10502 Z= 0.300 Chirality : 0.043 0.172 1124 Planarity : 0.004 0.051 1374 Dihedral : 4.377 27.479 1032 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.22 % Allowed : 16.95 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.00 (0.27), residues: 930 helix: 0.39 (0.29), residues: 330 sheet: -1.90 (0.39), residues: 158 loop : -0.89 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 53 HIS 0.004 0.001 HIS B 451 PHE 0.020 0.002 PHE A 173 TYR 0.015 0.002 TYR B 484 ARG 0.005 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 137 LEU cc_start: 0.8194 (tt) cc_final: 0.7741 (tt) REVERT: A 343 TYR cc_start: 0.3861 (m-10) cc_final: 0.3510 (m-80) REVERT: A 495 LEU cc_start: 0.5004 (OUTLIER) cc_final: 0.4048 (tp) REVERT: B 70 TYR cc_start: 0.7200 (t80) cc_final: 0.6850 (t80) REVERT: B 111 GLN cc_start: 0.6704 (mm110) cc_final: 0.6429 (mm-40) REVERT: B 465 PHE cc_start: 0.6547 (t80) cc_final: 0.6272 (t80) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.1955 time to fit residues: 27.9526 Evaluate side-chains 103 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 456 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.0030 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7766 Z= 0.169 Angle : 0.590 9.819 10502 Z= 0.289 Chirality : 0.042 0.144 1124 Planarity : 0.004 0.054 1374 Dihedral : 4.264 25.884 1032 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.85 % Allowed : 17.32 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.10 (0.28), residues: 930 helix: 0.50 (0.29), residues: 330 sheet: -2.29 (0.34), residues: 192 loop : -0.80 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 53 HIS 0.004 0.001 HIS B 451 PHE 0.022 0.002 PHE B 216 TYR 0.014 0.001 TYR B 70 ARG 0.004 0.000 ARG A 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 TYR cc_start: 0.7087 (t80) cc_final: 0.6722 (t80) REVERT: B 111 GLN cc_start: 0.6726 (mm110) cc_final: 0.6372 (mm-40) REVERT: B 465 PHE cc_start: 0.6526 (t80) cc_final: 0.6161 (t80) outliers start: 7 outliers final: 5 residues processed: 100 average time/residue: 0.1882 time to fit residues: 26.5187 Evaluate side-chains 95 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 456 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.0470 chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.251906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.224668 restraints weight = 9635.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.224188 restraints weight = 6922.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.225730 restraints weight = 5918.332| |-----------------------------------------------------------------------------| r_work (final): 0.4611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4610 r_free = 0.4610 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4610 r_free = 0.4610 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7766 Z= 0.213 Angle : 0.605 9.733 10502 Z= 0.298 Chirality : 0.043 0.142 1124 Planarity : 0.005 0.077 1374 Dihedral : 4.302 25.245 1032 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.10 % Allowed : 17.07 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.13 (0.28), residues: 930 helix: 0.47 (0.29), residues: 330 sheet: -2.37 (0.35), residues: 182 loop : -0.84 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 349 HIS 0.005 0.001 HIS B 451 PHE 0.018 0.002 PHE B 216 TYR 0.017 0.002 TYR B 484 ARG 0.005 0.000 ARG A 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1675.41 seconds wall clock time: 31 minutes 12.71 seconds (1872.71 seconds total)