Starting phenix.real_space_refine on Fri Jan 19 20:48:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsh_32758/01_2024/7wsh_32758.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsh_32758/01_2024/7wsh_32758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsh_32758/01_2024/7wsh_32758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsh_32758/01_2024/7wsh_32758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsh_32758/01_2024/7wsh_32758.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsh_32758/01_2024/7wsh_32758.pdb" } resolution = 2.89 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= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6216 atoms to isotropic. 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 Zn 1 6.06 5 S 37 5.16 5 C 4119 2.51 5 N 1082 2.21 5 O 1218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6457 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4899 Classifications: {'peptide': 598} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 568} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.69, per 1000 atoms: 0.57 Number of scatterers: 6457 At special positions: 0 Unit cell: (72.921, 84.963, 127.11, 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) Zn 1 29.99 S 37 16.00 O 1218 8.00 N 1082 7.00 C 4119 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 Links applied NAG-ASN " NAG B 601 " - " ASN B 343 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 56.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.720A pdb=" N GLU A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.655A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.550A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 removed outlier: 4.074A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.835A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.562A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.589A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.610A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 removed outlier: 3.688A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.577A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.636A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.083A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.835A pdb=" N MET A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.827A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.556A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.971A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.522A pdb=" N THR A 347 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.559A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 318 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2086 1.34 - 1.46: 1704 1.46 - 1.58: 2793 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6641 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C5 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C3 NAG B 601 " pdb=" O3 NAG B 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.02e+00 bond pdb=" CA ILE A 54 " pdb=" CB ILE A 54 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 7.03e-01 bond pdb=" C2 NAG B 601 " pdb=" N2 NAG B 601 " ideal model delta sigma weight residual 1.439 1.453 -0.014 2.00e-02 2.50e+03 5.22e-01 ... (remaining 6636 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.79: 226 106.79 - 113.59: 3475 113.59 - 120.40: 2593 120.40 - 127.20: 2632 127.20 - 134.01: 99 Bond angle restraints: 9025 Sorted by residual: angle pdb=" CA GLY A 352 " pdb=" C GLY A 352 " pdb=" N LYS A 353 " ideal model delta sigma weight residual 114.23 117.49 -3.26 8.80e-01 1.29e+00 1.37e+01 angle pdb=" CA GLY A 352 " pdb=" C GLY A 352 " pdb=" O GLY A 352 " ideal model delta sigma weight residual 122.33 119.83 2.50 8.10e-01 1.52e+00 9.53e+00 angle pdb=" CA GLN A 101 " pdb=" C GLN A 101 " pdb=" N HIS A 102 " ideal model delta sigma weight residual 118.27 121.46 -3.19 1.59e+00 3.96e-01 4.02e+00 angle pdb=" N GLY A 352 " pdb=" CA GLY A 352 " pdb=" C GLY A 352 " ideal model delta sigma weight residual 111.85 109.84 2.01 1.06e+00 8.90e-01 3.61e+00 angle pdb=" N GLY B 496 " pdb=" CA GLY B 496 " pdb=" C GLY B 496 " ideal model delta sigma weight residual 113.18 109.00 4.18 2.37e+00 1.78e-01 3.11e+00 ... (remaining 9020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.23: 3704 15.23 - 30.46: 177 30.46 - 45.68: 48 45.68 - 60.91: 9 60.91 - 76.14: 2 Dihedral angle restraints: 3940 sinusoidal: 1611 harmonic: 2329 Sorted by residual: dihedral pdb=" CA VAL A 342 " pdb=" C VAL A 342 " pdb=" N VAL A 343 " pdb=" CA VAL A 343 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.64e+00 dihedral pdb=" N GLN B 493 " pdb=" CA GLN B 493 " pdb=" CB GLN B 493 " pdb=" CG GLN B 493 " ideal model delta sinusoidal sigma weight residual -180.00 -125.71 -54.29 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CA TYR A 497 " pdb=" C TYR A 497 " pdb=" N CYS A 498 " pdb=" CA CYS A 498 " ideal model delta harmonic sigma weight residual 180.00 164.82 15.18 0 5.00e+00 4.00e-02 9.21e+00 ... (remaining 3937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 487 0.025 - 0.050: 279 0.050 - 0.075: 108 0.075 - 0.100: 45 0.100 - 0.124: 19 Chirality restraints: 938 Sorted by residual: chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA VAL A 343 " pdb=" N VAL A 343 " pdb=" C VAL A 343 " pdb=" CB VAL A 343 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 935 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO B 521 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO A 583 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 388 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO A 389 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " 0.015 5.00e-02 4.00e+02 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 123 2.69 - 3.24: 6431 3.24 - 3.80: 10582 3.80 - 4.35: 15128 4.35 - 4.90: 24081 Nonbonded interactions: 56345 Sorted by model distance: nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.140 2.440 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.152 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.163 2.230 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.174 2.440 nonbonded pdb=" OG1 THR A 276 " pdb=" OG1 THR A 445 " model vdw 2.282 2.440 ... (remaining 56340 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 10.160 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.410 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6641 Z= 0.165 Angle : 0.445 5.085 9025 Z= 0.237 Chirality : 0.039 0.124 938 Planarity : 0.003 0.030 1172 Dihedral : 10.058 76.137 2425 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.72 % Allowed : 3.87 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.03 (0.29), residues: 789 helix: 0.03 (0.26), residues: 391 sheet: 0.80 (0.87), residues: 41 loop : 0.02 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.009 0.001 PHE A 428 TYR 0.016 0.001 TYR A 385 ARG 0.002 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7481 (tp40) cc_final: 0.7241 (tp40) REVERT: A 114 GLN cc_start: 0.7554 (pt0) cc_final: 0.7232 (tp-100) REVERT: A 332 MET cc_start: 0.7917 (ttp) cc_final: 0.7660 (ttp) outliers start: 5 outliers final: 2 residues processed: 156 average time/residue: 1.2790 time to fit residues: 208.9417 Evaluate side-chains 102 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 82 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 228 GLN A 325 GLN A 586 ASN B 354 ASN B 409 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6641 Z= 0.229 Angle : 0.534 5.883 9025 Z= 0.283 Chirality : 0.043 0.152 938 Planarity : 0.004 0.037 1172 Dihedral : 5.146 51.306 892 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.30 % Allowed : 12.77 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.37 (0.29), residues: 789 helix: 0.43 (0.26), residues: 398 sheet: 0.69 (0.82), residues: 43 loop : 0.17 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.011 0.001 PHE A 428 TYR 0.021 0.002 TYR A 385 ARG 0.007 0.001 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7503 (tp40) cc_final: 0.7101 (tp40) REVERT: A 578 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7482 (p0) outliers start: 16 outliers final: 7 residues processed: 112 average time/residue: 1.1898 time to fit residues: 140.1410 Evaluate side-chains 96 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 322 ASN A 325 GLN A 401 HIS B 354 ASN B 493 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6641 Z= 0.179 Angle : 0.480 5.666 9025 Z= 0.251 Chirality : 0.041 0.133 938 Planarity : 0.004 0.037 1172 Dihedral : 4.800 40.957 892 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.58 % Allowed : 13.63 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.56 (0.29), residues: 789 helix: 0.68 (0.26), residues: 403 sheet: 0.58 (0.81), residues: 43 loop : 0.16 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.010 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.006 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7544 (tp40) cc_final: 0.7211 (tp40) REVERT: A 114 GLN cc_start: 0.7232 (tp-100) cc_final: 0.6944 (tp-100) REVERT: A 578 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7513 (p0) outliers start: 18 outliers final: 8 residues processed: 110 average time/residue: 1.2263 time to fit residues: 141.8063 Evaluate side-chains 99 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 472 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 98 GLN A 322 ASN A 325 GLN B 354 ASN B 493 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6641 Z= 0.413 Angle : 0.596 7.396 9025 Z= 0.311 Chirality : 0.047 0.154 938 Planarity : 0.004 0.042 1172 Dihedral : 5.156 33.832 892 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.59 % Allowed : 14.49 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.35 (0.29), residues: 789 helix: 0.47 (0.26), residues: 400 sheet: 0.40 (0.79), residues: 43 loop : 0.12 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 163 HIS 0.008 0.002 HIS A 239 PHE 0.020 0.002 PHE A 32 TYR 0.024 0.002 TYR A 385 ARG 0.009 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7577 (tp40) cc_final: 0.7218 (tp40) REVERT: A 143 LEU cc_start: 0.8407 (mt) cc_final: 0.8134 (mt) REVERT: A 578 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7571 (p0) outliers start: 25 outliers final: 12 residues processed: 113 average time/residue: 1.1832 time to fit residues: 140.7848 Evaluate side-chains 104 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 98 GLN A 325 GLN B 493 GLN B 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6641 Z= 0.196 Angle : 0.492 6.066 9025 Z= 0.257 Chirality : 0.041 0.134 938 Planarity : 0.004 0.040 1172 Dihedral : 4.701 27.844 892 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.16 % Allowed : 16.21 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.62 (0.29), residues: 789 helix: 0.77 (0.26), residues: 396 sheet: 0.45 (0.81), residues: 43 loop : 0.17 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.012 0.001 PHE A 428 TYR 0.019 0.001 TYR A 385 ARG 0.006 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7540 (tp40) cc_final: 0.7008 (tp-100) REVERT: A 406 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8139 (mm-30) REVERT: A 578 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7609 (p0) outliers start: 22 outliers final: 10 residues processed: 109 average time/residue: 1.2496 time to fit residues: 143.0851 Evaluate side-chains 103 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 322 ASN A 325 GLN B 493 GLN B 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6641 Z= 0.189 Angle : 0.489 5.748 9025 Z= 0.255 Chirality : 0.041 0.135 938 Planarity : 0.004 0.053 1172 Dihedral : 4.539 28.013 892 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.44 % Allowed : 15.78 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.76 (0.29), residues: 789 helix: 0.90 (0.26), residues: 396 sheet: 0.39 (0.79), residues: 43 loop : 0.22 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.011 0.001 PHE A 428 TYR 0.018 0.001 TYR A 385 ARG 0.010 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7503 (tp40) cc_final: 0.6986 (tp-100) REVERT: A 406 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8138 (mm-30) REVERT: A 470 LYS cc_start: 0.8258 (mtmp) cc_final: 0.8006 (mtmm) REVERT: A 578 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7618 (p0) outliers start: 24 outliers final: 16 residues processed: 113 average time/residue: 1.2034 time to fit residues: 143.0149 Evaluate side-chains 110 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 322 ASN A 325 GLN B 493 GLN B 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6641 Z= 0.158 Angle : 0.475 6.238 9025 Z= 0.247 Chirality : 0.040 0.155 938 Planarity : 0.004 0.047 1172 Dihedral : 4.407 27.564 892 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.16 % Allowed : 16.36 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.30), residues: 789 helix: 1.03 (0.26), residues: 395 sheet: 0.50 (0.80), residues: 43 loop : 0.27 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.010 0.001 PHE A 428 TYR 0.017 0.001 TYR A 385 ARG 0.008 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7513 (tp40) cc_final: 0.7018 (tp-100) REVERT: A 406 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8144 (mm-30) REVERT: A 419 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7790 (ttmm) REVERT: A 470 LYS cc_start: 0.8248 (mtmp) cc_final: 0.8003 (mtmm) REVERT: A 578 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7607 (p0) outliers start: 22 outliers final: 15 residues processed: 109 average time/residue: 1.3391 time to fit residues: 153.0867 Evaluate side-chains 105 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 72 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 322 ASN A 325 GLN B 493 GLN B 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6641 Z= 0.158 Angle : 0.477 6.332 9025 Z= 0.247 Chirality : 0.040 0.146 938 Planarity : 0.004 0.050 1172 Dihedral : 4.351 27.423 892 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.16 % Allowed : 16.50 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.98 (0.30), residues: 789 helix: 1.10 (0.26), residues: 395 sheet: 0.56 (0.80), residues: 43 loop : 0.31 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE A 428 TYR 0.017 0.001 TYR A 385 ARG 0.008 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7525 (tp40) cc_final: 0.7033 (tp-100) REVERT: A 98 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: A 578 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7608 (p0) REVERT: A 600 ARG cc_start: 0.7041 (mmm-85) cc_final: 0.6833 (ptm160) outliers start: 22 outliers final: 14 residues processed: 105 average time/residue: 1.2692 time to fit residues: 139.8577 Evaluate side-chains 105 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 299 ASN A 322 ASN A 325 GLN B 493 GLN B 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6641 Z= 0.174 Angle : 0.486 7.156 9025 Z= 0.252 Chirality : 0.041 0.148 938 Planarity : 0.004 0.043 1172 Dihedral : 4.350 27.288 892 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.73 % Allowed : 17.07 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.01 (0.29), residues: 789 helix: 1.17 (0.26), residues: 389 sheet: 0.55 (0.80), residues: 43 loop : 0.26 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.010 0.001 PHE A 428 TYR 0.018 0.001 TYR A 385 ARG 0.007 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7529 (tp40) cc_final: 0.7041 (tp-100) REVERT: A 98 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: A 578 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7609 (p0) REVERT: A 600 ARG cc_start: 0.7055 (mmm-85) cc_final: 0.6851 (ptm160) outliers start: 19 outliers final: 14 residues processed: 105 average time/residue: 1.1959 time to fit residues: 132.3385 Evaluate side-chains 104 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 322 ASN A 325 GLN A 401 HIS B 493 GLN B 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6641 Z= 0.160 Angle : 0.491 8.303 9025 Z= 0.253 Chirality : 0.040 0.145 938 Planarity : 0.004 0.038 1172 Dihedral : 4.312 26.943 892 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.15 % Allowed : 17.65 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.05 (0.29), residues: 789 helix: 1.22 (0.26), residues: 389 sheet: 0.52 (0.80), residues: 43 loop : 0.28 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.010 0.001 PHE A 523 TYR 0.016 0.001 TYR A 385 ARG 0.007 0.000 ARG A 600 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8342 (ttp) cc_final: 0.8091 (ttm) REVERT: A 79 GLN cc_start: 0.7536 (tp40) cc_final: 0.7053 (tp-100) REVERT: A 98 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: A 578 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7602 (p0) REVERT: A 600 ARG cc_start: 0.7056 (mmm-85) cc_final: 0.6852 (ptm160) REVERT: B 414 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7772 (tp40) outliers start: 15 outliers final: 12 residues processed: 100 average time/residue: 1.2062 time to fit residues: 126.9701 Evaluate side-chains 102 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 0.0050 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN B 493 GLN B 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.153342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120881 restraints weight = 7237.267| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.79 r_work: 0.3209 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6641 Z= 0.151 Angle : 0.485 9.179 9025 Z= 0.251 Chirality : 0.040 0.144 938 Planarity : 0.004 0.037 1172 Dihedral : 4.261 26.489 892 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.01 % Allowed : 18.22 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.12 (0.30), residues: 789 helix: 1.29 (0.26), residues: 389 sheet: 0.51 (0.81), residues: 43 loop : 0.29 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE A 523 TYR 0.016 0.001 TYR A 385 ARG 0.006 0.000 ARG A 600 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3182.01 seconds wall clock time: 56 minutes 58.93 seconds (3418.93 seconds total)