Starting phenix.real_space_refine on Mon Sep 23 14:51:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f63_31471/09_2024/7f63_31471.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f63_31471/09_2024/7f63_31471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f63_31471/09_2024/7f63_31471.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f63_31471/09_2024/7f63_31471.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f63_31471/09_2024/7f63_31471.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f63_31471/09_2024/7f63_31471.cif" } resolution = 3.9 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= 0.031 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 15 5.16 5 C 2149 2.51 5 N 555 2.21 5 O 656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3375 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1578 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 945 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 852 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Time building chain proxies: 3.10, per 1000 atoms: 0.92 Number of scatterers: 3375 At special positions: 0 Unit cell: (67.1, 80.3, 115.5, 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 15 16.00 O 656 8.00 N 555 7.00 C 2149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 427.7 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 790 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 8.6% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.402A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.479A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.599A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.721A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 439 through 442 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 5.006A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.127A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.760A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.750A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 22 removed outlier: 4.198A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 192 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: 0.80 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1061 1.34 - 1.46: 912 1.46 - 1.58: 1472 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3463 Sorted by residual: bond pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.23e-01 bond pdb=" CA ASN A 394 " pdb=" CB ASN A 394 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.61e-02 3.86e+03 8.66e-01 bond pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 1.808 1.779 0.029 3.30e-02 9.18e+02 7.56e-01 bond pdb=" N ASN A 394 " pdb=" CA ASN A 394 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.42e-02 4.96e+03 7.05e-01 bond pdb=" CA ILE L 75 " pdb=" C ILE L 75 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.16e-02 7.43e+03 6.11e-01 ... (remaining 3458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 4612 1.66 - 3.33: 71 3.33 - 4.99: 16 4.99 - 6.65: 3 6.65 - 8.31: 2 Bond angle restraints: 4704 Sorted by residual: angle pdb=" C LEU H 70 " pdb=" N THR H 71 " pdb=" CA THR H 71 " ideal model delta sigma weight residual 121.75 117.03 4.72 1.73e+00 3.34e-01 7.43e+00 angle pdb=" C TYR H 80 " pdb=" N MET H 81 " pdb=" CA MET H 81 " ideal model delta sigma weight residual 122.65 126.43 -3.78 1.49e+00 4.50e-01 6.45e+00 angle pdb=" C THR A 393 " pdb=" N ASN A 394 " pdb=" CA ASN A 394 " ideal model delta sigma weight residual 122.82 126.21 -3.39 1.42e+00 4.96e-01 5.72e+00 angle pdb=" CA LEU H 70 " pdb=" CB LEU H 70 " pdb=" CG LEU H 70 " ideal model delta sigma weight residual 116.30 124.61 -8.31 3.50e+00 8.16e-02 5.64e+00 angle pdb=" C ASN A 331 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 121.97 125.97 -4.00 1.80e+00 3.09e-01 4.94e+00 ... (remaining 4699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 1824 16.04 - 32.08: 153 32.08 - 48.12: 47 48.12 - 64.15: 8 64.15 - 80.19: 4 Dihedral angle restraints: 2036 sinusoidal: 788 harmonic: 1248 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 12.81 80.19 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 154.13 -61.13 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -46.16 -39.84 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 2033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 304 0.032 - 0.064: 132 0.064 - 0.096: 37 0.096 - 0.128: 23 0.128 - 0.160: 5 Chirality restraints: 501 Sorted by residual: chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CG LEU H 70 " pdb=" CB LEU H 70 " pdb=" CD1 LEU H 70 " pdb=" CD2 LEU H 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ASN A 394 " pdb=" N ASN A 394 " pdb=" C ASN A 394 " pdb=" CB ASN A 394 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 498 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 64 " 0.014 2.00e-02 2.50e+03 2.31e-02 9.32e+00 pdb=" CG PHE H 64 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE H 64 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE H 64 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE H 64 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE H 64 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 64 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 337 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 29 " 0.006 2.00e-02 2.50e+03 8.93e-03 1.40e+00 pdb=" CG PHE H 29 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE H 29 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE H 29 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE H 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE H 29 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE H 29 " -0.000 2.00e-02 2.50e+03 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 92 2.69 - 3.24: 3188 3.24 - 3.79: 5100 3.79 - 4.35: 6634 4.35 - 4.90: 10708 Nonbonded interactions: 25722 Sorted by model distance: nonbonded pdb=" O HIS L 61 " pdb=" OG SER L 76 " model vdw 2.136 3.040 nonbonded pdb=" O ALA H 106 " pdb=" OH TYR L 36 " model vdw 2.141 3.040 nonbonded pdb=" OG1 THR H 28 " pdb=" OE2 GLU H 31 " model vdw 2.170 3.040 nonbonded pdb=" O CYS H 22 " pdb=" OG1 THR H 78 " model vdw 2.290 3.040 nonbonded pdb=" NH2 ARG A 346 " pdb=" OH TYR A 451 " model vdw 2.330 3.120 ... (remaining 25717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 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 : 0.002 0.029 3463 Z= 0.130 Angle : 0.575 8.312 4704 Z= 0.299 Chirality : 0.044 0.160 501 Planarity : 0.004 0.047 605 Dihedral : 13.336 74.505 1228 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.31 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.39), residues: 421 helix: -3.88 (0.95), residues: 12 sheet: 0.31 (0.48), residues: 132 loop : -2.56 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.052 0.002 PHE H 64 TYR 0.016 0.001 TYR L 49 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.7649 (m-30) cc_final: 0.6909 (m-30) REVERT: A 406 GLU cc_start: 0.8120 (mp0) cc_final: 0.7712 (mp0) REVERT: H 101 TYR cc_start: 0.6569 (t80) cc_final: 0.6301 (t80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2227 time to fit residues: 29.9359 Evaluate side-chains 67 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3463 Z= 0.193 Angle : 0.710 11.196 4704 Z= 0.366 Chirality : 0.047 0.206 501 Planarity : 0.004 0.036 605 Dihedral : 4.847 25.931 472 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.74 % Favored : 89.79 % Rotamer: Outliers : 1.89 % Allowed : 13.21 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.39), residues: 421 helix: -2.95 (0.99), residues: 20 sheet: 0.33 (0.48), residues: 131 loop : -2.61 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 35 HIS 0.002 0.001 HIS L 61 PHE 0.023 0.002 PHE H 29 TYR 0.012 0.001 TYR L 53 ARG 0.005 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.7285 (m-30) cc_final: 0.7075 (m-30) REVERT: A 498 GLN cc_start: 0.7464 (mp10) cc_final: 0.6698 (mp10) REVERT: H 57 ASP cc_start: 0.7835 (t0) cc_final: 0.7577 (t0) outliers start: 7 outliers final: 2 residues processed: 86 average time/residue: 0.1722 time to fit residues: 17.6681 Evaluate side-chains 63 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 443 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN L 61 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3463 Z= 0.199 Angle : 0.692 11.797 4704 Z= 0.364 Chirality : 0.048 0.212 501 Planarity : 0.004 0.036 605 Dihedral : 5.153 17.255 472 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.45 % Favored : 89.07 % Rotamer: Outliers : 2.70 % Allowed : 18.06 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.40), residues: 421 helix: -3.10 (0.97), residues: 20 sheet: 0.23 (0.49), residues: 136 loop : -2.54 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 36 HIS 0.002 0.001 HIS L 61 PHE 0.017 0.002 PHE H 29 TYR 0.013 0.001 TYR H 80 ARG 0.005 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6946 (mt-10) REVERT: A 498 GLN cc_start: 0.7665 (mp10) cc_final: 0.6782 (mp10) REVERT: H 33 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8585 (t) REVERT: H 46 GLU cc_start: 0.8296 (mp0) cc_final: 0.8004 (mp0) REVERT: H 57 ASP cc_start: 0.8502 (t0) cc_final: 0.7751 (t0) REVERT: H 62 GLN cc_start: 0.7541 (tm-30) cc_final: 0.7100 (tm-30) REVERT: L 83 LEU cc_start: 0.7105 (tt) cc_final: 0.6578 (pp) REVERT: L 85 GLU cc_start: 0.7253 (tp30) cc_final: 0.6548 (tm-30) outliers start: 10 outliers final: 6 residues processed: 81 average time/residue: 0.2038 time to fit residues: 19.4217 Evaluate side-chains 66 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain L residue 15 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 0.0170 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 1.0222 ------------------------------------------------------------------------------- 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: 0.6741 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3463 Z= 0.240 Angle : 0.731 11.613 4704 Z= 0.383 Chirality : 0.048 0.218 501 Planarity : 0.005 0.039 605 Dihedral : 5.688 21.017 472 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.64 % Favored : 87.89 % Rotamer: Outliers : 2.70 % Allowed : 20.49 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.40), residues: 421 helix: -3.47 (0.85), residues: 20 sheet: 0.13 (0.49), residues: 132 loop : -2.53 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.003 0.001 HIS L 61 PHE 0.016 0.002 PHE H 29 TYR 0.038 0.002 TYR L 91 ARG 0.004 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8456 (tpt170) cc_final: 0.8152 (tpt90) REVERT: A 484 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7022 (mt-10) REVERT: A 498 GLN cc_start: 0.7379 (mp10) cc_final: 0.6353 (mp10) REVERT: H 33 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8967 (t) REVERT: H 46 GLU cc_start: 0.8345 (mp0) cc_final: 0.7951 (mp0) REVERT: H 57 ASP cc_start: 0.8329 (t0) cc_final: 0.7807 (t0) REVERT: H 108 ASP cc_start: 0.8215 (p0) cc_final: 0.7978 (p0) REVERT: L 55 TYR cc_start: 0.2324 (OUTLIER) cc_final: 0.1358 (m-10) REVERT: L 83 LEU cc_start: 0.7035 (tt) cc_final: 0.6524 (pp) REVERT: L 85 GLU cc_start: 0.7512 (tp30) cc_final: 0.6706 (tm-30) outliers start: 10 outliers final: 6 residues processed: 77 average time/residue: 0.1732 time to fit residues: 16.2388 Evaluate side-chains 65 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 55 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.6467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3463 Z= 0.265 Angle : 0.749 11.549 4704 Z= 0.399 Chirality : 0.049 0.211 501 Planarity : 0.006 0.077 605 Dihedral : 5.929 21.666 472 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.40 % Favored : 88.12 % Rotamer: Outliers : 5.39 % Allowed : 20.22 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.40), residues: 421 helix: -3.46 (0.87), residues: 20 sheet: 0.13 (0.50), residues: 132 loop : -2.62 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 36 HIS 0.002 0.001 HIS A 519 PHE 0.012 0.002 PHE H 109 TYR 0.036 0.002 TYR L 91 ARG 0.004 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.7396 (mp10) cc_final: 0.6525 (mp10) REVERT: H 46 GLU cc_start: 0.8390 (mp0) cc_final: 0.7973 (mp0) REVERT: H 57 ASP cc_start: 0.8474 (t0) cc_final: 0.8028 (t0) REVERT: H 108 ASP cc_start: 0.8453 (p0) cc_final: 0.8209 (p0) REVERT: H 109 PHE cc_start: 0.7775 (t80) cc_final: 0.7515 (t80) REVERT: L 24 LYS cc_start: 0.1461 (OUTLIER) cc_final: 0.0627 (tmtt) REVERT: L 55 TYR cc_start: 0.1997 (OUTLIER) cc_final: 0.0654 (m-10) REVERT: L 83 LEU cc_start: 0.7410 (tt) cc_final: 0.6879 (pp) REVERT: L 85 GLU cc_start: 0.7701 (tp30) cc_final: 0.6871 (tm-30) REVERT: L 91 TYR cc_start: 0.8474 (p90) cc_final: 0.8149 (p90) outliers start: 20 outliers final: 10 residues processed: 79 average time/residue: 0.1563 time to fit residues: 15.0631 Evaluate side-chains 69 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 55 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.6769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3463 Z= 0.223 Angle : 0.738 12.069 4704 Z= 0.388 Chirality : 0.049 0.222 501 Planarity : 0.005 0.057 605 Dihedral : 5.837 21.997 472 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.11 % Favored : 87.41 % Rotamer: Outliers : 2.70 % Allowed : 23.18 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.39), residues: 421 helix: -3.23 (0.77), residues: 26 sheet: -0.01 (0.50), residues: 131 loop : -2.81 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 35 HIS 0.003 0.001 HIS L 61 PHE 0.012 0.001 PHE H 29 TYR 0.034 0.002 TYR L 91 ARG 0.003 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8410 (mp0) cc_final: 0.8089 (mp0) REVERT: A 408 ARG cc_start: 0.8587 (tpt170) cc_final: 0.8383 (tpt170) REVERT: A 498 GLN cc_start: 0.7333 (mp10) cc_final: 0.6431 (mp10) REVERT: H 45 LEU cc_start: 0.8942 (mt) cc_final: 0.8591 (mm) REVERT: H 57 ASP cc_start: 0.8424 (t0) cc_final: 0.8038 (t0) REVERT: H 108 ASP cc_start: 0.8360 (p0) cc_final: 0.8035 (p0) REVERT: H 109 PHE cc_start: 0.7797 (t80) cc_final: 0.7589 (t80) REVERT: L 55 TYR cc_start: 0.2200 (OUTLIER) cc_final: 0.1174 (m-10) REVERT: L 83 LEU cc_start: 0.7076 (tt) cc_final: 0.6616 (pp) REVERT: L 85 GLU cc_start: 0.7773 (tp30) cc_final: 0.6843 (tm-30) outliers start: 10 outliers final: 4 residues processed: 69 average time/residue: 0.1552 time to fit residues: 13.2009 Evaluate side-chains 60 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3463 Z= 0.223 Angle : 0.753 12.016 4704 Z= 0.398 Chirality : 0.049 0.199 501 Planarity : 0.005 0.051 605 Dihedral : 5.805 22.659 472 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.88 % Favored : 87.65 % Rotamer: Outliers : 2.70 % Allowed : 23.45 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.39), residues: 421 helix: -3.74 (0.64), residues: 26 sheet: -0.09 (0.49), residues: 133 loop : -2.86 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS L 61 PHE 0.013 0.001 PHE H 29 TYR 0.032 0.002 TYR L 91 ARG 0.003 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8367 (mp0) cc_final: 0.8151 (mp0) REVERT: A 408 ARG cc_start: 0.8535 (tpt170) cc_final: 0.8316 (tpt170) REVERT: A 498 GLN cc_start: 0.7315 (mp10) cc_final: 0.6457 (mp10) REVERT: H 57 ASP cc_start: 0.8509 (t0) cc_final: 0.8114 (t0) REVERT: H 108 ASP cc_start: 0.8222 (p0) cc_final: 0.7855 (p0) REVERT: H 109 PHE cc_start: 0.7777 (t80) cc_final: 0.7567 (t80) REVERT: L 24 LYS cc_start: 0.1895 (OUTLIER) cc_final: 0.0963 (tmtt) REVERT: L 55 TYR cc_start: 0.2162 (OUTLIER) cc_final: 0.0789 (m-10) REVERT: L 83 LEU cc_start: 0.7104 (tt) cc_final: 0.6658 (pp) REVERT: L 85 GLU cc_start: 0.7764 (tp30) cc_final: 0.6850 (tm-30) outliers start: 10 outliers final: 6 residues processed: 71 average time/residue: 0.1612 time to fit residues: 14.2180 Evaluate side-chains 62 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.0010 chunk 34 optimal weight: 0.8980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3463 Z= 0.228 Angle : 0.768 12.485 4704 Z= 0.402 Chirality : 0.049 0.202 501 Planarity : 0.005 0.050 605 Dihedral : 5.794 23.637 472 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.59 % Favored : 86.94 % Rotamer: Outliers : 2.96 % Allowed : 22.91 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.39), residues: 421 helix: -4.11 (0.58), residues: 26 sheet: -0.22 (0.48), residues: 134 loop : -2.88 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.002 0.001 HIS L 61 PHE 0.012 0.001 PHE H 29 TYR 0.016 0.001 TYR L 91 ARG 0.003 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8442 (tpt170) cc_final: 0.8221 (tpt170) REVERT: A 498 GLN cc_start: 0.7430 (mp10) cc_final: 0.6699 (mp10) REVERT: H 57 ASP cc_start: 0.8571 (t0) cc_final: 0.8188 (t0) REVERT: H 74 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8571 (mmtt) REVERT: H 108 ASP cc_start: 0.8177 (p0) cc_final: 0.7829 (p0) REVERT: H 109 PHE cc_start: 0.7750 (t80) cc_final: 0.7523 (t80) REVERT: L 24 LYS cc_start: 0.2055 (OUTLIER) cc_final: 0.1137 (tmtt) REVERT: L 55 TYR cc_start: 0.2007 (OUTLIER) cc_final: 0.0668 (m-10) REVERT: L 79 GLN cc_start: -0.0817 (OUTLIER) cc_final: -0.2165 (mt0) REVERT: L 83 LEU cc_start: 0.7137 (tt) cc_final: 0.6692 (pp) REVERT: L 85 GLU cc_start: 0.7796 (tp30) cc_final: 0.7482 (tp30) outliers start: 11 outliers final: 6 residues processed: 70 average time/residue: 0.1415 time to fit residues: 12.3677 Evaluate side-chains 64 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3463 Z= 0.211 Angle : 0.764 12.499 4704 Z= 0.399 Chirality : 0.048 0.174 501 Planarity : 0.005 0.044 605 Dihedral : 5.762 21.439 472 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.16 % Favored : 88.36 % Rotamer: Outliers : 3.50 % Allowed : 22.91 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.39), residues: 421 helix: -4.15 (0.65), residues: 26 sheet: -0.28 (0.48), residues: 134 loop : -2.86 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS L 61 PHE 0.013 0.001 PHE H 29 TYR 0.014 0.001 TYR H 104 ARG 0.003 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8438 (tpt170) cc_final: 0.8217 (tpt170) REVERT: A 493 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6910 (mp10) REVERT: A 498 GLN cc_start: 0.7536 (mp10) cc_final: 0.6545 (mp10) REVERT: H 57 ASP cc_start: 0.8571 (t0) cc_final: 0.8223 (t0) REVERT: H 108 ASP cc_start: 0.8109 (p0) cc_final: 0.7741 (p0) REVERT: H 109 PHE cc_start: 0.7563 (t80) cc_final: 0.7296 (t80) REVERT: L 24 LYS cc_start: 0.2088 (OUTLIER) cc_final: 0.1247 (tmtt) REVERT: L 53 TYR cc_start: 0.5256 (m-10) cc_final: 0.4952 (m-10) REVERT: L 55 TYR cc_start: 0.1913 (OUTLIER) cc_final: 0.0716 (m-10) REVERT: L 79 GLN cc_start: -0.0908 (OUTLIER) cc_final: -0.2074 (mt0) REVERT: L 83 LEU cc_start: 0.7160 (tt) cc_final: 0.6706 (pp) REVERT: L 85 GLU cc_start: 0.7775 (tp30) cc_final: 0.7475 (tp30) outliers start: 13 outliers final: 7 residues processed: 73 average time/residue: 0.1538 time to fit residues: 13.8958 Evaluate side-chains 68 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.0770 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.7291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3463 Z= 0.218 Angle : 0.810 12.843 4704 Z= 0.424 Chirality : 0.050 0.226 501 Planarity : 0.005 0.045 605 Dihedral : 5.771 27.440 472 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.88 % Favored : 87.65 % Rotamer: Outliers : 2.70 % Allowed : 23.99 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.39), residues: 421 helix: -4.26 (0.57), residues: 26 sheet: -0.34 (0.48), residues: 134 loop : -2.86 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS L 61 PHE 0.012 0.001 PHE H 63 TYR 0.014 0.001 TYR H 104 ARG 0.002 0.000 ARG H 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 CYS cc_start: 0.2736 (p) cc_final: 0.2500 (p) REVERT: A 408 ARG cc_start: 0.8438 (tpt170) cc_final: 0.8213 (tpt170) REVERT: A 498 GLN cc_start: 0.7438 (mp10) cc_final: 0.6475 (mp10) REVERT: H 46 GLU cc_start: 0.8373 (mp0) cc_final: 0.8043 (mp0) REVERT: H 57 ASP cc_start: 0.8563 (t0) cc_final: 0.8226 (t0) REVERT: H 108 ASP cc_start: 0.8133 (p0) cc_final: 0.7750 (p0) REVERT: H 109 PHE cc_start: 0.7618 (t80) cc_final: 0.7313 (t80) REVERT: L 24 LYS cc_start: 0.2071 (OUTLIER) cc_final: 0.1226 (tmtt) REVERT: L 55 TYR cc_start: 0.2037 (OUTLIER) cc_final: 0.0565 (m-10) REVERT: L 79 GLN cc_start: -0.0737 (OUTLIER) cc_final: -0.1933 (mt0) REVERT: L 83 LEU cc_start: 0.7213 (tt) cc_final: 0.6727 (pp) REVERT: L 85 GLU cc_start: 0.7716 (tp30) cc_final: 0.7457 (tp30) outliers start: 10 outliers final: 7 residues processed: 69 average time/residue: 0.1550 time to fit residues: 13.1713 Evaluate side-chains 66 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 42 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 = 0.3978 r_free = 0.3978 target = 0.109648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.100144 restraints weight = 11754.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.101827 restraints weight = 7292.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.103008 restraints weight = 5094.449| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.7529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3463 Z= 0.230 Angle : 0.813 12.663 4704 Z= 0.426 Chirality : 0.049 0.197 501 Planarity : 0.005 0.047 605 Dihedral : 5.944 27.667 472 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.35 % Favored : 87.17 % Rotamer: Outliers : 3.23 % Allowed : 24.53 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.38), residues: 421 helix: -4.41 (0.49), residues: 26 sheet: -0.35 (0.48), residues: 133 loop : -2.92 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS L 61 PHE 0.011 0.001 PHE H 29 TYR 0.016 0.001 TYR L 55 ARG 0.003 0.001 ARG A 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1314.01 seconds wall clock time: 24 minutes 11.28 seconds (1451.28 seconds total)