Starting phenix.real_space_refine on Tue Feb 13 16:39:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyi_21461/02_2024/6vyi_21461_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyi_21461/02_2024/6vyi_21461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyi_21461/02_2024/6vyi_21461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyi_21461/02_2024/6vyi_21461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyi_21461/02_2024/6vyi_21461_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyi_21461/02_2024/6vyi_21461_updated.pdb" } resolution = 3.0 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 42 5.16 5 C 4620 2.51 5 N 1136 2.21 5 O 1114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 313": "OD1" <-> "OD2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 313": "OD1" <-> "OD2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B ARG 424": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6916 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3360 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3360 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 147 Unusual residues: {'6OU': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.57, per 1000 atoms: 0.66 Number of scatterers: 6916 At special positions: 0 Unit cell: (109.725, 91.575, 81.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 4 15.00 O 1114 8.00 N 1136 7.00 C 4620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 0 sheets defined 70.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.505A pdb=" N CYS A 92 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 removed outlier: 3.886A pdb=" N VAL A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 154 removed outlier: 4.299A pdb=" N ASN A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 184 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 191 through 227 removed outlier: 3.693A pdb=" N ARG A 222 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 275 through 299 Processing helix chain 'A' and resid 301 through 307 removed outlier: 4.089A pdb=" N SER A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 342 removed outlier: 3.838A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'A' and resid 400 through 419 Processing helix chain 'A' and resid 429 through 447 removed outlier: 4.071A pdb=" N ILE A 438 " --> pdb=" O MET A 434 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 450 through 462 Processing helix chain 'A' and resid 466 through 478 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 88 through 112 removed outlier: 3.505A pdb=" N CYS B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 127 removed outlier: 3.887A pdb=" N VAL B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 154 removed outlier: 4.298A pdb=" N ASN B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 184 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 191 through 227 removed outlier: 3.693A pdb=" N ARG B 222 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 275 through 299 Processing helix chain 'B' and resid 301 through 307 removed outlier: 4.089A pdb=" N SER B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 342 removed outlier: 3.838A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 344 through 352 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 379 through 388 Processing helix chain 'B' and resid 391 through 395 Processing helix chain 'B' and resid 400 through 419 Processing helix chain 'B' and resid 429 through 447 removed outlier: 4.071A pdb=" N ILE B 438 " --> pdb=" O MET B 434 " (cutoff:3.500A) Proline residue: B 439 - end of helix Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 466 through 478 382 hydrogen bonds defined for protein. 1146 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: 1.88 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1018 1.32 - 1.44: 2138 1.44 - 1.56: 3894 1.56 - 1.68: 8 1.68 - 1.80: 68 Bond restraints: 7126 Sorted by residual: bond pdb=" O22 6OU A 502 " pdb=" P23 6OU A 502 " ideal model delta sigma weight residual 1.643 1.557 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " ideal model delta sigma weight residual 1.643 1.566 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " ideal model delta sigma weight residual 1.643 1.568 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O22 6OU A 503 " pdb=" P23 6OU A 503 " ideal model delta sigma weight residual 1.643 1.573 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C27 6OU A 503 " pdb=" C28 6OU A 503 " ideal model delta sigma weight residual 1.512 1.563 -0.051 2.00e-02 2.50e+03 6.57e+00 ... (remaining 7121 not shown) Histogram of bond angle deviations from ideal: 97.53 - 104.94: 129 104.94 - 112.36: 3564 112.36 - 119.78: 2562 119.78 - 127.19: 3266 127.19 - 134.61: 127 Bond angle restraints: 9648 Sorted by residual: angle pdb=" C21 6OU A 502 " pdb=" O22 6OU A 502 " pdb=" P23 6OU A 502 " ideal model delta sigma weight residual 117.17 134.61 -17.44 3.00e+00 1.11e-01 3.38e+01 angle pdb=" C21 6OU A 501 " pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " ideal model delta sigma weight residual 117.17 134.50 -17.33 3.00e+00 1.11e-01 3.34e+01 angle pdb=" O22 6OU A 503 " pdb=" P23 6OU A 503 " pdb=" O26 6OU A 503 " ideal model delta sigma weight residual 93.95 110.09 -16.14 3.00e+00 1.11e-01 2.89e+01 angle pdb=" C21 6OU B 501 " pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " ideal model delta sigma weight residual 117.17 131.43 -14.26 3.00e+00 1.11e-01 2.26e+01 angle pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " pdb=" O26 6OU B 501 " ideal model delta sigma weight residual 93.95 108.05 -14.10 3.00e+00 1.11e-01 2.21e+01 ... (remaining 9643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 4045 34.83 - 69.66: 109 69.66 - 104.49: 21 104.49 - 139.31: 11 139.31 - 174.14: 4 Dihedral angle restraints: 4190 sinusoidal: 1778 harmonic: 2412 Sorted by residual: dihedral pdb=" CA GLY A 87 " pdb=" C GLY A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 156.65 23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA GLY B 87 " pdb=" C GLY B 87 " pdb=" N ILE B 88 " pdb=" CA ILE B 88 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" C19 6OU B 501 " pdb=" C20 6OU B 501 " pdb=" C21 6OU B 501 " pdb=" O22 6OU B 501 " ideal model delta sinusoidal sigma weight residual -59.00 115.14 -174.14 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 751 0.051 - 0.102: 242 0.102 - 0.153: 35 0.153 - 0.204: 1 0.204 - 0.255: 3 Chirality restraints: 1032 Sorted by residual: chirality pdb=" C20 6OU A 503 " pdb=" C19 6OU A 503 " pdb=" C21 6OU A 503 " pdb=" O30 6OU A 503 " both_signs ideal model delta sigma weight residual False 2.35 2.60 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C20 6OU B 501 " pdb=" C19 6OU B 501 " pdb=" C21 6OU B 501 " pdb=" O30 6OU B 501 " both_signs ideal model delta sigma weight residual False 2.35 2.57 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C20 6OU A 502 " pdb=" C19 6OU A 502 " pdb=" C21 6OU A 502 " pdb=" O30 6OU A 502 " both_signs ideal model delta sigma weight residual False 2.35 2.56 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1029 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 296 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C ILE A 296 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 296 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN A 297 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 296 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C ILE B 296 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE B 296 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN B 297 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 243 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO B 244 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 244 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 244 " 0.022 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 288 2.71 - 3.25: 7314 3.25 - 3.80: 11716 3.80 - 4.35: 14245 4.35 - 4.90: 24334 Nonbonded interactions: 57897 Sorted by model distance: nonbonded pdb=" OE1 GLU A 351 " pdb=" NH2 ARG A 358 " model vdw 2.157 2.520 nonbonded pdb=" OE1 GLU B 351 " pdb=" NH2 ARG B 358 " model vdw 2.158 2.520 nonbonded pdb=" O GLU B 416 " pdb=" OG SER B 420 " model vdw 2.193 2.440 nonbonded pdb=" O GLU A 416 " pdb=" OG SER A 420 " model vdw 2.194 2.440 nonbonded pdb=" ND2 ASN A 366 " pdb=" O ASN B 84 " model vdw 2.218 2.520 ... (remaining 57892 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 66 through 481 or resid 501)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.010 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: 4.000 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.850 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:16.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.010 0.086 7126 Z= 0.631 Angle : 0.941 17.441 9648 Z= 0.447 Chirality : 0.048 0.255 1032 Planarity : 0.005 0.039 1172 Dihedral : 19.278 174.143 2626 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % 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: -2.99 (0.26), residues: 804 helix: -1.16 (0.19), residues: 592 sheet: None (None), residues: 0 loop : -4.15 (0.33), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 334 HIS 0.005 0.001 HIS B 382 PHE 0.016 0.002 PHE B 338 TYR 0.015 0.002 TYR B 417 ARG 0.005 0.001 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 306 ASN cc_start: 0.8273 (m-40) cc_final: 0.7945 (m-40) REVERT: A 404 ARG cc_start: 0.7495 (mtt-85) cc_final: 0.6766 (mtm110) REVERT: B 404 ARG cc_start: 0.7480 (mtt-85) cc_final: 0.6777 (mtm110) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 1.4403 time to fit residues: 179.4327 Evaluate side-chains 92 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 119 GLN A 162 GLN A 239 HIS A 246 ASN ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN A 465 GLN B 119 GLN B 162 GLN B 239 HIS B 246 ASN B 266 ASN B 292 GLN B 465 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7126 Z= 0.240 Angle : 0.585 7.457 9648 Z= 0.292 Chirality : 0.039 0.127 1032 Planarity : 0.004 0.031 1172 Dihedral : 18.006 172.075 1082 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.22 % Allowed : 11.76 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.29), residues: 804 helix: 0.44 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -3.46 (0.35), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 340 HIS 0.004 0.001 HIS A 201 PHE 0.028 0.002 PHE B 443 TYR 0.013 0.001 TYR B 211 ARG 0.002 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 0.839 Fit side-chains REVERT: A 215 ASN cc_start: 0.8327 (m-40) cc_final: 0.8106 (m-40) REVERT: A 404 ARG cc_start: 0.7500 (mtt-85) cc_final: 0.6771 (mtm110) REVERT: B 215 ASN cc_start: 0.8337 (m-40) cc_final: 0.8108 (m-40) REVERT: B 316 TYR cc_start: 0.7483 (m-10) cc_final: 0.7232 (m-80) REVERT: B 404 ARG cc_start: 0.7491 (mtt-85) cc_final: 0.6763 (mtm110) outliers start: 23 outliers final: 2 residues processed: 117 average time/residue: 0.9680 time to fit residues: 120.7258 Evaluate side-chains 101 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 185 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7126 Z= 0.234 Angle : 0.567 7.360 9648 Z= 0.281 Chirality : 0.039 0.121 1032 Planarity : 0.004 0.028 1172 Dihedral : 16.678 170.174 1082 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.06 % Allowed : 12.89 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.30), residues: 804 helix: 1.10 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -3.24 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 340 HIS 0.004 0.001 HIS B 201 PHE 0.012 0.001 PHE B 443 TYR 0.011 0.001 TYR B 339 ARG 0.003 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 0.803 Fit side-chains REVERT: A 215 ASN cc_start: 0.8325 (m-40) cc_final: 0.8070 (m-40) REVERT: A 404 ARG cc_start: 0.7444 (mtt-85) cc_final: 0.6775 (mtm110) REVERT: B 215 ASN cc_start: 0.8328 (m-40) cc_final: 0.8066 (m-40) REVERT: B 404 ARG cc_start: 0.7483 (mtt-85) cc_final: 0.6765 (mtm110) outliers start: 29 outliers final: 7 residues processed: 123 average time/residue: 0.9156 time to fit residues: 120.7105 Evaluate side-chains 102 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 251 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.0470 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7126 Z= 0.208 Angle : 0.556 7.415 9648 Z= 0.275 Chirality : 0.038 0.118 1032 Planarity : 0.004 0.027 1172 Dihedral : 16.019 164.270 1082 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.78 % Allowed : 13.59 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.31), residues: 804 helix: 1.41 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -3.21 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 340 HIS 0.004 0.001 HIS A 474 PHE 0.029 0.001 PHE A 443 TYR 0.012 0.001 TYR B 211 ARG 0.003 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 0.770 Fit side-chains REVERT: A 73 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7302 (t0) REVERT: A 215 ASN cc_start: 0.8303 (m-40) cc_final: 0.8048 (m-40) REVERT: A 404 ARG cc_start: 0.7470 (mtt-85) cc_final: 0.6767 (mtm110) REVERT: B 215 ASN cc_start: 0.8322 (m-40) cc_final: 0.8064 (m-40) REVERT: B 316 TYR cc_start: 0.7317 (m-10) cc_final: 0.7092 (m-80) REVERT: B 404 ARG cc_start: 0.7518 (mtt-85) cc_final: 0.6806 (mtm110) outliers start: 27 outliers final: 7 residues processed: 119 average time/residue: 1.0198 time to fit residues: 129.6079 Evaluate side-chains 104 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 300 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 19 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7126 Z= 0.282 Angle : 0.594 7.905 9648 Z= 0.289 Chirality : 0.041 0.211 1032 Planarity : 0.004 0.028 1172 Dihedral : 15.880 154.368 1082 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 5.18 % Allowed : 14.29 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.31), residues: 804 helix: 1.45 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -3.12 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 340 HIS 0.004 0.001 HIS A 474 PHE 0.015 0.001 PHE B 443 TYR 0.012 0.001 TYR B 339 ARG 0.001 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 104 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 215 ASN cc_start: 0.8353 (m-40) cc_final: 0.8093 (m-40) REVERT: A 404 ARG cc_start: 0.7508 (mtt-85) cc_final: 0.6801 (mtm110) REVERT: B 215 ASN cc_start: 0.8361 (m-40) cc_final: 0.8094 (m-40) REVERT: B 316 TYR cc_start: 0.7337 (m-10) cc_final: 0.7132 (m-80) REVERT: B 400 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7969 (ttmt) REVERT: B 404 ARG cc_start: 0.7498 (mtt-85) cc_final: 0.6803 (mtm110) outliers start: 37 outliers final: 13 residues processed: 125 average time/residue: 1.0487 time to fit residues: 139.1952 Evaluate side-chains 104 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 19 optimal weight: 0.0370 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 6 optimal weight: 0.0570 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7126 Z= 0.178 Angle : 0.560 7.968 9648 Z= 0.275 Chirality : 0.039 0.179 1032 Planarity : 0.004 0.028 1172 Dihedral : 15.268 143.667 1082 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.64 % Allowed : 16.11 % Favored : 80.25 % 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: 0.79 (0.32), residues: 804 helix: 1.66 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.05 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 340 HIS 0.004 0.001 HIS B 474 PHE 0.030 0.001 PHE B 443 TYR 0.011 0.001 TYR B 339 ARG 0.002 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7223 (t0) REVERT: A 215 ASN cc_start: 0.8284 (m-40) cc_final: 0.8059 (m-40) REVERT: A 224 LYS cc_start: 0.8481 (ttpp) cc_final: 0.7911 (tmmt) REVERT: A 295 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8458 (mt) REVERT: A 404 ARG cc_start: 0.7508 (mtt-85) cc_final: 0.6806 (mtm110) REVERT: A 467 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8338 (mp) REVERT: B 215 ASN cc_start: 0.8298 (m-40) cc_final: 0.8047 (m-40) REVERT: B 224 LYS cc_start: 0.8508 (ttpp) cc_final: 0.7926 (tmmt) REVERT: B 404 ARG cc_start: 0.7507 (mtt-85) cc_final: 0.6787 (mtm110) outliers start: 26 outliers final: 8 residues processed: 119 average time/residue: 1.1656 time to fit residues: 146.5177 Evaluate side-chains 103 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 0.0060 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7126 Z= 0.225 Angle : 0.571 7.588 9648 Z= 0.280 Chirality : 0.040 0.177 1032 Planarity : 0.004 0.031 1172 Dihedral : 15.074 138.445 1082 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.92 % Allowed : 16.53 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.32), residues: 804 helix: 1.68 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.00 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 340 HIS 0.004 0.001 HIS B 474 PHE 0.016 0.001 PHE B 443 TYR 0.012 0.001 TYR A 339 ARG 0.002 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7244 (t0) REVERT: A 215 ASN cc_start: 0.8313 (m-40) cc_final: 0.8055 (m-40) REVERT: A 224 LYS cc_start: 0.8485 (ttpp) cc_final: 0.7913 (tmmt) REVERT: A 295 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8463 (mt) REVERT: A 404 ARG cc_start: 0.7532 (mtt-85) cc_final: 0.6812 (mtm110) REVERT: B 215 ASN cc_start: 0.8338 (m-40) cc_final: 0.8057 (m-40) REVERT: B 224 LYS cc_start: 0.8479 (ttpp) cc_final: 0.7909 (tmmt) REVERT: B 404 ARG cc_start: 0.7526 (mtt-85) cc_final: 0.7287 (mtt90) outliers start: 28 outliers final: 8 residues processed: 114 average time/residue: 1.1569 time to fit residues: 139.2250 Evaluate side-chains 103 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7126 Z= 0.174 Angle : 0.569 7.906 9648 Z= 0.282 Chirality : 0.039 0.150 1032 Planarity : 0.004 0.030 1172 Dihedral : 14.506 135.845 1082 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.94 % Allowed : 18.91 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.32), residues: 804 helix: 1.81 (0.23), residues: 598 sheet: None (None), residues: 0 loop : -2.96 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 340 HIS 0.004 0.001 HIS B 474 PHE 0.031 0.001 PHE A 443 TYR 0.012 0.001 TYR A 339 ARG 0.002 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7267 (t0) REVERT: A 215 ASN cc_start: 0.8256 (m-40) cc_final: 0.8026 (m-40) REVERT: A 224 LYS cc_start: 0.8469 (ttpp) cc_final: 0.7880 (tmmt) REVERT: B 215 ASN cc_start: 0.8282 (m-40) cc_final: 0.8026 (m-40) REVERT: B 224 LYS cc_start: 0.8452 (ttpp) cc_final: 0.7874 (tmmt) REVERT: B 404 ARG cc_start: 0.7524 (mtt-85) cc_final: 0.7252 (mtt90) outliers start: 21 outliers final: 9 residues processed: 113 average time/residue: 1.2285 time to fit residues: 146.0614 Evaluate side-chains 110 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 7126 Z= 0.447 Angle : 0.680 7.597 9648 Z= 0.338 Chirality : 0.045 0.210 1032 Planarity : 0.005 0.034 1172 Dihedral : 15.197 137.122 1082 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 3.22 % Allowed : 19.19 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.31), residues: 804 helix: 1.43 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -2.94 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 340 HIS 0.004 0.001 HIS A 382 PHE 0.031 0.002 PHE B 443 TYR 0.015 0.002 TYR B 417 ARG 0.002 0.000 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 224 LYS cc_start: 0.8477 (ttpp) cc_final: 0.7976 (tmmt) REVERT: A 404 ARG cc_start: 0.7891 (mtt180) cc_final: 0.7502 (mtt90) REVERT: B 404 ARG cc_start: 0.7541 (mtt-85) cc_final: 0.7086 (mtt90) outliers start: 23 outliers final: 11 residues processed: 106 average time/residue: 1.2783 time to fit residues: 142.7656 Evaluate side-chains 102 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 6 optimal weight: 0.0060 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN B 162 GLN B 266 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7126 Z= 0.184 Angle : 0.589 7.749 9648 Z= 0.294 Chirality : 0.040 0.155 1032 Planarity : 0.004 0.029 1172 Dihedral : 14.531 134.829 1082 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.10 % Allowed : 20.59 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.32), residues: 804 helix: 1.72 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -2.93 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 340 HIS 0.003 0.001 HIS A 474 PHE 0.031 0.002 PHE B 443 TYR 0.013 0.001 TYR B 339 ARG 0.002 0.000 ARG A 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.690 Fit side-chains REVERT: A 73 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7254 (t0) REVERT: A 215 ASN cc_start: 0.8290 (m-40) cc_final: 0.8036 (m-40) REVERT: A 224 LYS cc_start: 0.8453 (ttpp) cc_final: 0.7891 (tmmt) REVERT: A 353 MET cc_start: 0.7650 (pmt) cc_final: 0.5325 (pmt) REVERT: B 215 ASN cc_start: 0.8296 (m-40) cc_final: 0.8035 (m-40) REVERT: B 353 MET cc_start: 0.7636 (pmt) cc_final: 0.5311 (pmt) REVERT: B 404 ARG cc_start: 0.7524 (mtt-85) cc_final: 0.7299 (mtt90) outliers start: 15 outliers final: 7 residues processed: 109 average time/residue: 1.2414 time to fit residues: 142.4872 Evaluate side-chains 107 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 0.0470 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN B 292 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.106158 restraints weight = 9440.110| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.98 r_work: 0.3099 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 7126 Z= 0.308 Angle : 1.273 59.194 9648 Z= 0.760 Chirality : 0.043 0.223 1032 Planarity : 0.004 0.029 1172 Dihedral : 14.539 134.845 1082 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.40 % Allowed : 21.85 % Favored : 76.75 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.32), residues: 804 helix: 1.71 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -2.91 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 340 HIS 0.004 0.001 HIS A 474 PHE 0.030 0.002 PHE B 443 TYR 0.012 0.001 TYR B 339 ARG 0.008 0.000 ARG A 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2703.29 seconds wall clock time: 49 minutes 16.09 seconds (2956.09 seconds total)