Starting phenix.real_space_refine on Tue Jun 25 09:24:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b91_44365/06_2024/9b91_44365_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b91_44365/06_2024/9b91_44365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b91_44365/06_2024/9b91_44365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b91_44365/06_2024/9b91_44365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b91_44365/06_2024/9b91_44365_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b91_44365/06_2024/9b91_44365_updated.pdb" } resolution = 3.3 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= 0.000 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 3 5.49 5 S 38 5.16 5 C 4854 2.51 5 N 1327 2.21 5 O 1287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 7511 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7478 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 43, 'TRANS': 949} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 411 Unresolved non-hydrogen angles: 510 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 19, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 285 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.86, per 1000 atoms: 0.78 Number of scatterers: 7511 At special positions: 0 Unit cell: (87.768, 120.06, 153.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 38 16.00 P 3 15.00 O 1287 8.00 N 1327 7.00 C 4854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.59 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.6 seconds 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 4 sheets defined 60.6% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 Proline residue: A 12 - end of helix Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 132 through 149 removed outlier: 3.724A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 282 through 294 Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 326 through 335 removed outlier: 4.358A pdb=" N GLU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 357 removed outlier: 3.609A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 422 through 434 removed outlier: 4.076A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 451 through 454 No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'A' and resid 457 through 466 Processing helix chain 'A' and resid 472 through 479 Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 572 through 581 Processing helix chain 'A' and resid 585 through 602 Processing helix chain 'A' and resid 608 through 633 Processing helix chain 'A' and resid 635 through 644 removed outlier: 3.541A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 667 No H-bonds generated for 'chain 'A' and resid 664 through 667' Processing helix chain 'A' and resid 670 through 680 Processing helix chain 'A' and resid 690 through 698 Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 767 through 777 Processing helix chain 'A' and resid 779 through 802 Processing helix chain 'A' and resid 812 through 833 Processing helix chain 'A' and resid 852 through 861 Processing helix chain 'A' and resid 863 through 883 Processing helix chain 'A' and resid 888 through 911 removed outlier: 3.598A pdb=" N LEU A 906 " --> pdb=" O PHE A 902 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 952 Proline residue: A 918 - end of helix removed outlier: 4.081A pdb=" N MET A 927 " --> pdb=" O VAL A 923 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LYS A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASP A 929 " --> pdb=" O LYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 966 Processing helix chain 'A' and resid 968 through 975 removed outlier: 3.624A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE A 975 " --> pdb=" O TYR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 982 No H-bonds generated for 'chain 'A' and resid 980 through 982' Processing helix chain 'A' and resid 985 through 987 No H-bonds generated for 'chain 'A' and resid 985 through 987' Processing helix chain 'A' and resid 1017 through 1032 Processing helix chain 'A' and resid 1034 through 1070 removed outlier: 4.877A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1087 Processing helix chain 'A' and resid 1116 through 1142 Processing helix chain 'A' and resid 1144 through 1175 Processing sheet with id= A, first strand: chain 'A' and resid 16 through 19 Processing sheet with id= B, first strand: chain 'A' and resid 76 through 78 removed outlier: 7.086A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 117 through 122 removed outlier: 8.027A pdb=" N SER A 120 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 274 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU A 122 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 276 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N LEU A 277 " --> pdb=" O PRO A 297 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 299 " --> pdb=" O LEU A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 989 through 991 removed outlier: 4.062A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP A1000 " --> pdb=" O SER A 991 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2433 1.34 - 1.46: 1693 1.46 - 1.57: 3494 1.57 - 1.69: 5 1.69 - 1.81: 57 Bond restraints: 7682 Sorted by residual: bond pdb=" CB THR A 823 " pdb=" CG2 THR A 823 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.45e+00 bond pdb=" CB TRP A1124 " pdb=" CG TRP A1124 " ideal model delta sigma weight residual 1.498 1.462 0.036 3.10e-02 1.04e+03 1.34e+00 bond pdb=" CB GLN A 669 " pdb=" CG GLN A 669 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CB TRP A 681 " pdb=" CG TRP A 681 " ideal model delta sigma weight residual 1.498 1.468 0.030 3.10e-02 1.04e+03 9.61e-01 bond pdb=" CB CYS A1011 " pdb=" SG CYS A1011 " ideal model delta sigma weight residual 1.808 1.776 0.032 3.30e-02 9.18e+02 9.17e-01 ... (remaining 7677 not shown) Histogram of bond angle deviations from ideal: 99.73 - 107.77: 331 107.77 - 115.81: 4694 115.81 - 123.84: 5202 123.84 - 131.88: 205 131.88 - 139.92: 27 Bond angle restraints: 10459 Sorted by residual: angle pdb=" C3' ATP A2003 " pdb=" C4' ATP A2003 " pdb=" C5' ATP A2003 " ideal model delta sigma weight residual 115.19 110.95 4.24 1.76e+00 3.23e-01 5.81e+00 angle pdb=" C2' ATP A2003 " pdb=" C3' ATP A2003 " pdb=" O3' ATP A2003 " ideal model delta sigma weight residual 111.83 105.58 6.25 2.67e+00 1.40e-01 5.48e+00 angle pdb=" N GLY A 220 " pdb=" CA GLY A 220 " pdb=" C GLY A 220 " ideal model delta sigma weight residual 110.77 115.28 -4.51 1.93e+00 2.68e-01 5.46e+00 angle pdb=" C1' ATP A2003 " pdb=" C2' ATP A2003 " pdb=" O2' ATP A2003 " ideal model delta sigma weight residual 110.58 104.21 6.37 2.79e+00 1.28e-01 5.20e+00 angle pdb=" C3' ATP A2003 " pdb=" C2' ATP A2003 " pdb=" O2' ATP A2003 " ideal model delta sigma weight residual 111.83 106.09 5.74 2.67e+00 1.40e-01 4.62e+00 ... (remaining 10454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 4256 16.86 - 33.72: 205 33.72 - 50.59: 41 50.59 - 67.45: 19 67.45 - 84.31: 5 Dihedral angle restraints: 4526 sinusoidal: 1679 harmonic: 2847 Sorted by residual: dihedral pdb=" CB CYS A 993 " pdb=" SG CYS A 993 " pdb=" SG CYS A1011 " pdb=" CB CYS A1011 " ideal model delta sinusoidal sigma weight residual -86.00 -146.15 60.15 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N PRO A 208 " pdb=" CA PRO A 208 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ARG A 139 " pdb=" CB ARG A 139 " pdb=" CG ARG A 139 " pdb=" CD ARG A 139 " ideal model delta sinusoidal sigma weight residual -60.00 -118.74 58.74 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1097 0.059 - 0.117: 101 0.117 - 0.176: 5 0.176 - 0.235: 0 0.235 - 0.294: 3 Chirality restraints: 1206 Sorted by residual: chirality pdb=" C2' ATP A2003 " pdb=" C1' ATP A2003 " pdb=" C3' ATP A2003 " pdb=" O2' ATP A2003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C3' ATP A2003 " pdb=" C2' ATP A2003 " pdb=" C4' ATP A2003 " pdb=" O3' ATP A2003 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C4' ATP A2003 " pdb=" C3' ATP A2003 " pdb=" C5' ATP A2003 " pdb=" O4' ATP A2003 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1203 not shown) Planarity restraints: 1315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 699 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 700 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 700 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 700 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1076 " 0.016 5.00e-02 4.00e+02 2.34e-02 8.79e-01 pdb=" N PRO A1077 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A1077 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A1077 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 456 " -0.013 5.00e-02 4.00e+02 1.94e-02 6.05e-01 pdb=" N PRO A 457 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " -0.011 5.00e-02 4.00e+02 ... (remaining 1312 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 148 2.67 - 3.23: 8284 3.23 - 3.79: 12049 3.79 - 4.34: 14955 4.34 - 4.90: 24731 Nonbonded interactions: 60167 Sorted by model distance: nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.119 2.510 nonbonded pdb=" OE1 GLN A 831 " pdb="CA CA A2001 " model vdw 2.170 2.510 nonbonded pdb=" N GLU A 374 " pdb=" OE1 GLU A 374 " model vdw 2.204 2.520 nonbonded pdb=" O PHE A 454 " pdb=" NH1 ARG A 459 " model vdw 2.236 2.520 nonbonded pdb=" N GLU A 389 " pdb=" OE1 GLU A 389 " model vdw 2.238 2.520 ... (remaining 60162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 11.960 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.470 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 : 0.005 0.040 7682 Z= 0.335 Angle : 0.499 6.369 10459 Z= 0.270 Chirality : 0.036 0.294 1206 Planarity : 0.003 0.041 1315 Dihedral : 11.380 84.310 2683 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.28 % Allowed : 5.79 % Favored : 93.93 % 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: 1.45 (0.27), residues: 975 helix: 2.00 (0.21), residues: 605 sheet: -2.01 (0.59), residues: 59 loop : -0.46 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 213 HIS 0.003 0.001 HIS A 173 PHE 0.007 0.001 PHE A 223 TYR 0.007 0.001 TYR A1015 ARG 0.003 0.000 ARG A1062 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1037 ASN cc_start: 0.8974 (m-40) cc_final: 0.8671 (m110) REVERT: A 1038 LEU cc_start: 0.9535 (tp) cc_final: 0.9307 (tt) outliers start: 2 outliers final: 2 residues processed: 110 average time/residue: 0.1832 time to fit residues: 27.6405 Evaluate side-chains 66 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 373 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 0.0010 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 973 GLN A1032 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7682 Z= 0.289 Angle : 0.579 8.434 10459 Z= 0.293 Chirality : 0.038 0.154 1206 Planarity : 0.004 0.039 1315 Dihedral : 6.765 68.630 1108 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.34 % Allowed : 10.07 % Favored : 87.59 % 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: 2.08 (0.28), residues: 975 helix: 2.47 (0.21), residues: 615 sheet: -1.20 (0.63), residues: 64 loop : -0.38 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 772 HIS 0.004 0.001 HIS A1128 PHE 0.023 0.001 PHE A 249 TYR 0.009 0.001 TYR A 227 ARG 0.014 0.001 ARG A 601 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1037 ASN cc_start: 0.8967 (m-40) cc_final: 0.8696 (m110) REVERT: A 1051 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8124 (tm-30) outliers start: 17 outliers final: 10 residues processed: 82 average time/residue: 0.1654 time to fit residues: 19.7351 Evaluate side-chains 68 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1032 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7682 Z= 0.174 Angle : 0.513 8.493 10459 Z= 0.257 Chirality : 0.035 0.140 1206 Planarity : 0.004 0.039 1315 Dihedral : 6.555 76.879 1108 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.07 % Allowed : 12.69 % Favored : 85.24 % 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: 2.24 (0.28), residues: 975 helix: 2.60 (0.21), residues: 617 sheet: -1.11 (0.64), residues: 64 loop : -0.36 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1124 HIS 0.002 0.001 HIS A 505 PHE 0.022 0.001 PHE A 697 TYR 0.009 0.001 TYR A 227 ARG 0.011 0.000 ARG A 601 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.8608 (ptp) cc_final: 0.8062 (ptp) REVERT: A 1037 ASN cc_start: 0.8826 (m-40) cc_final: 0.8561 (m110) REVERT: A 1051 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7947 (tm-30) outliers start: 15 outliers final: 10 residues processed: 81 average time/residue: 0.1740 time to fit residues: 20.2848 Evaluate side-chains 71 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1032 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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: 0.8385 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7682 Z= 0.228 Angle : 0.530 7.790 10459 Z= 0.265 Chirality : 0.036 0.142 1206 Planarity : 0.004 0.038 1315 Dihedral : 6.278 83.179 1108 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.62 % Allowed : 13.38 % Favored : 84.00 % 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: 2.15 (0.28), residues: 975 helix: 2.54 (0.21), residues: 618 sheet: -1.66 (0.64), residues: 59 loop : -0.29 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1124 HIS 0.003 0.001 HIS A 505 PHE 0.015 0.001 PHE A 697 TYR 0.009 0.001 TYR A 227 ARG 0.005 0.000 ARG A 601 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 186 MET cc_start: 0.8758 (ptp) cc_final: 0.8217 (ptp) REVERT: A 412 GLU cc_start: 0.8666 (mp0) cc_final: 0.8437 (mp0) REVERT: A 574 MET cc_start: 0.8735 (mmm) cc_final: 0.8525 (mmt) REVERT: A 1037 ASN cc_start: 0.8797 (m-40) cc_final: 0.8520 (m110) REVERT: A 1051 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7980 (tm-30) outliers start: 19 outliers final: 13 residues processed: 75 average time/residue: 0.1630 time to fit residues: 17.9838 Evaluate side-chains 71 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 988 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.0060 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7682 Z= 0.216 Angle : 0.525 7.198 10459 Z= 0.261 Chirality : 0.036 0.151 1206 Planarity : 0.004 0.037 1315 Dihedral : 5.936 89.027 1107 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.62 % Allowed : 14.48 % Favored : 82.90 % 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: 2.17 (0.28), residues: 975 helix: 2.56 (0.21), residues: 618 sheet: -1.69 (0.65), residues: 59 loop : -0.30 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1124 HIS 0.002 0.001 HIS A 505 PHE 0.024 0.001 PHE A 697 TYR 0.009 0.001 TYR A 227 ARG 0.006 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.8824 (ptp) cc_final: 0.8313 (ptp) REVERT: A 412 GLU cc_start: 0.8713 (mp0) cc_final: 0.8501 (mp0) REVERT: A 784 MET cc_start: 0.8582 (tmm) cc_final: 0.8150 (tmm) REVERT: A 1037 ASN cc_start: 0.8807 (m-40) cc_final: 0.8564 (m110) REVERT: A 1051 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7894 (tm-30) outliers start: 19 outliers final: 13 residues processed: 74 average time/residue: 0.1593 time to fit residues: 17.5416 Evaluate side-chains 69 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 988 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 79 optimal weight: 0.0870 chunk 44 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- 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: 0.8412 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7682 Z= 0.233 Angle : 0.523 7.695 10459 Z= 0.260 Chirality : 0.036 0.158 1206 Planarity : 0.004 0.036 1315 Dihedral : 5.619 85.742 1105 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.03 % Allowed : 15.45 % Favored : 81.52 % 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 (0.28), residues: 975 helix: 2.61 (0.21), residues: 620 sheet: -1.63 (0.64), residues: 59 loop : -0.15 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1124 HIS 0.002 0.001 HIS A 173 PHE 0.027 0.001 PHE A 373 TYR 0.009 0.001 TYR A 227 ARG 0.007 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8824 (tm-30) REVERT: A 186 MET cc_start: 0.8854 (ptp) cc_final: 0.8340 (ptp) REVERT: A 784 MET cc_start: 0.8617 (tmm) cc_final: 0.8227 (tmm) REVERT: A 1037 ASN cc_start: 0.8797 (m-40) cc_final: 0.8538 (m110) REVERT: A 1051 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7931 (tm-30) outliers start: 22 outliers final: 17 residues processed: 74 average time/residue: 0.1597 time to fit residues: 17.7273 Evaluate side-chains 72 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1139 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.8428 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7682 Z= 0.256 Angle : 0.530 8.363 10459 Z= 0.266 Chirality : 0.037 0.168 1206 Planarity : 0.004 0.036 1315 Dihedral : 5.499 83.738 1105 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.90 % Allowed : 16.41 % Favored : 80.69 % 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: 2.22 (0.28), residues: 975 helix: 2.57 (0.21), residues: 620 sheet: -1.81 (0.62), residues: 65 loop : -0.14 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1124 HIS 0.002 0.001 HIS A 447 PHE 0.026 0.001 PHE A 697 TYR 0.008 0.001 TYR A 227 ARG 0.006 0.000 ARG A1138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 56 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 135 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8824 (tm-30) REVERT: A 186 MET cc_start: 0.8887 (ptp) cc_final: 0.8417 (ptp) REVERT: A 784 MET cc_start: 0.8625 (tmm) cc_final: 0.8263 (tmm) REVERT: A 1037 ASN cc_start: 0.8846 (m-40) cc_final: 0.8577 (m110) REVERT: A 1051 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7937 (tm-30) outliers start: 21 outliers final: 15 residues processed: 71 average time/residue: 0.1582 time to fit residues: 17.0583 Evaluate side-chains 70 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 988 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 60 optimal weight: 0.0570 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 83 optimal weight: 0.0970 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1007 GLN A1061 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7682 Z= 0.142 Angle : 0.520 8.798 10459 Z= 0.255 Chirality : 0.035 0.165 1206 Planarity : 0.004 0.038 1315 Dihedral : 5.332 80.086 1105 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.76 % Allowed : 16.41 % Favored : 80.83 % 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: 2.20 (0.28), residues: 975 helix: 2.55 (0.21), residues: 622 sheet: -1.70 (0.64), residues: 65 loop : -0.20 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1124 HIS 0.002 0.000 HIS A 505 PHE 0.021 0.001 PHE A 697 TYR 0.006 0.001 TYR A 227 ARG 0.008 0.000 ARG A1138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8776 (tm-30) REVERT: A 186 MET cc_start: 0.8841 (ptp) cc_final: 0.8304 (ptp) REVERT: A 1037 ASN cc_start: 0.8704 (m-40) cc_final: 0.8459 (m110) REVERT: A 1051 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7759 (tm-30) outliers start: 20 outliers final: 15 residues processed: 83 average time/residue: 0.1632 time to fit residues: 19.8223 Evaluate side-chains 76 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 988 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1061 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7682 Z= 0.180 Angle : 0.541 9.811 10459 Z= 0.262 Chirality : 0.035 0.171 1206 Planarity : 0.004 0.038 1315 Dihedral : 5.273 79.778 1105 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.48 % Allowed : 17.24 % Favored : 80.28 % 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: 2.24 (0.29), residues: 975 helix: 2.58 (0.21), residues: 622 sheet: -1.70 (0.64), residues: 65 loop : -0.17 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1124 HIS 0.002 0.000 HIS A 447 PHE 0.018 0.001 PHE A 697 TYR 0.006 0.001 TYR A1063 ARG 0.007 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8793 (tm-30) REVERT: A 186 MET cc_start: 0.8878 (ptp) cc_final: 0.8326 (ptp) REVERT: A 430 MET cc_start: 0.9268 (mmm) cc_final: 0.9005 (tpp) REVERT: A 1037 ASN cc_start: 0.8745 (m-40) cc_final: 0.8503 (m110) REVERT: A 1051 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7805 (tm-30) outliers start: 18 outliers final: 16 residues processed: 76 average time/residue: 0.1588 time to fit residues: 18.2267 Evaluate side-chains 77 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1061 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0870 chunk 65 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- 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: 0.8393 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7682 Z= 0.181 Angle : 0.548 10.018 10459 Z= 0.268 Chirality : 0.036 0.177 1206 Planarity : 0.004 0.038 1315 Dihedral : 5.257 79.262 1105 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.48 % Allowed : 17.24 % Favored : 80.28 % 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: 2.23 (0.29), residues: 975 helix: 2.56 (0.21), residues: 622 sheet: -1.70 (0.64), residues: 65 loop : -0.17 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1124 HIS 0.002 0.000 HIS A 173 PHE 0.031 0.001 PHE A 697 TYR 0.006 0.001 TYR A1063 ARG 0.006 0.000 ARG A 632 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8795 (tm-30) REVERT: A 186 MET cc_start: 0.8886 (ptp) cc_final: 0.8330 (ptp) REVERT: A 430 MET cc_start: 0.9272 (mmm) cc_final: 0.9025 (tpp) REVERT: A 599 MET cc_start: 0.8656 (ttm) cc_final: 0.8346 (ttm) REVERT: A 1037 ASN cc_start: 0.8736 (m-40) cc_final: 0.8492 (m110) REVERT: A 1051 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7782 (tm-30) outliers start: 18 outliers final: 15 residues processed: 77 average time/residue: 0.1616 time to fit residues: 18.5505 Evaluate side-chains 76 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 988 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 80 optimal weight: 0.0050 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 69 optimal weight: 0.0020 chunk 4 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.075917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059280 restraints weight = 29454.677| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 4.20 r_work: 0.2943 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7682 Z= 0.156 Angle : 0.557 10.342 10459 Z= 0.269 Chirality : 0.036 0.194 1206 Planarity : 0.004 0.038 1315 Dihedral : 5.212 77.754 1105 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.48 % Allowed : 17.10 % Favored : 80.41 % 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: 2.24 (0.28), residues: 975 helix: 2.50 (0.21), residues: 628 sheet: -1.05 (0.73), residues: 52 loop : -0.27 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1124 HIS 0.001 0.000 HIS A 447 PHE 0.027 0.001 PHE A 697 TYR 0.005 0.001 TYR A 227 ARG 0.006 0.000 ARG A1138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1809.15 seconds wall clock time: 32 minutes 58.96 seconds (1978.96 seconds total)