Starting phenix.real_space_refine on Mon Sep 23 20:17:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtk_14143/09_2024/7qtk_14143.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtk_14143/09_2024/7qtk_14143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtk_14143/09_2024/7qtk_14143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtk_14143/09_2024/7qtk_14143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtk_14143/09_2024/7qtk_14143.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtk_14143/09_2024/7qtk_14143.cif" } resolution = 3.84 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 3171 2.51 5 N 845 2.21 5 O 974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5009 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "C" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.02, per 1000 atoms: 0.80 Number of scatterers: 5009 At special positions: 0 Unit cell: (71.9316, 103.747, 125.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 974 8.00 N 845 7.00 C 3171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN D 343 " Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 717.8 milliseconds 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1194 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 13 sheets defined 11.7% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.320A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.875A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 4.035A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.756A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.766A pdb=" N ASP B 31 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.853A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 removed outlier: 3.654A pdb=" N LYS C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.731A pdb=" N HIS C 189 " --> pdb=" O ASP C 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 354 through 358 removed outlier: 4.132A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'D' and resid 473 through 474 removed outlier: 4.001A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.334A pdb=" N GLY B 10 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 50 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 59 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.334A pdb=" N GLY B 10 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE B 114 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 136 removed outlier: 3.547A pdb=" N GLY B 151 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 144 Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 166 removed outlier: 3.650A pdb=" N THR B 163 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR B 206 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.665A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 removed outlier: 7.135A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 114 through 118 removed outlier: 3.804A pdb=" N VAL C 133 " --> pdb=" O PHE C 118 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.260A pdb=" N TRP C 148 " --> pdb=" O GLN C 155 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 145 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 207 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 196 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 205 " --> pdb=" O VAL C 196 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 408 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: 1.45 Time building geometry restraints manager: 1.46 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: 859 1.32 - 1.45: 1457 1.45 - 1.57: 2798 1.57 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 5134 Sorted by residual: bond pdb=" N VAL C 96 " pdb=" CA VAL C 96 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.32e-02 5.74e+03 1.53e+01 bond pdb=" CA SER C 93 " pdb=" CB SER C 93 " ideal model delta sigma weight residual 1.530 1.470 0.060 1.69e-02 3.50e+03 1.26e+01 bond pdb=" N THR C 109 " pdb=" CA THR C 109 " ideal model delta sigma weight residual 1.455 1.498 -0.042 1.33e-02 5.65e+03 1.00e+01 bond pdb=" N VAL C 110 " pdb=" CA VAL C 110 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.22e-02 6.72e+03 9.37e+00 bond pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.45e+00 ... (remaining 5129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6696 1.64 - 3.28: 220 3.28 - 4.92: 50 4.92 - 6.57: 13 6.57 - 8.21: 4 Bond angle restraints: 6983 Sorted by residual: angle pdb=" C VAL C 96 " pdb=" N THR C 97 " pdb=" CA THR C 97 " ideal model delta sigma weight residual 122.39 115.93 6.46 1.48e+00 4.57e-01 1.90e+01 angle pdb=" N PRO C 95 " pdb=" CA PRO C 95 " pdb=" C PRO C 95 " ideal model delta sigma weight residual 112.47 104.26 8.21 2.06e+00 2.36e-01 1.59e+01 angle pdb=" N TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta sigma weight residual 110.37 117.38 -7.01 1.78e+00 3.16e-01 1.55e+01 angle pdb=" CA TYR C 94 " pdb=" C TYR C 94 " pdb=" N PRO C 95 " ideal model delta sigma weight residual 118.44 124.39 -5.95 1.59e+00 3.96e-01 1.40e+01 angle pdb=" CA LYS B 129 " pdb=" C LYS B 129 " pdb=" O LYS B 129 " ideal model delta sigma weight residual 121.40 117.32 4.08 1.11e+00 8.12e-01 1.35e+01 ... (remaining 6978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 2781 16.64 - 33.28: 240 33.28 - 49.92: 47 49.92 - 66.56: 13 66.56 - 83.20: 4 Dihedral angle restraints: 3085 sinusoidal: 1216 harmonic: 1869 Sorted by residual: dihedral pdb=" N TYR C 94 " pdb=" C TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta harmonic sigma weight residual 122.80 138.48 -15.68 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" C TYR C 94 " pdb=" N TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta harmonic sigma weight residual -122.60 -135.93 13.33 0 2.50e+00 1.60e-01 2.84e+01 dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual 93.00 50.33 42.67 1 1.00e+01 1.00e-02 2.54e+01 ... (remaining 3082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 755 0.122 - 0.245: 18 0.245 - 0.367: 1 0.367 - 0.489: 0 0.489 - 0.611: 1 Chirality restraints: 775 Sorted by residual: chirality pdb=" CA TYR C 94 " pdb=" N TYR C 94 " pdb=" C TYR C 94 " pdb=" CB TYR C 94 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.34e+00 chirality pdb=" CA VAL B 123 " pdb=" N VAL B 123 " pdb=" C VAL B 123 " pdb=" CB VAL B 123 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA LYS B 129 " pdb=" N LYS B 129 " pdb=" C LYS B 129 " pdb=" CB LYS B 129 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 772 not shown) Planarity restraints: 899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 92 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C HIS C 92 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS C 92 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 93 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 97 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C THR C 97 " -0.033 2.00e-02 2.50e+03 pdb=" O THR C 97 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE C 98 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 94 " 0.018 2.00e-02 2.50e+03 1.06e-02 2.23e+00 pdb=" CG TYR C 94 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 94 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 94 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 94 " 0.005 2.00e-02 2.50e+03 ... (remaining 896 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 260 2.73 - 3.27: 4783 3.27 - 3.81: 7745 3.81 - 4.36: 9078 4.36 - 4.90: 15883 Nonbonded interactions: 37749 Sorted by model distance: nonbonded pdb=" OD1 ASP B 99 " pdb=" N ARG B 100 " model vdw 2.182 3.120 nonbonded pdb=" OG SER C 14 " pdb=" OD2 ASP C 17 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU D 406 " pdb=" NE2 GLN D 409 " model vdw 2.279 3.120 nonbonded pdb=" O TYR C 192 " pdb=" OG SER C 208 " model vdw 2.287 3.040 nonbonded pdb=" OG SER B 17 " pdb=" ND2 ASN B 84 " model vdw 2.299 3.120 ... (remaining 37744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.200 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5134 Z= 0.264 Angle : 0.731 8.208 6983 Z= 0.420 Chirality : 0.054 0.611 775 Planarity : 0.004 0.033 898 Dihedral : 13.163 83.203 1864 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.98 % Rotamer: Outliers : 0.54 % Allowed : 1.44 % Favored : 98.02 % Cbeta Deviations : 0.17 % 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: -0.03 (0.34), residues: 637 helix: -2.54 (0.93), residues: 22 sheet: 0.89 (0.34), residues: 244 loop : -0.47 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 115 HIS 0.003 0.001 HIS C 189 PHE 0.019 0.001 PHE D 392 TYR 0.023 0.002 TYR C 94 ARG 0.010 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.599 Fit side-chains REVERT: B 89 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7709 (mp0) REVERT: B 152 CYS cc_start: 0.3391 (m) cc_final: 0.3030 (m) REVERT: B 216 ASN cc_start: 0.7341 (m-40) cc_final: 0.6990 (p0) REVERT: C 49 TYR cc_start: 0.8696 (p90) cc_final: 0.8487 (p90) outliers start: 3 outliers final: 0 residues processed: 84 average time/residue: 0.2408 time to fit residues: 24.6816 Evaluate side-chains 61 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN B 183 GLN B 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5134 Z= 0.296 Angle : 0.686 10.526 6983 Z= 0.353 Chirality : 0.049 0.392 775 Planarity : 0.004 0.034 898 Dihedral : 6.216 53.332 744 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.81 % Favored : 94.03 % Rotamer: Outliers : 1.08 % Allowed : 9.91 % Favored : 89.01 % 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: -0.35 (0.34), residues: 637 helix: -2.51 (0.81), residues: 28 sheet: 0.74 (0.34), residues: 243 loop : -0.71 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 115 HIS 0.005 0.002 HIS C 198 PHE 0.018 0.002 PHE B 29 TYR 0.020 0.002 TYR D 369 ARG 0.007 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.576 Fit side-chains REVERT: D 406 GLU cc_start: 0.8415 (pt0) cc_final: 0.8107 (pt0) REVERT: B 29 PHE cc_start: 0.8346 (t80) cc_final: 0.8073 (t80) REVERT: B 89 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7899 (mp0) REVERT: B 114 ILE cc_start: 0.9228 (mm) cc_final: 0.8921 (mm) REVERT: B 216 ASN cc_start: 0.7751 (m-40) cc_final: 0.6811 (p0) REVERT: C 48 ILE cc_start: 0.9418 (tp) cc_final: 0.9096 (tp) outliers start: 6 outliers final: 2 residues processed: 73 average time/residue: 0.2492 time to fit residues: 22.3096 Evaluate side-chains 64 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.0050 chunk 19 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5134 Z= 0.154 Angle : 0.612 11.843 6983 Z= 0.307 Chirality : 0.046 0.355 775 Planarity : 0.003 0.031 898 Dihedral : 5.541 47.135 744 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.45 % Rotamer: Outliers : 0.54 % Allowed : 13.15 % Favored : 86.31 % 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: -0.25 (0.34), residues: 637 helix: -2.25 (0.96), residues: 26 sheet: 0.77 (0.34), residues: 239 loop : -0.63 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 115 HIS 0.003 0.001 HIS C 189 PHE 0.013 0.001 PHE D 515 TYR 0.031 0.001 TYR C 49 ARG 0.004 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.611 Fit side-chains REVERT: D 378 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8675 (pttm) REVERT: B 28 ARG cc_start: 0.7686 (ttp80) cc_final: 0.7103 (ttp80) REVERT: B 29 PHE cc_start: 0.8169 (t80) cc_final: 0.7808 (t80) REVERT: B 89 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7852 (mp0) REVERT: B 156 ASP cc_start: 0.6127 (m-30) cc_final: 0.4928 (t0) REVERT: B 206 TYR cc_start: 0.4803 (m-80) cc_final: 0.4545 (m-80) REVERT: C 18 ARG cc_start: 0.7121 (tpp80) cc_final: 0.6774 (mmm-85) REVERT: C 48 ILE cc_start: 0.9374 (tp) cc_final: 0.9046 (tp) outliers start: 3 outliers final: 1 residues processed: 72 average time/residue: 0.2472 time to fit residues: 21.8230 Evaluate side-chains 60 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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: 0.7931 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5134 Z= 0.293 Angle : 0.670 11.046 6983 Z= 0.340 Chirality : 0.048 0.365 775 Planarity : 0.004 0.034 898 Dihedral : 5.803 48.749 744 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.12 % Favored : 93.56 % Rotamer: Outliers : 2.16 % Allowed : 12.61 % Favored : 85.23 % 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: -0.40 (0.34), residues: 637 helix: -2.09 (0.99), residues: 26 sheet: 0.62 (0.34), residues: 239 loop : -0.71 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 115 HIS 0.005 0.001 HIS B 101 PHE 0.021 0.002 PHE D 515 TYR 0.024 0.002 TYR C 49 ARG 0.007 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.571 Fit side-chains REVERT: D 378 LYS cc_start: 0.9058 (ttpt) cc_final: 0.8845 (pttm) REVERT: B 29 PHE cc_start: 0.8346 (t80) cc_final: 0.7876 (t80) REVERT: B 32 TYR cc_start: 0.8795 (m-80) cc_final: 0.8215 (m-80) REVERT: B 89 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7898 (mp0) REVERT: C 1 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7719 (p0) REVERT: C 18 ARG cc_start: 0.7278 (tpp80) cc_final: 0.6899 (mmm-85) REVERT: C 48 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9041 (mm) outliers start: 12 outliers final: 5 residues processed: 71 average time/residue: 0.2540 time to fit residues: 22.2644 Evaluate side-chains 64 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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: 0.7934 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5134 Z= 0.270 Angle : 0.672 11.305 6983 Z= 0.335 Chirality : 0.048 0.376 775 Planarity : 0.004 0.037 898 Dihedral : 5.758 46.729 744 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.98 % Rotamer: Outliers : 1.80 % Allowed : 13.33 % Favored : 84.86 % 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: -0.48 (0.34), residues: 637 helix: -1.99 (0.99), residues: 26 sheet: 0.51 (0.34), residues: 239 loop : -0.74 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 115 HIS 0.006 0.001 HIS B 101 PHE 0.020 0.001 PHE D 515 TYR 0.026 0.002 TYR C 49 ARG 0.005 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.604 Fit side-chains REVERT: D 402 ILE cc_start: 0.8410 (mm) cc_final: 0.7932 (pt) REVERT: B 29 PHE cc_start: 0.8340 (t80) cc_final: 0.7971 (t80) REVERT: B 32 TYR cc_start: 0.8804 (m-80) cc_final: 0.8205 (m-80) REVERT: B 89 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7878 (mp0) REVERT: B 162 VAL cc_start: 0.7528 (OUTLIER) cc_final: 0.7229 (p) REVERT: C 1 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7838 (p0) REVERT: C 18 ARG cc_start: 0.7336 (tpp80) cc_final: 0.6972 (mmm-85) REVERT: C 48 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9026 (mm) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.2367 time to fit residues: 20.1651 Evaluate side-chains 68 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5134 Z= 0.210 Angle : 0.639 11.332 6983 Z= 0.318 Chirality : 0.047 0.370 775 Planarity : 0.004 0.034 898 Dihedral : 5.580 46.574 744 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 2.70 % Allowed : 13.51 % Favored : 83.78 % 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: -0.56 (0.34), residues: 637 helix: -2.24 (0.84), residues: 32 sheet: 0.52 (0.34), residues: 232 loop : -0.77 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 115 HIS 0.005 0.001 HIS B 101 PHE 0.020 0.001 PHE D 515 TYR 0.024 0.001 TYR C 49 ARG 0.003 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.532 Fit side-chains REVERT: D 402 ILE cc_start: 0.8234 (mm) cc_final: 0.7826 (pt) REVERT: B 29 PHE cc_start: 0.8387 (t80) cc_final: 0.8036 (t80) REVERT: B 32 TYR cc_start: 0.8774 (m-80) cc_final: 0.8143 (m-80) REVERT: B 83 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7352 (mmm) REVERT: B 89 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7879 (mp0) REVERT: B 162 VAL cc_start: 0.7440 (OUTLIER) cc_final: 0.7132 (p) REVERT: C 1 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8101 (p0) REVERT: C 18 ARG cc_start: 0.7192 (tpp80) cc_final: 0.6959 (mmm-85) REVERT: C 48 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9018 (mm) outliers start: 15 outliers final: 9 residues processed: 76 average time/residue: 0.2161 time to fit residues: 20.3837 Evaluate side-chains 77 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 38 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 28 optimal weight: 0.0980 chunk 24 optimal weight: 0.0670 chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.4720 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5134 Z= 0.149 Angle : 0.612 10.463 6983 Z= 0.302 Chirality : 0.047 0.360 775 Planarity : 0.003 0.034 898 Dihedral : 5.367 50.612 744 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.77 % Favored : 96.08 % Rotamer: Outliers : 2.52 % Allowed : 15.32 % Favored : 82.16 % 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: -0.35 (0.34), residues: 637 helix: -1.97 (0.93), residues: 32 sheet: 0.66 (0.35), residues: 236 loop : -0.66 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.002 0.001 HIS B 101 PHE 0.015 0.001 PHE D 515 TYR 0.029 0.001 TYR C 49 ARG 0.005 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.559 Fit side-chains REVERT: B 29 PHE cc_start: 0.8333 (t80) cc_final: 0.7970 (t80) REVERT: B 32 TYR cc_start: 0.8634 (m-80) cc_final: 0.7998 (m-80) REVERT: B 83 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7070 (mtp) REVERT: B 89 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7877 (mp0) REVERT: B 156 ASP cc_start: 0.6130 (m-30) cc_final: 0.5013 (t0) REVERT: B 162 VAL cc_start: 0.7427 (OUTLIER) cc_final: 0.7138 (p) REVERT: B 185 SER cc_start: 0.8147 (m) cc_final: 0.7646 (p) REVERT: C 1 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7910 (p0) REVERT: C 48 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.8998 (mm) outliers start: 14 outliers final: 8 residues processed: 78 average time/residue: 0.2168 time to fit residues: 20.9975 Evaluate side-chains 74 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 5134 Z= 0.394 Angle : 0.749 11.686 6983 Z= 0.377 Chirality : 0.049 0.361 775 Planarity : 0.004 0.035 898 Dihedral : 5.840 43.941 744 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.38 % Favored : 92.46 % Rotamer: Outliers : 2.88 % Allowed : 15.32 % Favored : 81.80 % 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: -0.70 (0.34), residues: 637 helix: -2.18 (0.86), residues: 32 sheet: 0.40 (0.35), residues: 226 loop : -0.86 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 148 HIS 0.016 0.002 HIS B 101 PHE 0.024 0.002 PHE D 515 TYR 0.016 0.002 TYR C 49 ARG 0.005 0.001 ARG D 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.595 Fit side-chains REVERT: B 29 PHE cc_start: 0.8471 (t80) cc_final: 0.8078 (t80) REVERT: B 32 TYR cc_start: 0.8859 (m-80) cc_final: 0.8304 (m-80) REVERT: B 83 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.7543 (mmm) REVERT: C 48 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9023 (mm) outliers start: 16 outliers final: 8 residues processed: 71 average time/residue: 0.2420 time to fit residues: 21.3145 Evaluate side-chains 68 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 17 optimal weight: 0.0470 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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: 0.7874 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5134 Z= 0.168 Angle : 0.675 11.500 6983 Z= 0.332 Chirality : 0.047 0.365 775 Planarity : 0.004 0.036 898 Dihedral : 5.458 44.058 744 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.29 % Rotamer: Outliers : 1.62 % Allowed : 16.94 % Favored : 81.44 % 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: -0.49 (0.34), residues: 637 helix: -2.04 (0.86), residues: 32 sheet: 0.55 (0.35), residues: 227 loop : -0.72 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 115 HIS 0.002 0.001 HIS C 189 PHE 0.019 0.001 PHE D 515 TYR 0.027 0.001 TYR C 49 ARG 0.006 0.001 ARG D 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: B 29 PHE cc_start: 0.8343 (t80) cc_final: 0.7995 (t80) REVERT: B 32 TYR cc_start: 0.8690 (m-80) cc_final: 0.8157 (m-80) REVERT: B 83 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7375 (mmm) REVERT: B 156 ASP cc_start: 0.6005 (m-30) cc_final: 0.4935 (t0) REVERT: C 48 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9042 (mm) outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 0.2284 time to fit residues: 19.7163 Evaluate side-chains 69 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7897 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5134 Z= 0.202 Angle : 0.688 13.065 6983 Z= 0.335 Chirality : 0.046 0.359 775 Planarity : 0.004 0.035 898 Dihedral : 5.196 31.912 744 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 1.80 % Allowed : 16.40 % Favored : 81.80 % 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: -0.46 (0.34), residues: 637 helix: -2.04 (0.86), residues: 32 sheet: 0.65 (0.35), residues: 234 loop : -0.77 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 115 HIS 0.002 0.000 HIS C 189 PHE 0.021 0.001 PHE D 515 TYR 0.022 0.001 TYR C 49 ARG 0.005 0.001 ARG D 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: B 29 PHE cc_start: 0.8424 (t80) cc_final: 0.8149 (t80) REVERT: B 32 TYR cc_start: 0.8743 (m-80) cc_final: 0.8172 (m-80) REVERT: B 83 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7360 (mmm) REVERT: B 156 ASP cc_start: 0.6072 (m-30) cc_final: 0.4974 (t0) REVERT: C 48 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9066 (tp) outliers start: 10 outliers final: 8 residues processed: 66 average time/residue: 0.2372 time to fit residues: 19.3005 Evaluate side-chains 68 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 43 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.121049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.095839 restraints weight = 12300.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.097627 restraints weight = 8395.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.098846 restraints weight = 6555.131| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5134 Z= 0.183 Angle : 0.669 12.395 6983 Z= 0.326 Chirality : 0.046 0.371 775 Planarity : 0.004 0.034 898 Dihedral : 5.195 37.386 744 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.45 % Rotamer: Outliers : 1.80 % Allowed : 16.40 % Favored : 81.80 % 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: -0.47 (0.34), residues: 637 helix: -2.15 (0.87), residues: 32 sheet: 0.62 (0.35), residues: 236 loop : -0.76 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 115 HIS 0.002 0.001 HIS C 189 PHE 0.020 0.001 PHE D 515 TYR 0.023 0.001 TYR C 49 ARG 0.004 0.001 ARG C 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1412.91 seconds wall clock time: 26 minutes 11.29 seconds (1571.29 seconds total)