Starting phenix.real_space_refine on Mon Sep 23 21:28:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymd_33927/09_2024/7ymd_33927.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymd_33927/09_2024/7ymd_33927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.176 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymd_33927/09_2024/7ymd_33927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymd_33927/09_2024/7ymd_33927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymd_33927/09_2024/7ymd_33927.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymd_33927/09_2024/7ymd_33927.cif" } resolution = 4.176 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= 0.007 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 25 5.16 5 C 3575 2.51 5 N 969 2.21 5 O 1084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 5653 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 816 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2573 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2264 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Time building chain proxies: 3.75, per 1000 atoms: 0.66 Number of scatterers: 5653 At special positions: 0 Unit cell: (77.256, 83.52, 99.18, 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 25 16.00 O 1084 8.00 N 969 7.00 C 3575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 670.1 milliseconds 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 5 sheets defined 50.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.523A pdb=" N ARG A 202 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS A 203 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR A 205 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN A 207 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLN A 208 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 210 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS A 211 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 227 removed outlier: 4.243A pdb=" N ILE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 27 removed outlier: 3.529A pdb=" N ALA B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 49 removed outlier: 5.015A pdb=" N ASP B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 77 removed outlier: 4.064A pdb=" N LEU B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 97 removed outlier: 4.346A pdb=" N LYS B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 168 Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.881A pdb=" N GLU B 186 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 223 through 237 Processing helix chain 'B' and resid 251 through 258 removed outlier: 3.575A pdb=" N ILE B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 266 Processing helix chain 'B' and resid 306 through 316 Processing helix chain 'C' and resid 8 through 25 removed outlier: 4.549A pdb=" N LEU C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 42 removed outlier: 4.054A pdb=" N ARG C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 63 Processing helix chain 'C' and resid 68 through 83 Processing helix chain 'C' and resid 94 through 99 removed outlier: 4.030A pdb=" N ASN C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 146 removed outlier: 3.522A pdb=" N PHE C 138 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR C 146 " --> pdb=" O GLN C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 151 removed outlier: 3.744A pdb=" N ILE C 151 " --> pdb=" O TYR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 Processing helix chain 'C' and resid 177 through 195 Processing helix chain 'C' and resid 201 through 209 Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' Processing helix chain 'C' and resid 226 through 237 Processing helix chain 'C' and resid 259 through 266 Processing helix chain 'C' and resid 267 through 280 Processing helix chain 'C' and resid 282 through 287 removed outlier: 4.455A pdb=" N LYS C 287 " --> pdb=" O GLU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 298 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 33 removed outlier: 3.573A pdb=" N CYS B 32 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 133 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.194A pdb=" N SER B 207 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 281 " --> pdb=" O VAL B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 240 through 242 Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 47 removed outlier: 4.690A pdb=" N LYS C 122 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE C 124 " --> pdb=" O GLN C 89 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 89 " --> pdb=" O ILE C 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 199 through 200 removed outlier: 3.954A pdb=" N ILE C 199 " --> pdb=" O TYR C 256 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 669 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: 1.29 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1877 1.34 - 1.46: 874 1.46 - 1.58: 2954 1.58 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 5744 Sorted by residual: bond pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ASP C 7 " pdb=" CA ASP C 7 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ASN B 286 " pdb=" CA ASN B 286 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.99e-01 bond pdb=" CB GLU B 45 " pdb=" CG GLU B 45 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.84e-01 bond pdb=" N THR C 168 " pdb=" CA THR C 168 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.69e-01 ... (remaining 5739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 7412 1.04 - 2.08: 278 2.08 - 3.12: 41 3.12 - 4.15: 16 4.15 - 5.19: 3 Bond angle restraints: 7750 Sorted by residual: angle pdb=" C ASN B 286 " pdb=" CA ASN B 286 " pdb=" CB ASN B 286 " ideal model delta sigma weight residual 110.42 115.61 -5.19 1.99e+00 2.53e-01 6.81e+00 angle pdb=" C TYR A 212 " pdb=" N ASN A 213 " pdb=" CA ASN A 213 " ideal model delta sigma weight residual 121.54 125.73 -4.19 1.91e+00 2.74e-01 4.81e+00 angle pdb=" C LYS C 196 " pdb=" N ASN C 197 " pdb=" CA ASN C 197 " ideal model delta sigma weight residual 121.54 125.46 -3.92 1.91e+00 2.74e-01 4.20e+00 angle pdb=" C THR C 168 " pdb=" CA THR C 168 " pdb=" CB THR C 168 " ideal model delta sigma weight residual 110.42 114.48 -4.06 1.99e+00 2.53e-01 4.15e+00 angle pdb=" C ARG A 127 " pdb=" CA ARG A 127 " pdb=" CB ARG A 127 " ideal model delta sigma weight residual 109.54 112.83 -3.29 1.84e+00 2.95e-01 3.19e+00 ... (remaining 7745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3220 17.94 - 35.88: 219 35.88 - 53.82: 40 53.82 - 71.76: 7 71.76 - 89.69: 3 Dihedral angle restraints: 3489 sinusoidal: 1422 harmonic: 2067 Sorted by residual: dihedral pdb=" CA ARG A 127 " pdb=" C ARG A 127 " pdb=" N SER A 128 " pdb=" CA SER A 128 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA CYS B 32 " pdb=" C CYS B 32 " pdb=" N HIS B 33 " pdb=" CA HIS B 33 " ideal model delta harmonic sigma weight residual -180.00 -163.01 -16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA MET B 265 " pdb=" C MET B 265 " pdb=" N TYR B 266 " pdb=" CA TYR B 266 " ideal model delta harmonic sigma weight residual 180.00 163.73 16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 3486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 562 0.025 - 0.050: 190 0.050 - 0.075: 73 0.075 - 0.100: 34 0.100 - 0.125: 25 Chirality restraints: 884 Sorted by residual: chirality pdb=" CA VAL C 129 " pdb=" N VAL C 129 " pdb=" C VAL C 129 " pdb=" CB VAL C 129 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA ILE C 254 " pdb=" N ILE C 254 " pdb=" C ILE C 254 " pdb=" CB ILE C 254 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 881 not shown) Planarity restraints: 993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 160 " 0.009 2.00e-02 2.50e+03 7.84e-03 1.54e+00 pdb=" CG TRP B 160 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP B 160 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 160 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 160 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 160 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 160 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 160 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 160 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 160 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 242 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO A 243 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 196 " 0.005 2.00e-02 2.50e+03 1.11e-02 1.22e+00 pdb=" C LYS C 196 " -0.019 2.00e-02 2.50e+03 pdb=" O LYS C 196 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN C 197 " 0.006 2.00e-02 2.50e+03 ... (remaining 990 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 79 2.60 - 3.18: 5545 3.18 - 3.75: 8420 3.75 - 4.33: 11466 4.33 - 4.90: 18681 Nonbonded interactions: 44191 Sorted by model distance: nonbonded pdb=" O SER B 213 " pdb=" OG1 THR B 214 " model vdw 2.026 3.040 nonbonded pdb=" OE2 GLU A 214 " pdb=" CG GLN A 217 " model vdw 2.216 3.440 nonbonded pdb=" O LEU C 80 " pdb=" N GLY C 85 " model vdw 2.219 3.120 nonbonded pdb=" OH TYR B 20 " pdb=" O PRO C 130 " model vdw 2.247 3.040 nonbonded pdb=" O LYS C 287 " pdb=" OG SER C 288 " model vdw 2.263 3.040 ... (remaining 44186 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: 0.140 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.690 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5744 Z= 0.131 Angle : 0.481 5.193 7750 Z= 0.278 Chirality : 0.037 0.125 884 Planarity : 0.002 0.028 993 Dihedral : 12.735 89.694 2145 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 0.16 (0.35), residues: 693 helix: 1.35 (0.31), residues: 330 sheet: -0.54 (1.16), residues: 22 loop : -1.13 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 160 HIS 0.007 0.001 HIS C 56 PHE 0.015 0.001 PHE B 165 TYR 0.008 0.001 TYR B 261 ARG 0.005 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 MET cc_start: 0.8043 (tpp) cc_final: 0.7781 (tpp) REVERT: B 222 LEU cc_start: 0.8632 (mm) cc_final: 0.7899 (tp) REVERT: C 197 ASN cc_start: 0.7333 (p0) cc_final: 0.7112 (p0) REVERT: C 224 ASN cc_start: 0.8580 (m-40) cc_final: 0.8119 (t0) REVERT: C 257 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7442 (tpt-90) REVERT: C 299 ASP cc_start: 0.7148 (p0) cc_final: 0.6436 (p0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1477 time to fit residues: 34.7653 Evaluate side-chains 145 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 GLN C 89 GLN C 145 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5744 Z= 0.178 Angle : 0.559 9.641 7750 Z= 0.294 Chirality : 0.042 0.143 884 Planarity : 0.003 0.044 993 Dihedral : 4.040 18.222 757 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % 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: -0.14 (0.34), residues: 693 helix: 0.91 (0.30), residues: 335 sheet: -1.63 (0.96), residues: 26 loop : -0.99 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 160 HIS 0.006 0.001 HIS C 56 PHE 0.015 0.002 PHE C 207 TYR 0.013 0.002 TYR C 84 ARG 0.003 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 PHE cc_start: 0.6226 (t80) cc_final: 0.5966 (t80) REVERT: A 226 LEU cc_start: 0.8376 (mp) cc_final: 0.8164 (mp) REVERT: B 163 GLU cc_start: 0.8569 (tt0) cc_final: 0.8103 (mm-30) REVERT: B 222 LEU cc_start: 0.8591 (mm) cc_final: 0.7965 (tp) REVERT: C 31 MET cc_start: 0.8637 (tpp) cc_final: 0.8390 (tpp) REVERT: C 139 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8600 (tttt) REVERT: C 148 GLU cc_start: 0.8353 (pt0) cc_final: 0.8071 (pt0) REVERT: C 197 ASN cc_start: 0.7623 (p0) cc_final: 0.7403 (p0) REVERT: C 299 ASP cc_start: 0.7163 (p0) cc_final: 0.6866 (p0) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1522 time to fit residues: 36.3525 Evaluate side-chains 147 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 55 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 chunk 47 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN B 23 GLN C 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5744 Z= 0.167 Angle : 0.577 8.884 7750 Z= 0.301 Chirality : 0.042 0.188 884 Planarity : 0.003 0.040 993 Dihedral : 4.109 21.250 757 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.16 % Allowed : 2.07 % Favored : 97.77 % 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: -0.32 (0.33), residues: 693 helix: 0.73 (0.29), residues: 336 sheet: -1.88 (0.92), residues: 26 loop : -1.04 (0.36), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 160 HIS 0.008 0.001 HIS C 56 PHE 0.021 0.002 PHE C 193 TYR 0.019 0.001 TYR B 313 ARG 0.002 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 PHE cc_start: 0.6315 (t80) cc_final: 0.6039 (t80) REVERT: B 89 ILE cc_start: 0.9042 (mp) cc_final: 0.8794 (pt) REVERT: B 158 MET cc_start: 0.8194 (tpp) cc_final: 0.7846 (mmm) REVERT: B 163 GLU cc_start: 0.8515 (tt0) cc_final: 0.8060 (mm-30) REVERT: C 31 MET cc_start: 0.8653 (tpp) cc_final: 0.8349 (tpp) REVERT: C 48 ARG cc_start: 0.8617 (tpt-90) cc_final: 0.8280 (mmm160) outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.1803 time to fit residues: 43.9119 Evaluate side-chains 149 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 0.0170 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 overall best weight: 3.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 GLN C 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5744 Z= 0.300 Angle : 0.669 8.955 7750 Z= 0.351 Chirality : 0.045 0.175 884 Planarity : 0.004 0.041 993 Dihedral : 4.623 22.948 757 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.16 % Allowed : 4.13 % Favored : 95.71 % 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: -0.57 (0.33), residues: 693 helix: 0.53 (0.29), residues: 333 sheet: -2.16 (0.89), residues: 26 loop : -1.14 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 160 HIS 0.005 0.002 HIS C 56 PHE 0.024 0.002 PHE A 215 TYR 0.021 0.002 TYR A 227 ARG 0.003 0.001 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9083 (mtmm) cc_final: 0.8829 (mtmm) REVERT: A 226 LEU cc_start: 0.8406 (mp) cc_final: 0.8146 (mp) REVERT: B 33 HIS cc_start: 0.8879 (t70) cc_final: 0.8001 (t-90) REVERT: B 206 PHE cc_start: 0.6639 (m-10) cc_final: 0.6401 (m-10) REVERT: C 52 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8188 (mm-40) REVERT: C 149 GLU cc_start: 0.8302 (mp0) cc_final: 0.8054 (mp0) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.1526 time to fit residues: 34.3299 Evaluate side-chains 137 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 0.0370 chunk 56 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 34 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 overall best weight: 3.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN C 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5744 Z= 0.281 Angle : 0.659 8.428 7750 Z= 0.341 Chirality : 0.044 0.152 884 Planarity : 0.004 0.039 993 Dihedral : 4.826 23.708 757 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: -0.81 (0.33), residues: 693 helix: 0.34 (0.29), residues: 342 sheet: -2.08 (0.90), residues: 26 loop : -1.33 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 160 HIS 0.011 0.002 HIS A 147 PHE 0.023 0.002 PHE C 207 TYR 0.023 0.002 TYR A 227 ARG 0.003 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.5798 (ttt) cc_final: 0.5432 (ttt) REVERT: B 33 HIS cc_start: 0.8590 (t70) cc_final: 0.7611 (t-90) REVERT: B 89 ILE cc_start: 0.9052 (mp) cc_final: 0.8685 (pt) REVERT: B 206 PHE cc_start: 0.6482 (m-10) cc_final: 0.6275 (m-10) REVERT: C 31 MET cc_start: 0.8812 (tpp) cc_final: 0.8159 (tpp) REVERT: C 149 GLU cc_start: 0.8029 (mp0) cc_final: 0.7793 (mp0) REVERT: C 197 ASN cc_start: 0.7605 (p0) cc_final: 0.7398 (p0) REVERT: C 237 ARG cc_start: 0.8967 (mtt180) cc_final: 0.8649 (ttm170) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1472 time to fit residues: 32.2650 Evaluate side-chains 140 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 228 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN B 280 GLN C 56 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5744 Z= 0.172 Angle : 0.601 9.644 7750 Z= 0.313 Chirality : 0.042 0.149 884 Planarity : 0.003 0.039 993 Dihedral : 4.712 24.731 757 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.33), residues: 693 helix: 0.47 (0.29), residues: 335 sheet: -1.99 (0.94), residues: 26 loop : -1.40 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 160 HIS 0.007 0.001 HIS C 56 PHE 0.020 0.002 PHE C 207 TYR 0.019 0.002 TYR A 227 ARG 0.002 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 PHE cc_start: 0.6447 (t80) cc_final: 0.6241 (t80) REVERT: B 89 ILE cc_start: 0.9061 (mp) cc_final: 0.8729 (pt) REVERT: B 305 TRP cc_start: 0.5803 (m-90) cc_final: 0.5240 (m-90) REVERT: C 31 MET cc_start: 0.8864 (tpp) cc_final: 0.8311 (tpp) REVERT: C 149 GLU cc_start: 0.8030 (mp0) cc_final: 0.7759 (mp0) REVERT: C 237 ARG cc_start: 0.8909 (mtt180) cc_final: 0.8641 (ttm170) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1549 time to fit residues: 34.4955 Evaluate side-chains 147 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 280 GLN C 56 HIS C 118 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5744 Z= 0.163 Angle : 0.608 9.598 7750 Z= 0.313 Chirality : 0.042 0.188 884 Planarity : 0.003 0.041 993 Dihedral : 4.545 24.468 757 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: -0.77 (0.33), residues: 693 helix: 0.40 (0.29), residues: 342 sheet: -1.89 (0.98), residues: 26 loop : -1.37 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 160 HIS 0.008 0.001 HIS C 56 PHE 0.019 0.002 PHE C 207 TYR 0.035 0.002 TYR B 266 ARG 0.002 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 PHE cc_start: 0.6575 (t80) cc_final: 0.6232 (t80) REVERT: A 226 LEU cc_start: 0.8275 (mp) cc_final: 0.7839 (mp) REVERT: A 228 ASN cc_start: 0.7479 (t0) cc_final: 0.7181 (t0) REVERT: B 29 ARG cc_start: 0.8546 (mmt-90) cc_final: 0.8183 (mmt-90) REVERT: B 41 LEU cc_start: 0.9208 (tt) cc_final: 0.8980 (tt) REVERT: B 42 MET cc_start: 0.8997 (mtt) cc_final: 0.8527 (mtt) REVERT: B 158 MET cc_start: 0.8215 (tpp) cc_final: 0.7985 (mmm) REVERT: B 305 TRP cc_start: 0.5636 (m-90) cc_final: 0.5161 (m-90) REVERT: C 31 MET cc_start: 0.8823 (tpp) cc_final: 0.8314 (tpp) REVERT: C 72 MET cc_start: 0.8190 (tpt) cc_final: 0.7807 (tpp) REVERT: C 142 GLN cc_start: 0.8185 (tp40) cc_final: 0.7917 (tp40) REVERT: C 149 GLU cc_start: 0.8075 (mp0) cc_final: 0.7799 (mp0) REVERT: C 197 ASN cc_start: 0.7427 (p0) cc_final: 0.6871 (p0) REVERT: C 257 ARG cc_start: 0.7164 (tpt90) cc_final: 0.6458 (tpt90) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1658 time to fit residues: 36.9922 Evaluate side-chains 145 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 63 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN C 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5744 Z= 0.172 Angle : 0.602 9.201 7750 Z= 0.310 Chirality : 0.042 0.150 884 Planarity : 0.003 0.042 993 Dihedral : 4.495 24.380 757 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.33), residues: 693 helix: 0.41 (0.29), residues: 335 sheet: -1.79 (0.98), residues: 26 loop : -1.34 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 160 HIS 0.007 0.001 HIS C 56 PHE 0.017 0.002 PHE C 207 TYR 0.024 0.002 TYR B 266 ARG 0.002 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 PHE cc_start: 0.6685 (t80) cc_final: 0.6282 (t80) REVERT: A 226 LEU cc_start: 0.8271 (mp) cc_final: 0.7798 (mp) REVERT: A 228 ASN cc_start: 0.7640 (t0) cc_final: 0.7378 (t0) REVERT: B 29 ARG cc_start: 0.8555 (mmt-90) cc_final: 0.8149 (mmt-90) REVERT: B 33 HIS cc_start: 0.8717 (t70) cc_final: 0.8361 (t-90) REVERT: B 41 LEU cc_start: 0.9221 (tt) cc_final: 0.8982 (tt) REVERT: B 42 MET cc_start: 0.9077 (mtt) cc_final: 0.8606 (mtt) REVERT: B 89 ILE cc_start: 0.9017 (mp) cc_final: 0.8692 (pt) REVERT: B 305 TRP cc_start: 0.5600 (m-90) cc_final: 0.5140 (m-90) REVERT: C 31 MET cc_start: 0.8816 (tpp) cc_final: 0.8310 (tpp) REVERT: C 72 MET cc_start: 0.8152 (tpt) cc_final: 0.7805 (tpp) REVERT: C 142 GLN cc_start: 0.8178 (tp40) cc_final: 0.7901 (tp40) REVERT: C 149 GLU cc_start: 0.8081 (mp0) cc_final: 0.7781 (mp0) REVERT: C 237 ARG cc_start: 0.8891 (ttm170) cc_final: 0.8659 (ttm170) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1538 time to fit residues: 34.4827 Evaluate side-chains 142 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN C 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5744 Z= 0.170 Angle : 0.648 11.097 7750 Z= 0.328 Chirality : 0.043 0.176 884 Planarity : 0.003 0.041 993 Dihedral : 4.561 24.441 757 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -0.82 (0.33), residues: 693 helix: 0.29 (0.29), residues: 344 sheet: -1.61 (1.02), residues: 26 loop : -1.35 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 160 HIS 0.010 0.001 HIS A 147 PHE 0.021 0.002 PHE A 215 TYR 0.023 0.002 TYR B 313 ARG 0.002 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 PHE cc_start: 0.6619 (t80) cc_final: 0.6280 (t80) REVERT: A 226 LEU cc_start: 0.8175 (mp) cc_final: 0.7733 (mp) REVERT: A 244 LEU cc_start: 0.9187 (tp) cc_final: 0.8966 (tp) REVERT: B 29 ARG cc_start: 0.8554 (mmt-90) cc_final: 0.8125 (mmt-90) REVERT: B 33 HIS cc_start: 0.8552 (t70) cc_final: 0.8071 (t-90) REVERT: B 41 LEU cc_start: 0.9209 (tt) cc_final: 0.8982 (tt) REVERT: B 42 MET cc_start: 0.8975 (mtt) cc_final: 0.8642 (mtt) REVERT: B 89 ILE cc_start: 0.9038 (mp) cc_final: 0.8711 (pt) REVERT: B 206 PHE cc_start: 0.6576 (m-10) cc_final: 0.6337 (m-10) REVERT: B 261 TYR cc_start: 0.8081 (t80) cc_final: 0.7789 (t80) REVERT: B 305 TRP cc_start: 0.5568 (m-90) cc_final: 0.5123 (m-90) REVERT: C 31 MET cc_start: 0.8783 (tpp) cc_final: 0.8297 (tpp) REVERT: C 72 MET cc_start: 0.8129 (tpt) cc_final: 0.7781 (tpp) REVERT: C 140 ILE cc_start: 0.8398 (pt) cc_final: 0.8188 (pt) REVERT: C 142 GLN cc_start: 0.8148 (tp40) cc_final: 0.7875 (tp40) REVERT: C 149 GLU cc_start: 0.8070 (mp0) cc_final: 0.7773 (mp0) REVERT: C 237 ARG cc_start: 0.8813 (ttm170) cc_final: 0.8589 (mtm180) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1490 time to fit residues: 33.7665 Evaluate side-chains 146 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 5 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS B 280 GLN C 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5744 Z= 0.167 Angle : 0.633 10.848 7750 Z= 0.323 Chirality : 0.043 0.176 884 Planarity : 0.003 0.041 993 Dihedral : 4.429 24.368 757 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -0.75 (0.33), residues: 693 helix: 0.35 (0.29), residues: 339 sheet: -1.68 (1.01), residues: 26 loop : -1.28 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 160 HIS 0.008 0.001 HIS C 56 PHE 0.016 0.002 PHE C 207 TYR 0.027 0.002 TYR A 227 ARG 0.003 0.000 ARG B 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 PHE cc_start: 0.6719 (t80) cc_final: 0.6412 (t80) REVERT: A 219 ASN cc_start: 0.8654 (t0) cc_final: 0.8444 (t0) REVERT: A 226 LEU cc_start: 0.8035 (mp) cc_final: 0.7626 (mp) REVERT: B 29 ARG cc_start: 0.8546 (mmt-90) cc_final: 0.8258 (mmt-90) REVERT: B 89 ILE cc_start: 0.9033 (mp) cc_final: 0.8748 (pt) REVERT: B 305 TRP cc_start: 0.5458 (m-90) cc_final: 0.5057 (m-90) REVERT: C 31 MET cc_start: 0.8764 (tpp) cc_final: 0.8171 (tpp) REVERT: C 72 MET cc_start: 0.8147 (tpt) cc_final: 0.7803 (tpp) REVERT: C 142 GLN cc_start: 0.8089 (tp40) cc_final: 0.7781 (tp40) REVERT: C 149 GLU cc_start: 0.8060 (mp0) cc_final: 0.7742 (mp0) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1465 time to fit residues: 33.4236 Evaluate side-chains 144 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.191633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.145671 restraints weight = 9321.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150475 restraints weight = 6142.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.153997 restraints weight = 4729.301| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5744 Z= 0.221 Angle : 0.659 10.185 7750 Z= 0.338 Chirality : 0.043 0.147 884 Planarity : 0.003 0.042 993 Dihedral : 4.547 24.035 757 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.32), residues: 693 helix: 0.31 (0.28), residues: 344 sheet: -1.66 (0.97), residues: 26 loop : -1.40 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 160 HIS 0.008 0.001 HIS C 56 PHE 0.029 0.002 PHE A 215 TYR 0.032 0.003 TYR A 227 ARG 0.008 0.001 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1425.79 seconds wall clock time: 26 minutes 8.22 seconds (1568.22 seconds total)