Starting phenix.real_space_refine on Wed Sep 17 14:02:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jul_61829/09_2025/9jul_61829.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jul_61829/09_2025/9jul_61829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jul_61829/09_2025/9jul_61829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jul_61829/09_2025/9jul_61829.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jul_61829/09_2025/9jul_61829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jul_61829/09_2025/9jul_61829.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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 41 5.16 5 C 5764 2.51 5 N 1543 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9005 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 8971 Classifications: {'peptide': 1165} Link IDs: {'PTRANS': 30, 'TRANS': 1134} Chain breaks: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'BLD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.26, per 1000 atoms: 0.25 Number of scatterers: 9005 At special positions: 0 Unit cell: (106.95, 99.51, 127.41, 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 41 16.00 O 1657 8.00 N 1543 7.00 C 5764 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: 0.93 Conformation dependent library (CDL) restraints added in 363.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 3 sheets defined 69.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 37 through 75 removed outlier: 4.229A pdb=" N LEU A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 78 through 132 Processing helix chain 'A' and resid 134 through 141 removed outlier: 3.674A pdb=" N PHE A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 164 removed outlier: 4.309A pdb=" N VAL A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 187 Processing helix chain 'A' and resid 187 through 236 Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 245 through 299 Processing helix chain 'A' and resid 303 through 347 Proline residue: A 326 - end of helix removed outlier: 3.503A pdb=" N HIS A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 removed outlier: 3.782A pdb=" N VAL A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 413 " --> pdb=" O LYS A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 removed outlier: 4.253A pdb=" N LYS A 438 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.529A pdb=" N ALA A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 522 Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.835A pdb=" N GLU A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 696 through 729 removed outlier: 3.650A pdb=" N TYR A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 787 removed outlier: 4.178A pdb=" N SER A 752 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 787 " --> pdb=" O ALA A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 794 Processing helix chain 'A' and resid 799 through 852 removed outlier: 3.537A pdb=" N ALA A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL A 813 " --> pdb=" O ASP A 809 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 828 " --> pdb=" O ILE A 824 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ARG A 844 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 852 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 869 Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 878 through 891 Processing helix chain 'A' and resid 891 through 898 Processing helix chain 'A' and resid 900 through 954 Proline residue: A 914 - end of helix Processing helix chain 'A' and resid 958 through 981 Processing helix chain 'A' and resid 985 through 1001 Processing helix chain 'A' and resid 1064 through 1073 removed outlier: 3.536A pdb=" N VAL A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1100 removed outlier: 3.762A pdb=" N LYS A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1122 Processing helix chain 'A' and resid 1129 through 1139 Processing helix chain 'A' and resid 1141 through 1148 removed outlier: 3.849A pdb=" N ALA A1147 " --> pdb=" O LYS A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1154 removed outlier: 3.705A pdb=" N THR A1154 " --> pdb=" O GLY A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1179 removed outlier: 3.593A pdb=" N ARG A1179 " --> pdb=" O ARG A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1210 Processing helix chain 'A' and resid 1234 through 1237 Processing helix chain 'A' and resid 1243 through 1250 removed outlier: 4.003A pdb=" N ASN A1250 " --> pdb=" O HIS A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1264 Processing sheet with id=AA1, first strand: chain 'A' and resid 447 through 448 removed outlier: 6.410A pdb=" N GLY A 447 " --> pdb=" O LEU A 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1042 through 1048 removed outlier: 4.347A pdb=" N ILE A1029 " --> pdb=" O ASP A1044 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N SER A1046 " --> pdb=" O LYS A1027 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LYS A1027 " --> pdb=" O SER A1046 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG A1048 " --> pdb=" O GLU A1025 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU A1025 " --> pdb=" O ARG A1048 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1102 through 1104 removed outlier: 7.096A pdb=" N ALA A1103 " --> pdb=" O LEU A1185 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N MET A1184 " --> pdb=" O ILE A1215 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL A1217 " --> pdb=" O MET A1184 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU A1186 " --> pdb=" O VAL A1217 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A1229 " --> pdb=" O THR A1054 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1812 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: 1.61 Time building geometry restraints manager: 1.17 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: 1619 1.32 - 1.45: 2245 1.45 - 1.57: 5242 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 9174 Sorted by residual: bond pdb=" N PHE A 243 " pdb=" CA PHE A 243 " ideal model delta sigma weight residual 1.457 1.487 -0.030 6.40e-03 2.44e+04 2.22e+01 bond pdb=" N VAL A1058 " pdb=" CA VAL A1058 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.15e-02 7.56e+03 9.65e+00 bond pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 8.72e+00 bond pdb=" N VAL A 198 " pdb=" CA VAL A 198 " ideal model delta sigma weight residual 1.463 1.498 -0.035 1.20e-02 6.94e+03 8.36e+00 bond pdb=" N ILE A1039 " pdb=" CA ILE A1039 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.25e+00 ... (remaining 9169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 11716 1.61 - 3.21: 633 3.21 - 4.82: 59 4.82 - 6.42: 15 6.42 - 8.03: 2 Bond angle restraints: 12425 Sorted by residual: angle pdb=" C PHE A 243 " pdb=" CA PHE A 243 " pdb=" CB PHE A 243 " ideal model delta sigma weight residual 117.07 111.28 5.79 1.44e+00 4.82e-01 1.62e+01 angle pdb=" CA LEU A1026 " pdb=" C LEU A1026 " pdb=" O LEU A1026 " ideal model delta sigma weight residual 122.64 117.85 4.79 1.25e+00 6.40e-01 1.47e+01 angle pdb=" N PHE A1075 " pdb=" CA PHE A1075 " pdb=" C PHE A1075 " ideal model delta sigma weight residual 111.28 107.30 3.98 1.09e+00 8.42e-01 1.34e+01 angle pdb=" N GLN A1073 " pdb=" CA GLN A1073 " pdb=" C GLN A1073 " ideal model delta sigma weight residual 113.20 109.00 4.20 1.21e+00 6.83e-01 1.21e+01 angle pdb=" O PHE A 243 " pdb=" C PHE A 243 " pdb=" N VAL A 244 " ideal model delta sigma weight residual 121.47 124.07 -2.60 7.50e-01 1.78e+00 1.20e+01 ... (remaining 12420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5006 17.59 - 35.18: 425 35.18 - 52.77: 71 52.77 - 70.36: 41 70.36 - 87.96: 5 Dihedral angle restraints: 5548 sinusoidal: 2194 harmonic: 3354 Sorted by residual: dihedral pdb=" CA VAL A 156 " pdb=" C VAL A 156 " pdb=" N MET A 157 " pdb=" CA MET A 157 " ideal model delta harmonic sigma weight residual -180.00 -160.64 -19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA LEU A 982 " pdb=" C LEU A 982 " pdb=" N ALA A 983 " pdb=" CA ALA A 983 " ideal model delta harmonic sigma weight residual -180.00 -162.75 -17.25 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA PRO A 525 " pdb=" C PRO A 525 " pdb=" N ALA A 526 " pdb=" CA ALA A 526 " ideal model delta harmonic sigma weight residual 180.00 164.37 15.63 0 5.00e+00 4.00e-02 9.78e+00 ... (remaining 5545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1178 0.064 - 0.129: 208 0.129 - 0.193: 47 0.193 - 0.257: 6 0.257 - 0.321: 2 Chirality restraints: 1441 Sorted by residual: chirality pdb=" C10 BLD A1301 " pdb=" C01 BLD A1301 " pdb=" C05 BLD A1301 " pdb=" C09 BLD A1301 " both_signs ideal model delta sigma weight residual False -3.02 -2.70 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C08 BLD A1301 " pdb=" C07 BLD A1301 " pdb=" C09 BLD A1301 " pdb=" C14 BLD A1301 " both_signs ideal model delta sigma weight residual False 2.71 2.44 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C23 BLD A1301 " pdb=" C22 BLD A1301 " pdb=" C24 BLD A1301 " pdb=" O23 BLD A1301 " both_signs ideal model delta sigma weight residual False -2.29 -2.53 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 1438 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 238 " 0.218 9.50e-02 1.11e+02 9.77e-02 5.87e+00 pdb=" NE ARG A 238 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 238 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 238 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 238 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 705 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.44e+00 pdb=" C VAL A 705 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL A 705 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 706 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 721 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C LEU A 721 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU A 721 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 722 " 0.011 2.00e-02 2.50e+03 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1654 2.77 - 3.30: 9829 3.30 - 3.84: 15542 3.84 - 4.37: 18034 4.37 - 4.90: 30048 Nonbonded interactions: 75107 Sorted by model distance: nonbonded pdb=" O SER A 704 " pdb=" OG SER A 707 " model vdw 2.238 3.040 nonbonded pdb=" O ALA A1130 " pdb=" NE2 GLN A1134 " model vdw 2.258 3.120 nonbonded pdb=" O GLY A1123 " pdb=" NH1 ARG A1179 " model vdw 2.277 3.120 nonbonded pdb=" O ARG A1220 " pdb=" OG1 THR A1223 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASP A1089 " pdb=" N ARG A1091 " model vdw 2.313 3.120 ... (remaining 75102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.350 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9174 Z= 0.369 Angle : 0.757 8.030 12425 Z= 0.511 Chirality : 0.055 0.321 1441 Planarity : 0.006 0.098 1573 Dihedral : 14.486 87.955 3390 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.74 % Allowed : 1.05 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.25), residues: 1161 helix: 1.62 (0.19), residues: 754 sheet: -0.30 (0.96), residues: 25 loop : -2.07 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 801 TYR 0.015 0.001 TYR A 938 PHE 0.021 0.002 PHE A 72 TRP 0.014 0.001 TRP A 697 HIS 0.006 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 9174) covalent geometry : angle 0.75728 (12425) hydrogen bonds : bond 0.13394 ( 616) hydrogen bonds : angle 5.41651 ( 1812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8176 (mtp) REVERT: A 432 GLN cc_start: 0.7998 (mp10) cc_final: 0.7532 (mp10) REVERT: A 465 LEU cc_start: 0.9112 (mm) cc_final: 0.8827 (mm) REVERT: A 492 LEU cc_start: 0.7901 (tp) cc_final: 0.7626 (tp) REVERT: A 553 MET cc_start: 0.7270 (pmm) cc_final: 0.7047 (pmm) REVERT: A 970 MET cc_start: 0.8999 (mmt) cc_final: 0.8361 (mmt) outliers start: 7 outliers final: 1 residues processed: 155 average time/residue: 0.1209 time to fit residues: 24.8013 Evaluate side-chains 119 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 1042 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.0970 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 236 GLN A 251 GLN ** A 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.170121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.105983 restraints weight = 11863.759| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.23 r_work: 0.3170 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9174 Z= 0.189 Angle : 0.593 9.472 12425 Z= 0.320 Chirality : 0.043 0.173 1441 Planarity : 0.004 0.050 1573 Dihedral : 6.074 76.847 1344 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.37 % Allowed : 9.27 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.25), residues: 1161 helix: 1.92 (0.19), residues: 755 sheet: 0.12 (1.12), residues: 18 loop : -1.86 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1199 TYR 0.017 0.002 TYR A 938 PHE 0.023 0.002 PHE A 72 TRP 0.012 0.001 TRP A 441 HIS 0.006 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 9174) covalent geometry : angle 0.59322 (12425) hydrogen bonds : bond 0.06447 ( 616) hydrogen bonds : angle 4.41932 ( 1812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.7753 (mmt180) cc_final: 0.7425 (tpp-160) REVERT: A 149 PHE cc_start: 0.7484 (t80) cc_final: 0.7128 (t80) REVERT: A 225 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: A 228 ASN cc_start: 0.7725 (t0) cc_final: 0.6778 (t0) REVERT: A 371 LYS cc_start: 0.8727 (mmtm) cc_final: 0.8438 (mmtt) REVERT: A 380 ARG cc_start: 0.7484 (ptp90) cc_final: 0.6935 (ptp-170) REVERT: A 432 GLN cc_start: 0.8170 (mp10) cc_final: 0.7538 (tm-30) REVERT: A 465 LEU cc_start: 0.9096 (mm) cc_final: 0.8856 (mm) REVERT: A 492 LEU cc_start: 0.7948 (tp) cc_final: 0.7581 (tp) REVERT: A 1053 LYS cc_start: 0.7443 (mtpt) cc_final: 0.7161 (mtpt) REVERT: A 1107 GLN cc_start: 0.8377 (pm20) cc_final: 0.7486 (tm-30) REVERT: A 1118 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7857 (pt0) REVERT: A 1202 GLN cc_start: 0.8113 (mt0) cc_final: 0.7760 (mm-40) REVERT: A 1259 MET cc_start: 0.8470 (mmm) cc_final: 0.8120 (ppp) outliers start: 13 outliers final: 7 residues processed: 144 average time/residue: 0.1031 time to fit residues: 20.3044 Evaluate side-chains 136 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1118 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 57 optimal weight: 0.0570 chunk 11 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN A 513 GLN ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 ASN ** A1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.174287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115027 restraints weight = 11642.058| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.44 r_work: 0.3231 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9174 Z= 0.126 Angle : 0.521 7.391 12425 Z= 0.280 Chirality : 0.040 0.166 1441 Planarity : 0.004 0.044 1573 Dihedral : 5.653 70.693 1341 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.58 % Allowed : 10.75 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.25), residues: 1161 helix: 2.23 (0.19), residues: 756 sheet: -0.31 (0.99), residues: 18 loop : -1.85 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1036 TYR 0.007 0.001 TYR A 938 PHE 0.019 0.001 PHE A 757 TRP 0.008 0.001 TRP A 697 HIS 0.005 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9174) covalent geometry : angle 0.52126 (12425) hydrogen bonds : bond 0.05399 ( 616) hydrogen bonds : angle 4.21139 ( 1812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7147 (mp10) REVERT: A 241 MET cc_start: 0.8668 (mtp) cc_final: 0.8460 (mtp) REVERT: A 371 LYS cc_start: 0.8721 (mmtm) cc_final: 0.8352 (mmtt) REVERT: A 380 ARG cc_start: 0.7414 (ptp90) cc_final: 0.6936 (ptp-170) REVERT: A 432 GLN cc_start: 0.8269 (mp10) cc_final: 0.7620 (tm-30) REVERT: A 465 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8795 (mm) REVERT: A 492 LEU cc_start: 0.7948 (tp) cc_final: 0.7551 (tp) REVERT: A 970 MET cc_start: 0.9110 (mmt) cc_final: 0.8750 (mmt) REVERT: A 1107 GLN cc_start: 0.8273 (pm20) cc_final: 0.7542 (tm-30) REVERT: A 1118 GLU cc_start: 0.8183 (pt0) cc_final: 0.7802 (pp20) REVERT: A 1259 MET cc_start: 0.8517 (mmm) cc_final: 0.8194 (ppp) outliers start: 15 outliers final: 11 residues processed: 140 average time/residue: 0.1171 time to fit residues: 22.0135 Evaluate side-chains 137 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1116 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 7.9990 chunk 97 optimal weight: 0.5980 chunk 114 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.172740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109571 restraints weight = 11936.422| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.22 r_work: 0.3226 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9174 Z= 0.131 Angle : 0.514 6.736 12425 Z= 0.277 Chirality : 0.040 0.182 1441 Planarity : 0.004 0.045 1573 Dihedral : 5.692 71.405 1341 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.21 % Allowed : 12.01 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.25), residues: 1161 helix: 2.25 (0.19), residues: 756 sheet: -0.46 (0.96), residues: 18 loop : -1.79 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 238 TYR 0.011 0.001 TYR A 938 PHE 0.016 0.001 PHE A 757 TRP 0.006 0.001 TRP A 697 HIS 0.004 0.001 HIS A1251 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9174) covalent geometry : angle 0.51375 (12425) hydrogen bonds : bond 0.05414 ( 616) hydrogen bonds : angle 4.14497 ( 1812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7057 (mp10) REVERT: A 236 GLN cc_start: 0.6866 (mt0) cc_final: 0.6550 (mm110) REVERT: A 371 LYS cc_start: 0.8694 (mmtm) cc_final: 0.8345 (mmtt) REVERT: A 380 ARG cc_start: 0.7425 (ptp90) cc_final: 0.7008 (ptp-170) REVERT: A 432 GLN cc_start: 0.8255 (mp10) cc_final: 0.7649 (tm-30) REVERT: A 461 LYS cc_start: 0.7844 (tmtt) cc_final: 0.7615 (tptm) REVERT: A 465 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8809 (mm) REVERT: A 492 LEU cc_start: 0.8027 (tp) cc_final: 0.7611 (tp) REVERT: A 512 LYS cc_start: 0.7734 (ptmm) cc_final: 0.7415 (ptmm) REVERT: A 970 MET cc_start: 0.9160 (mmt) cc_final: 0.8754 (mmt) REVERT: A 1042 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7097 (m-80) REVERT: A 1082 ARG cc_start: 0.7142 (ttp80) cc_final: 0.6935 (ttp80) REVERT: A 1084 MET cc_start: 0.7163 (tpp) cc_final: 0.6921 (tpp) REVERT: A 1107 GLN cc_start: 0.8290 (pm20) cc_final: 0.7629 (tm-30) REVERT: A 1118 GLU cc_start: 0.8143 (pt0) cc_final: 0.7823 (pp20) REVERT: A 1259 MET cc_start: 0.8513 (mmm) cc_final: 0.8175 (ppp) outliers start: 21 outliers final: 10 residues processed: 143 average time/residue: 0.1219 time to fit residues: 23.2666 Evaluate side-chains 142 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1104 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN ** A1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.167428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106016 restraints weight = 11985.165| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.58 r_work: 0.3114 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9174 Z= 0.216 Angle : 0.584 6.774 12425 Z= 0.316 Chirality : 0.043 0.196 1441 Planarity : 0.004 0.045 1573 Dihedral : 6.098 77.962 1341 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.63 % Allowed : 13.17 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.25), residues: 1161 helix: 1.99 (0.19), residues: 756 sheet: -0.51 (1.00), residues: 18 loop : -1.79 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 238 TYR 0.020 0.002 TYR A 938 PHE 0.020 0.002 PHE A 72 TRP 0.008 0.001 TRP A 291 HIS 0.007 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 9174) covalent geometry : angle 0.58435 (12425) hydrogen bonds : bond 0.06521 ( 616) hydrogen bonds : angle 4.32346 ( 1812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.7796 (mmt180) cc_final: 0.7445 (tpp-160) REVERT: A 225 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6982 (mp10) REVERT: A 306 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8328 (mp) REVERT: A 380 ARG cc_start: 0.7599 (ptp90) cc_final: 0.7153 (ptp-170) REVERT: A 432 GLN cc_start: 0.8138 (mp10) cc_final: 0.7607 (tm-30) REVERT: A 465 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8875 (mm) REVERT: A 492 LEU cc_start: 0.7962 (tp) cc_final: 0.7499 (tp) REVERT: A 521 MET cc_start: 0.8685 (mtm) cc_final: 0.8206 (mtm) REVERT: A 1042 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7162 (m-80) REVERT: A 1107 GLN cc_start: 0.8315 (pm20) cc_final: 0.7669 (tm-30) REVERT: A 1134 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8206 (mm-40) REVERT: A 1138 LEU cc_start: 0.8262 (mp) cc_final: 0.7902 (mp) REVERT: A 1259 MET cc_start: 0.8533 (mmm) cc_final: 0.8175 (ppp) outliers start: 25 outliers final: 15 residues processed: 142 average time/residue: 0.1183 time to fit residues: 22.4770 Evaluate side-chains 145 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1184 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 46 optimal weight: 0.0070 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.170298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.106543 restraints weight = 11814.934| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.21 r_work: 0.3187 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9174 Z= 0.138 Angle : 0.527 7.656 12425 Z= 0.284 Chirality : 0.040 0.213 1441 Planarity : 0.004 0.044 1573 Dihedral : 5.835 74.384 1341 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.11 % Allowed : 15.17 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.25), residues: 1161 helix: 2.19 (0.19), residues: 757 sheet: -0.59 (0.98), residues: 18 loop : -1.78 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 238 TYR 0.011 0.001 TYR A 938 PHE 0.017 0.001 PHE A 757 TRP 0.007 0.001 TRP A 291 HIS 0.005 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9174) covalent geometry : angle 0.52686 (12425) hydrogen bonds : bond 0.05761 ( 616) hydrogen bonds : angle 4.18842 ( 1812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.7783 (mmt180) cc_final: 0.7427 (tpp-160) REVERT: A 225 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: A 315 MET cc_start: 0.9012 (mmt) cc_final: 0.8772 (mmm) REVERT: A 371 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8213 (mmtt) REVERT: A 380 ARG cc_start: 0.7594 (ptp90) cc_final: 0.7175 (ptp-170) REVERT: A 432 GLN cc_start: 0.8149 (mp10) cc_final: 0.7650 (tm-30) REVERT: A 461 LYS cc_start: 0.7840 (tmtt) cc_final: 0.7633 (tttm) REVERT: A 465 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8882 (mm) REVERT: A 492 LEU cc_start: 0.7959 (tp) cc_final: 0.7490 (tp) REVERT: A 521 MET cc_start: 0.8643 (mtm) cc_final: 0.8190 (mtm) REVERT: A 1042 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7225 (m-80) REVERT: A 1084 MET cc_start: 0.7023 (tpp) cc_final: 0.6686 (tpp) REVERT: A 1089 ASP cc_start: 0.8636 (t0) cc_final: 0.8328 (t0) REVERT: A 1107 GLN cc_start: 0.8289 (pm20) cc_final: 0.7752 (tm-30) REVERT: A 1134 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8167 (mm-40) REVERT: A 1138 LEU cc_start: 0.8269 (mp) cc_final: 0.7963 (mp) REVERT: A 1259 MET cc_start: 0.8492 (mmm) cc_final: 0.8174 (ppp) outliers start: 20 outliers final: 10 residues processed: 138 average time/residue: 0.1209 time to fit residues: 22.4249 Evaluate side-chains 142 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1116 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 54 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 0.0030 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.171104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.111273 restraints weight = 11821.096| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.28 r_work: 0.3190 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9174 Z= 0.136 Angle : 0.526 8.482 12425 Z= 0.282 Chirality : 0.040 0.224 1441 Planarity : 0.003 0.044 1573 Dihedral : 5.767 73.674 1341 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.42 % Allowed : 15.49 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.25), residues: 1161 helix: 2.26 (0.19), residues: 757 sheet: -0.84 (0.95), residues: 18 loop : -1.77 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1199 TYR 0.011 0.001 TYR A 938 PHE 0.015 0.001 PHE A 757 TRP 0.006 0.001 TRP A 291 HIS 0.004 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9174) covalent geometry : angle 0.52582 (12425) hydrogen bonds : bond 0.05581 ( 616) hydrogen bonds : angle 4.11053 ( 1812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7427 (mp10) REVERT: A 236 GLN cc_start: 0.7493 (mt0) cc_final: 0.7271 (mt0) REVERT: A 306 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8393 (mp) REVERT: A 315 MET cc_start: 0.9018 (mmt) cc_final: 0.8805 (mmm) REVERT: A 371 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8184 (mmtt) REVERT: A 380 ARG cc_start: 0.7611 (ptp90) cc_final: 0.7212 (ptp-170) REVERT: A 432 GLN cc_start: 0.8151 (mp10) cc_final: 0.7669 (tm-30) REVERT: A 461 LYS cc_start: 0.7902 (tmtt) cc_final: 0.7679 (tttm) REVERT: A 465 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8874 (mm) REVERT: A 492 LEU cc_start: 0.7975 (tp) cc_final: 0.7487 (tp) REVERT: A 512 LYS cc_start: 0.7707 (ptmm) cc_final: 0.7162 (ptmm) REVERT: A 553 MET cc_start: 0.7469 (pmm) cc_final: 0.7194 (pmm) REVERT: A 1042 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7221 (m-80) REVERT: A 1082 ARG cc_start: 0.6839 (ttp80) cc_final: 0.6555 (ttp80) REVERT: A 1089 ASP cc_start: 0.8658 (t0) cc_final: 0.8418 (t0) REVERT: A 1107 GLN cc_start: 0.8323 (pm20) cc_final: 0.7788 (tm-30) REVERT: A 1118 GLU cc_start: 0.8144 (pt0) cc_final: 0.7874 (pp20) REVERT: A 1134 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8183 (mm-40) REVERT: A 1138 LEU cc_start: 0.8296 (mp) cc_final: 0.7945 (mp) REVERT: A 1259 MET cc_start: 0.8452 (mmm) cc_final: 0.8163 (ppp) outliers start: 23 outliers final: 16 residues processed: 145 average time/residue: 0.1192 time to fit residues: 23.1764 Evaluate side-chains 146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1184 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 19 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 92 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.171134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.111535 restraints weight = 11858.509| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.24 r_work: 0.3197 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9174 Z= 0.137 Angle : 0.533 8.304 12425 Z= 0.285 Chirality : 0.040 0.203 1441 Planarity : 0.004 0.044 1573 Dihedral : 5.749 73.529 1341 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.63 % Allowed : 15.70 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.25), residues: 1161 helix: 2.26 (0.19), residues: 757 sheet: -0.75 (1.02), residues: 18 loop : -1.76 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1199 TYR 0.011 0.001 TYR A 938 PHE 0.016 0.002 PHE A1075 TRP 0.006 0.001 TRP A 291 HIS 0.004 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9174) covalent geometry : angle 0.53314 (12425) hydrogen bonds : bond 0.05540 ( 616) hydrogen bonds : angle 4.10081 ( 1812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 GLN cc_start: 0.7464 (mt0) cc_final: 0.7263 (mt0) REVERT: A 306 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8386 (mp) REVERT: A 315 MET cc_start: 0.9011 (mmt) cc_final: 0.8625 (mmm) REVERT: A 380 ARG cc_start: 0.7675 (ptp90) cc_final: 0.7281 (ptp-170) REVERT: A 432 GLN cc_start: 0.8157 (mp10) cc_final: 0.7682 (tm-30) REVERT: A 461 LYS cc_start: 0.7900 (tmtt) cc_final: 0.7667 (tttm) REVERT: A 465 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8860 (mm) REVERT: A 492 LEU cc_start: 0.7976 (tp) cc_final: 0.7475 (tp) REVERT: A 512 LYS cc_start: 0.7762 (ptmm) cc_final: 0.7215 (ptmm) REVERT: A 553 MET cc_start: 0.7451 (pmm) cc_final: 0.7120 (pmm) REVERT: A 1042 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: A 1082 ARG cc_start: 0.6892 (ttp80) cc_final: 0.6598 (ttp80) REVERT: A 1084 MET cc_start: 0.6970 (tpp) cc_final: 0.6717 (tpp) REVERT: A 1089 ASP cc_start: 0.8607 (t0) cc_final: 0.8378 (t0) REVERT: A 1107 GLN cc_start: 0.8327 (pm20) cc_final: 0.7805 (tm-30) REVERT: A 1118 GLU cc_start: 0.8143 (pt0) cc_final: 0.7884 (pp20) REVERT: A 1134 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8141 (mm-40) REVERT: A 1138 LEU cc_start: 0.8304 (mp) cc_final: 0.7943 (mp) REVERT: A 1259 MET cc_start: 0.8444 (mmm) cc_final: 0.8188 (ppp) outliers start: 25 outliers final: 18 residues processed: 140 average time/residue: 0.1255 time to fit residues: 23.2926 Evaluate side-chains 146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1184 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.171874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.112073 restraints weight = 11870.792| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.26 r_work: 0.3208 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9174 Z= 0.131 Angle : 0.533 12.054 12425 Z= 0.281 Chirality : 0.041 0.353 1441 Planarity : 0.004 0.044 1573 Dihedral : 5.708 72.838 1341 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.21 % Allowed : 16.02 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.25), residues: 1161 helix: 2.29 (0.19), residues: 757 sheet: -0.76 (1.08), residues: 18 loop : -1.79 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1199 TYR 0.010 0.001 TYR A 938 PHE 0.017 0.001 PHE A1075 TRP 0.007 0.001 TRP A 188 HIS 0.004 0.001 HIS A1251 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9174) covalent geometry : angle 0.53306 (12425) hydrogen bonds : bond 0.05422 ( 616) hydrogen bonds : angle 4.06974 ( 1812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 GLN cc_start: 0.7430 (mt0) cc_final: 0.7199 (mt0) REVERT: A 238 ARG cc_start: 0.8467 (mtt90) cc_final: 0.8242 (mmm160) REVERT: A 315 MET cc_start: 0.9005 (mmt) cc_final: 0.8621 (mmm) REVERT: A 380 ARG cc_start: 0.7664 (ptp90) cc_final: 0.7277 (ptp-170) REVERT: A 432 GLN cc_start: 0.8183 (mp10) cc_final: 0.7737 (mp10) REVERT: A 461 LYS cc_start: 0.7920 (tmtt) cc_final: 0.7681 (tttm) REVERT: A 465 LEU cc_start: 0.9142 (mm) cc_final: 0.8842 (mm) REVERT: A 492 LEU cc_start: 0.7993 (tp) cc_final: 0.7464 (tp) REVERT: A 512 LYS cc_start: 0.7654 (ptmm) cc_final: 0.7168 (ptmm) REVERT: A 553 MET cc_start: 0.7450 (pmm) cc_final: 0.7120 (pmm) REVERT: A 1042 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7324 (m-80) REVERT: A 1082 ARG cc_start: 0.6923 (ttp80) cc_final: 0.6566 (ttp80) REVERT: A 1084 MET cc_start: 0.7021 (tpp) cc_final: 0.6769 (tpp) REVERT: A 1089 ASP cc_start: 0.8614 (t0) cc_final: 0.8362 (t0) REVERT: A 1107 GLN cc_start: 0.8328 (pm20) cc_final: 0.7826 (tm-30) REVERT: A 1118 GLU cc_start: 0.8135 (pt0) cc_final: 0.7872 (pp20) REVERT: A 1134 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8187 (mm-40) REVERT: A 1138 LEU cc_start: 0.8324 (mp) cc_final: 0.7959 (mp) REVERT: A 1259 MET cc_start: 0.8441 (mmm) cc_final: 0.8195 (ppp) outliers start: 21 outliers final: 17 residues processed: 137 average time/residue: 0.1208 time to fit residues: 22.1530 Evaluate side-chains 145 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1184 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.0270 chunk 68 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.171731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.111666 restraints weight = 11805.139| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.32 r_work: 0.3201 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9174 Z= 0.134 Angle : 0.534 12.609 12425 Z= 0.282 Chirality : 0.041 0.333 1441 Planarity : 0.004 0.044 1573 Dihedral : 5.712 72.952 1341 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.11 % Allowed : 16.33 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.25), residues: 1161 helix: 2.31 (0.19), residues: 757 sheet: -1.56 (0.87), residues: 26 loop : -1.80 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1199 TYR 0.011 0.001 TYR A 938 PHE 0.018 0.001 PHE A1075 TRP 0.006 0.001 TRP A 291 HIS 0.004 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9174) covalent geometry : angle 0.53395 (12425) hydrogen bonds : bond 0.05445 ( 616) hydrogen bonds : angle 4.06303 ( 1812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 GLN cc_start: 0.7540 (mt0) cc_final: 0.7144 (mm110) REVERT: A 238 ARG cc_start: 0.8517 (mtt90) cc_final: 0.8255 (mmm160) REVERT: A 315 MET cc_start: 0.9011 (mmt) cc_final: 0.8625 (mmm) REVERT: A 371 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8419 (mmtt) REVERT: A 380 ARG cc_start: 0.7647 (ptp90) cc_final: 0.7260 (ptp-170) REVERT: A 432 GLN cc_start: 0.8183 (mp10) cc_final: 0.7735 (mp10) REVERT: A 461 LYS cc_start: 0.7943 (tmtt) cc_final: 0.7698 (tttm) REVERT: A 465 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8822 (mm) REVERT: A 492 LEU cc_start: 0.7988 (tp) cc_final: 0.7453 (tp) REVERT: A 512 LYS cc_start: 0.7713 (ptmm) cc_final: 0.7196 (ptmm) REVERT: A 521 MET cc_start: 0.8449 (mtt) cc_final: 0.8228 (mtm) REVERT: A 553 MET cc_start: 0.7450 (pmm) cc_final: 0.7130 (pmm) REVERT: A 1042 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: A 1082 ARG cc_start: 0.6962 (ttp80) cc_final: 0.6607 (ttp80) REVERT: A 1084 MET cc_start: 0.6993 (tpp) cc_final: 0.6748 (tpp) REVERT: A 1089 ASP cc_start: 0.8618 (t0) cc_final: 0.8375 (t0) REVERT: A 1107 GLN cc_start: 0.8338 (pm20) cc_final: 0.7873 (tm-30) REVERT: A 1118 GLU cc_start: 0.8145 (pt0) cc_final: 0.7898 (pp20) REVERT: A 1134 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8188 (mm-40) REVERT: A 1138 LEU cc_start: 0.8315 (mp) cc_final: 0.7947 (mp) REVERT: A 1259 MET cc_start: 0.8434 (mmm) cc_final: 0.8206 (ppp) outliers start: 20 outliers final: 17 residues processed: 139 average time/residue: 0.1218 time to fit residues: 22.5553 Evaluate side-chains 146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1184 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN ** A1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.169510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109755 restraints weight = 11737.256| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.35 r_work: 0.3150 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9174 Z= 0.166 Angle : 0.565 12.810 12425 Z= 0.300 Chirality : 0.042 0.323 1441 Planarity : 0.004 0.045 1573 Dihedral : 5.893 75.869 1341 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.21 % Allowed : 16.65 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.25), residues: 1161 helix: 2.23 (0.19), residues: 757 sheet: -1.62 (0.88), residues: 26 loop : -1.81 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1199 TYR 0.015 0.001 TYR A 938 PHE 0.021 0.002 PHE A1075 TRP 0.007 0.001 TRP A 291 HIS 0.005 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9174) covalent geometry : angle 0.56473 (12425) hydrogen bonds : bond 0.05870 ( 616) hydrogen bonds : angle 4.13534 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3023.92 seconds wall clock time: 52 minutes 21.67 seconds (3141.67 seconds total)