Starting phenix.real_space_refine on Sun Apr 27 04:00:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrv_37791/04_2025/8wrv_37791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrv_37791/04_2025/8wrv_37791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrv_37791/04_2025/8wrv_37791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrv_37791/04_2025/8wrv_37791.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrv_37791/04_2025/8wrv_37791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrv_37791/04_2025/8wrv_37791.cif" } resolution = 3.28 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 92 5.49 5 S 11 5.16 5 C 2479 2.51 5 N 813 2.21 5 O 1076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4471 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 580 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2537 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 3 Chain: "B" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1188 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 23, 'rna3p_pyr': 27} Link IDs: {'rna2p': 6, 'rna3p': 49} Time building chain proxies: 4.70, per 1000 atoms: 1.05 Number of scatterers: 4471 At special positions: 0 Unit cell: (60.72, 77.22, 114.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 P 92 15.00 O 1076 8.00 N 813 7.00 C 2479 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: 1.23 Conformation dependent library (CDL) restraints added in 330.4 milliseconds 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 598 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 4 sheets defined 37.3% alpha, 20.9% beta 24 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 15 through 41 removed outlier: 3.756A pdb=" N HIS A 26 " --> pdb=" O TYR A 22 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.506A pdb=" N THR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 4.118A pdb=" N SER A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.534A pdb=" N LEU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.597A pdb=" N LEU A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 199 removed outlier: 3.552A pdb=" N LEU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 237 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 3.998A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 6 removed outlier: 5.852A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG A 428 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A 434 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A 426 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A 436 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE A 424 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ASP A 438 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS A 422 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 417 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 407 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 394 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR A 408 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN A 392 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 360 through 363 removed outlier: 3.817A pdb=" N PHE A 369 " --> pdb=" O ALA A 384 " (cutoff:3.500A) 106 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1019 1.33 - 1.45: 1438 1.45 - 1.57: 2091 1.57 - 1.69: 181 1.69 - 1.81: 16 Bond restraints: 4745 Sorted by residual: bond pdb=" O3' A B -10 " pdb=" P G B -9 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.31e+01 bond pdb=" C SER A 345 " pdb=" N PRO A 346 " ideal model delta sigma weight residual 1.331 1.368 -0.037 1.31e-02 5.83e+03 8.06e+00 bond pdb=" O3' C B 14 " pdb=" P C B 15 " ideal model delta sigma weight residual 1.607 1.649 -0.042 1.50e-02 4.44e+03 7.67e+00 bond pdb=" O3' G B -36 " pdb=" P U B -35 " ideal model delta sigma weight residual 1.607 1.647 -0.040 1.50e-02 4.44e+03 7.11e+00 bond pdb=" O3' U B -35 " pdb=" P G B -34 " ideal model delta sigma weight residual 1.607 1.642 -0.035 1.50e-02 4.44e+03 5.35e+00 ... (remaining 4740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 6625 2.05 - 4.11: 178 4.11 - 6.16: 20 6.16 - 8.21: 2 8.21 - 10.27: 1 Bond angle restraints: 6826 Sorted by residual: angle pdb=" O3' C B -6 " pdb=" C3' C B -6 " pdb=" C2' C B -6 " ideal model delta sigma weight residual 113.70 107.79 5.91 1.50e+00 4.44e-01 1.55e+01 angle pdb=" O2' U B -5 " pdb=" C2' U B -5 " pdb=" C1' U B -5 " ideal model delta sigma weight residual 111.80 106.16 5.64 1.50e+00 4.44e-01 1.41e+01 angle pdb=" C4' A B -7 " pdb=" C3' A B -7 " pdb=" O3' A B -7 " ideal model delta sigma weight residual 113.00 107.73 5.27 1.50e+00 4.44e-01 1.24e+01 angle pdb=" N VAL A 395 " pdb=" CA VAL A 395 " pdb=" C VAL A 395 " ideal model delta sigma weight residual 108.46 113.41 -4.95 1.49e+00 4.50e-01 1.10e+01 angle pdb=" N PHE A 202 " pdb=" CA PHE A 202 " pdb=" C PHE A 202 " ideal model delta sigma weight residual 109.81 117.06 -7.25 2.21e+00 2.05e-01 1.08e+01 ... (remaining 6821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 2533 35.81 - 71.62: 278 71.62 - 107.43: 26 107.43 - 143.24: 2 143.24 - 179.05: 3 Dihedral angle restraints: 2842 sinusoidal: 1921 harmonic: 921 Sorted by residual: dihedral pdb=" O4' C B -6 " pdb=" C1' C B -6 " pdb=" N1 C B -6 " pdb=" C2 C B -6 " ideal model delta sinusoidal sigma weight residual 200.00 50.44 149.56 1 1.50e+01 4.44e-03 7.95e+01 dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual 200.00 53.31 146.69 1 1.50e+01 4.44e-03 7.83e+01 dihedral pdb=" O4' U B -5 " pdb=" C1' U B -5 " pdb=" N1 U B -5 " pdb=" C2 U B -5 " ideal model delta sinusoidal sigma weight residual -128.00 51.05 -179.05 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 2839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 714 0.070 - 0.141: 62 0.141 - 0.211: 21 0.211 - 0.282: 1 0.282 - 0.352: 2 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA ARG A 41 " pdb=" N ARG A 41 " pdb=" C ARG A 41 " pdb=" CB ARG A 41 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA ARG A 172 " pdb=" N ARG A 172 " pdb=" C ARG A 172 " pdb=" CB ARG A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2' G B -36 " pdb=" C3' G B -36 " pdb=" O2' G B -36 " pdb=" C1' G B -36 " both_signs ideal model delta sigma weight residual False -2.75 -2.53 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 797 not shown) Planarity restraints: 547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 92 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A 93 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 205 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.26e+00 pdb=" C SER A 205 " -0.031 2.00e-02 2.50e+03 pdb=" O SER A 205 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 206 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 202 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO A 203 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " -0.023 5.00e-02 4.00e+02 ... (remaining 544 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1207 2.82 - 3.34: 3916 3.34 - 3.86: 8362 3.86 - 4.38: 9413 4.38 - 4.90: 13668 Nonbonded interactions: 36566 Sorted by model distance: nonbonded pdb=" NH2 ARG A 47 " pdb=" OE2 GLU A 53 " model vdw 2.301 3.120 nonbonded pdb=" O2' C B -30 " pdb=" OP2 U B -29 " model vdw 2.351 3.040 nonbonded pdb=" O2 U B -27 " pdb=" N2 G B -12 " model vdw 2.358 2.496 nonbonded pdb=" OG1 THR A 338 " pdb=" OP1 A B 5 " model vdw 2.368 3.040 nonbonded pdb=" OP1 DA C 2 " pdb=" NZ LYS A 422 " model vdw 2.397 3.120 ... (remaining 36561 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 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.500 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4745 Z= 0.243 Angle : 0.736 10.266 6826 Z= 0.435 Chirality : 0.050 0.352 800 Planarity : 0.005 0.051 547 Dihedral : 23.712 179.047 2244 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.85 % Allowed : 0.74 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.47), residues: 308 helix: -0.50 (0.48), residues: 109 sheet: -1.31 (0.54), residues: 77 loop : -1.51 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 229 HIS 0.002 0.001 HIS A 26 PHE 0.021 0.001 PHE A 83 TYR 0.010 0.001 TYR A 22 ARG 0.004 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.16282 ( 165) hydrogen bonds : angle 7.07049 ( 412) covalent geometry : bond 0.00407 ( 4745) covalent geometry : angle 0.73630 ( 6826) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.314 Fit side-chains REVERT: A 102 GLU cc_start: 0.7126 (pm20) cc_final: 0.6910 (pm20) REVERT: A 437 ILE cc_start: 0.8140 (mm) cc_final: 0.7937 (mm) outliers start: 5 outliers final: 0 residues processed: 62 average time/residue: 0.2992 time to fit residues: 21.3196 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.0060 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.0270 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 18 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.2254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.187090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.150048 restraints weight = 6611.979| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.52 r_work: 0.3727 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4745 Z= 0.135 Angle : 0.596 7.218 6826 Z= 0.316 Chirality : 0.036 0.232 800 Planarity : 0.005 0.050 547 Dihedral : 25.301 176.098 1619 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % 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: -0.80 (0.48), residues: 308 helix: 0.76 (0.48), residues: 112 sheet: -0.99 (0.54), residues: 76 loop : -1.37 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 229 HIS 0.001 0.000 HIS A 26 PHE 0.011 0.001 PHE A 169 TYR 0.007 0.001 TYR A 439 ARG 0.007 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 165) hydrogen bonds : angle 4.04149 ( 412) covalent geometry : bond 0.00269 ( 4745) covalent geometry : angle 0.59564 ( 6826) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.376 Fit side-chains REVERT: A 20 ASP cc_start: 0.7099 (m-30) cc_final: 0.6711 (t0) REVERT: A 96 ARG cc_start: 0.8113 (mmt90) cc_final: 0.7774 (mmm-85) REVERT: A 102 GLU cc_start: 0.7564 (pm20) cc_final: 0.7355 (pm20) REVERT: A 438 ASP cc_start: 0.7141 (m-30) cc_final: 0.6905 (m-30) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2337 time to fit residues: 13.4803 Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.0270 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.183355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.147178 restraints weight = 6524.022| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.53 r_work: 0.3664 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4745 Z= 0.153 Angle : 0.595 7.638 6826 Z= 0.315 Chirality : 0.037 0.232 800 Planarity : 0.005 0.049 547 Dihedral : 25.274 177.931 1619 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.37 % Allowed : 10.74 % Favored : 88.89 % 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: -0.58 (0.49), residues: 308 helix: 1.14 (0.49), residues: 113 sheet: -1.09 (0.56), residues: 77 loop : -1.31 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 229 HIS 0.003 0.001 HIS A 26 PHE 0.014 0.001 PHE A 369 TYR 0.007 0.001 TYR A 22 ARG 0.004 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 165) hydrogen bonds : angle 3.76531 ( 412) covalent geometry : bond 0.00321 ( 4745) covalent geometry : angle 0.59530 ( 6826) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.346 Fit side-chains REVERT: A 56 VAL cc_start: 0.6942 (p) cc_final: 0.6695 (p) REVERT: A 96 ARG cc_start: 0.8150 (mmt90) cc_final: 0.7788 (mmm-85) REVERT: A 102 GLU cc_start: 0.7584 (pm20) cc_final: 0.7341 (pm20) REVERT: A 438 ASP cc_start: 0.7292 (m-30) cc_final: 0.7092 (m-30) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.2371 time to fit residues: 13.6292 Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.179819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143705 restraints weight = 6576.013| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.52 r_work: 0.3621 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4745 Z= 0.227 Angle : 0.659 6.971 6826 Z= 0.348 Chirality : 0.041 0.232 800 Planarity : 0.006 0.052 547 Dihedral : 25.503 177.847 1619 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.11 % Allowed : 12.59 % Favored : 86.30 % 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: -0.84 (0.49), residues: 308 helix: 0.97 (0.49), residues: 113 sheet: -0.96 (0.58), residues: 75 loop : -1.72 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 229 HIS 0.004 0.002 HIS A 26 PHE 0.016 0.002 PHE A 369 TYR 0.012 0.002 TYR A 22 ARG 0.004 0.001 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 165) hydrogen bonds : angle 3.94868 ( 412) covalent geometry : bond 0.00484 ( 4745) covalent geometry : angle 0.65869 ( 6826) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.330 Fit side-chains REVERT: A 56 VAL cc_start: 0.7018 (p) cc_final: 0.6769 (p) REVERT: A 102 GLU cc_start: 0.7621 (pm20) cc_final: 0.7340 (pm20) REVERT: A 437 ILE cc_start: 0.8554 (mm) cc_final: 0.8073 (mm) outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.3415 time to fit residues: 22.1505 Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.0170 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.181431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145080 restraints weight = 6667.475| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.59 r_work: 0.3635 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4745 Z= 0.174 Angle : 0.618 8.126 6826 Z= 0.325 Chirality : 0.038 0.213 800 Planarity : 0.005 0.050 547 Dihedral : 25.298 177.987 1619 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.48 % Allowed : 13.70 % Favored : 84.81 % 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: -0.60 (0.49), residues: 308 helix: 1.22 (0.50), residues: 113 sheet: -1.01 (0.58), residues: 75 loop : -1.51 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 229 HIS 0.003 0.001 HIS A 26 PHE 0.015 0.001 PHE A 169 TYR 0.011 0.002 TYR A 125 ARG 0.007 0.001 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 165) hydrogen bonds : angle 3.76411 ( 412) covalent geometry : bond 0.00368 ( 4745) covalent geometry : angle 0.61765 ( 6826) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.376 Fit side-chains REVERT: A 102 GLU cc_start: 0.7650 (pm20) cc_final: 0.7362 (pm20) REVERT: A 129 LYS cc_start: 0.7854 (ttmm) cc_final: 0.7598 (ttmm) REVERT: A 416 ARG cc_start: 0.7973 (tpt170) cc_final: 0.7741 (tpt170) outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.3198 time to fit residues: 19.9181 Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 5 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 16 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.182128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.146053 restraints weight = 6585.104| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.51 r_work: 0.3644 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4745 Z= 0.146 Angle : 0.606 8.683 6826 Z= 0.319 Chirality : 0.038 0.212 800 Planarity : 0.005 0.057 547 Dihedral : 25.274 178.442 1619 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.96 % Allowed : 11.85 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.45 (0.49), residues: 308 helix: 1.38 (0.50), residues: 113 sheet: -1.02 (0.57), residues: 75 loop : -1.40 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.002 0.001 HIS A 26 PHE 0.014 0.001 PHE A 169 TYR 0.008 0.001 TYR A 22 ARG 0.005 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 165) hydrogen bonds : angle 3.68211 ( 412) covalent geometry : bond 0.00302 ( 4745) covalent geometry : angle 0.60633 ( 6826) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.308 Fit side-chains REVERT: A 102 GLU cc_start: 0.7591 (pm20) cc_final: 0.7326 (pm20) REVERT: A 129 LYS cc_start: 0.7826 (ttmm) cc_final: 0.7575 (ttmm) REVERT: A 416 ARG cc_start: 0.7972 (tpt170) cc_final: 0.7567 (tpt170) outliers start: 8 outliers final: 7 residues processed: 54 average time/residue: 0.2663 time to fit residues: 17.6889 Evaluate side-chains 54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 408 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.0170 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.180560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144015 restraints weight = 6572.393| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.57 r_work: 0.3620 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4745 Z= 0.201 Angle : 0.646 9.251 6826 Z= 0.338 Chirality : 0.040 0.202 800 Planarity : 0.006 0.058 547 Dihedral : 25.274 177.410 1619 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.96 % Allowed : 13.33 % Favored : 83.70 % 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: -0.61 (0.49), residues: 308 helix: 1.17 (0.50), residues: 113 sheet: -1.17 (0.58), residues: 78 loop : -1.34 (0.59), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 229 HIS 0.004 0.001 HIS A 89 PHE 0.013 0.002 PHE A 369 TYR 0.010 0.002 TYR A 22 ARG 0.007 0.001 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 165) hydrogen bonds : angle 3.82146 ( 412) covalent geometry : bond 0.00427 ( 4745) covalent geometry : angle 0.64577 ( 6826) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.342 Fit side-chains REVERT: A 96 ARG cc_start: 0.8262 (mmt-90) cc_final: 0.8050 (mmt-90) REVERT: A 102 GLU cc_start: 0.7687 (pm20) cc_final: 0.7398 (pm20) REVERT: A 107 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7259 (mt) REVERT: A 129 LYS cc_start: 0.7810 (ttmm) cc_final: 0.7422 (ttmm) REVERT: A 437 ILE cc_start: 0.8405 (mm) cc_final: 0.8169 (mm) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.2270 time to fit residues: 14.2073 Evaluate side-chains 54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 408 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.0370 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.180719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.144442 restraints weight = 6500.758| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.52 r_work: 0.3627 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4745 Z= 0.193 Angle : 0.637 8.490 6826 Z= 0.335 Chirality : 0.039 0.203 800 Planarity : 0.006 0.060 547 Dihedral : 25.261 177.495 1619 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.33 % Allowed : 12.96 % Favored : 83.70 % 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: -0.63 (0.50), residues: 308 helix: 1.18 (0.50), residues: 113 sheet: -1.17 (0.58), residues: 78 loop : -1.40 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 229 HIS 0.004 0.001 HIS A 26 PHE 0.010 0.001 PHE A 369 TYR 0.010 0.001 TYR A 22 ARG 0.007 0.001 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 165) hydrogen bonds : angle 3.80195 ( 412) covalent geometry : bond 0.00411 ( 4745) covalent geometry : angle 0.63716 ( 6826) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.312 Fit side-chains REVERT: A 102 GLU cc_start: 0.7620 (pm20) cc_final: 0.7351 (pm20) REVERT: A 107 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7275 (mt) REVERT: A 129 LYS cc_start: 0.7796 (ttmm) cc_final: 0.7501 (ttmm) REVERT: A 437 ILE cc_start: 0.8418 (mm) cc_final: 0.8166 (mm) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.2266 time to fit residues: 14.1949 Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 408 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 0.0570 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.181926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145891 restraints weight = 6594.732| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.50 r_work: 0.3641 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4745 Z= 0.152 Angle : 0.622 8.451 6826 Z= 0.327 Chirality : 0.038 0.201 800 Planarity : 0.005 0.060 547 Dihedral : 25.232 178.163 1619 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.22 % Allowed : 13.70 % Favored : 84.07 % 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: -0.58 (0.50), residues: 308 helix: 1.18 (0.49), residues: 113 sheet: -1.15 (0.58), residues: 78 loop : -1.29 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 229 HIS 0.002 0.001 HIS A 89 PHE 0.009 0.001 PHE A 369 TYR 0.009 0.001 TYR A 22 ARG 0.006 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 165) hydrogen bonds : angle 3.74098 ( 412) covalent geometry : bond 0.00316 ( 4745) covalent geometry : angle 0.62191 ( 6826) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.314 Fit side-chains REVERT: A 102 GLU cc_start: 0.7618 (pm20) cc_final: 0.7409 (pm20) REVERT: A 437 ILE cc_start: 0.8410 (mm) cc_final: 0.8159 (mm) outliers start: 6 outliers final: 6 residues processed: 48 average time/residue: 0.2214 time to fit residues: 12.8409 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 408 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.181282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145139 restraints weight = 6511.439| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.51 r_work: 0.3633 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4745 Z= 0.187 Angle : 0.638 9.638 6826 Z= 0.333 Chirality : 0.039 0.200 800 Planarity : 0.005 0.062 547 Dihedral : 25.199 177.936 1619 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 2.59 % Allowed : 13.33 % Favored : 84.07 % 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: -0.60 (0.50), residues: 308 helix: 1.19 (0.49), residues: 113 sheet: -1.18 (0.59), residues: 78 loop : -1.34 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 229 HIS 0.003 0.001 HIS A 26 PHE 0.010 0.001 PHE A 369 TYR 0.010 0.001 TYR A 22 ARG 0.006 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 165) hydrogen bonds : angle 3.77824 ( 412) covalent geometry : bond 0.00397 ( 4745) covalent geometry : angle 0.63790 ( 6826) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.476 Fit side-chains REVERT: A 96 ARG cc_start: 0.8169 (mmt-90) cc_final: 0.7904 (mmt-90) REVERT: A 102 GLU cc_start: 0.7636 (pm20) cc_final: 0.7427 (pm20) REVERT: A 437 ILE cc_start: 0.8426 (mm) cc_final: 0.8175 (mm) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.2621 time to fit residues: 15.5836 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 408 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.180484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144325 restraints weight = 6457.104| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.52 r_work: 0.3618 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4745 Z= 0.214 Angle : 0.653 9.311 6826 Z= 0.340 Chirality : 0.040 0.201 800 Planarity : 0.006 0.064 547 Dihedral : 25.211 177.730 1619 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.22 % Allowed : 13.33 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.50), residues: 308 helix: 1.12 (0.49), residues: 113 sheet: -1.02 (0.60), residues: 76 loop : -1.47 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 229 HIS 0.005 0.002 HIS A 26 PHE 0.013 0.002 PHE A 369 TYR 0.012 0.002 TYR A 22 ARG 0.006 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 165) hydrogen bonds : angle 3.82374 ( 412) covalent geometry : bond 0.00461 ( 4745) covalent geometry : angle 0.65285 ( 6826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3368.74 seconds wall clock time: 60 minutes 30.77 seconds (3630.77 seconds total)