Starting phenix.real_space_refine on Mon Jan 13 20:57:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9w_51159/01_2025/9g9w_51159.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9w_51159/01_2025/9g9w_51159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g9w_51159/01_2025/9g9w_51159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9w_51159/01_2025/9g9w_51159.map" model { file = "/net/cci-nas-00/data/ceres_data/9g9w_51159/01_2025/9g9w_51159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9w_51159/01_2025/9g9w_51159.cif" } resolution = 2.48 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= 0.048 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 K 3 8.98 5 S 32 5.16 5 C 2732 2.51 5 N 616 2.21 5 O 706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4089 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1938 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 4, 'TRANS': 253} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 108 Unusual residues: {' K': 3, 'Y01': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Restraints were copied for chains: B Time building chain proxies: 3.62, per 1000 atoms: 0.89 Number of scatterers: 4089 At special positions: 0 Unit cell: (60.736, 80.704, 94.848, 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) K 3 19.00 S 32 16.00 O 706 8.00 N 616 7.00 C 2732 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: 1.17 Conformation dependent library (CDL) restraints added in 534.9 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 53 removed outlier: 5.573A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 Proline residue: A 71 - end of helix removed outlier: 3.979A pdb=" N ALA A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 147 removed outlier: 3.675A pdb=" N LEU A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 182 Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 248 removed outlier: 5.290A pdb=" N ARG A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'B' and resid 3 through 53 removed outlier: 5.573A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 74 Proline residue: B 71 - end of helix removed outlier: 3.980A pdb=" N ALA B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 147 removed outlier: 3.675A pdb=" N LEU B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 182 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 248 removed outlier: 5.290A pdb=" N ARG B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 343 hydrogen bonds defined for protein. 1029 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: 1.10 Time building geometry restraints manager: 1.32 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: 632 1.32 - 1.44: 1134 1.44 - 1.56: 2376 1.56 - 1.68: 0 1.68 - 1.81: 50 Bond restraints: 4192 Sorted by residual: bond pdb=" CAL Y01 A 302 " pdb=" CAX Y01 A 302 " ideal model delta sigma weight residual 1.540 1.513 0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" CAL Y01 B 302 " pdb=" CAX Y01 B 302 " ideal model delta sigma weight residual 1.540 1.514 0.026 2.00e-02 2.50e+03 1.64e+00 bond pdb=" CAL Y01 B 303 " pdb=" CAX Y01 B 303 " ideal model delta sigma weight residual 1.540 1.515 0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" CAL Y01 A 303 " pdb=" CAX Y01 A 303 " ideal model delta sigma weight residual 1.540 1.515 0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" CAL Y01 B 301 " pdb=" CAX Y01 B 301 " ideal model delta sigma weight residual 1.540 1.516 0.024 2.00e-02 2.50e+03 1.48e+00 ... (remaining 4187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 4931 0.95 - 1.90: 653 1.90 - 2.86: 94 2.86 - 3.81: 34 3.81 - 4.76: 18 Bond angle restraints: 5730 Sorted by residual: angle pdb=" N SER B 31 " pdb=" CA SER B 31 " pdb=" C SER B 31 " ideal model delta sigma weight residual 111.82 115.38 -3.56 1.16e+00 7.43e-01 9.41e+00 angle pdb=" N SER A 31 " pdb=" CA SER A 31 " pdb=" C SER A 31 " ideal model delta sigma weight residual 111.82 115.34 -3.52 1.16e+00 7.43e-01 9.22e+00 angle pdb=" CA TYR A 96 " pdb=" CB TYR A 96 " pdb=" CG TYR A 96 " ideal model delta sigma weight residual 113.90 118.00 -4.10 1.80e+00 3.09e-01 5.20e+00 angle pdb=" CA TYR B 96 " pdb=" CB TYR B 96 " pdb=" CG TYR B 96 " ideal model delta sigma weight residual 113.90 117.99 -4.09 1.80e+00 3.09e-01 5.16e+00 angle pdb=" N PHE A 80 " pdb=" CA PHE A 80 " pdb=" C PHE A 80 " ideal model delta sigma weight residual 111.11 113.66 -2.55 1.20e+00 6.94e-01 4.53e+00 ... (remaining 5725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 2486 15.06 - 30.13: 160 30.13 - 45.19: 34 45.19 - 60.25: 20 60.25 - 75.31: 2 Dihedral angle restraints: 2702 sinusoidal: 1202 harmonic: 1500 Sorted by residual: dihedral pdb=" CA LYS B 79 " pdb=" C LYS B 79 " pdb=" N PHE B 80 " pdb=" CA PHE B 80 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LYS A 79 " pdb=" C LYS A 79 " pdb=" N PHE A 80 " pdb=" CA PHE A 80 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA HIS A 98 " pdb=" C HIS A 98 " pdb=" N ALA A 99 " pdb=" CA ALA A 99 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 2699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 341 0.034 - 0.068: 253 0.068 - 0.103: 60 0.103 - 0.137: 22 0.137 - 0.171: 6 Chirality restraints: 682 Sorted by residual: chirality pdb=" CA LEU A 208 " pdb=" N LEU A 208 " pdb=" C LEU A 208 " pdb=" CB LEU A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA LEU B 208 " pdb=" N LEU B 208 " pdb=" C LEU B 208 " pdb=" CB LEU B 208 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA TRP B 78 " pdb=" N TRP B 78 " pdb=" C TRP B 78 " pdb=" CB TRP B 78 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.93e-01 ... (remaining 679 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 137 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.73e+00 pdb=" C ARG B 137 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG B 137 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR B 138 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 137 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.73e+00 pdb=" C ARG A 137 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG A 137 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 138 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 39 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C GLU A 39 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU A 39 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A 40 " -0.012 2.00e-02 2.50e+03 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 1394 2.86 - 3.43: 4737 3.43 - 4.00: 7582 4.00 - 4.57: 11233 4.57 - 5.14: 15661 Nonbonded interactions: 40607 Sorted by model distance: nonbonded pdb=" OE2 GLU A 182 " pdb=" OH TYR A 220 " model vdw 2.295 3.040 nonbonded pdb=" OE2 GLU B 182 " pdb=" OH TYR B 220 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR A 52 " pdb=" OD2 ASP B 58 " model vdw 2.301 3.040 nonbonded pdb=" OD2 ASP A 58 " pdb=" OH TYR B 52 " model vdw 2.301 3.040 nonbonded pdb=" O THR A 198 " pdb=" OG1 THR A 199 " model vdw 2.420 3.040 ... (remaining 40602 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 259 or resid 301 through 303)) selection = chain 'B' } 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: 1.000 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.670 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 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 : 0.007 0.044 4192 Z= 0.468 Angle : 0.724 4.758 5730 Z= 0.446 Chirality : 0.050 0.171 682 Planarity : 0.006 0.022 680 Dihedral : 11.378 75.314 1742 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: 0.55 (0.33), residues: 512 helix: 0.52 (0.22), residues: 420 sheet: None (None), residues: 0 loop : 0.25 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 78 HIS 0.003 0.001 HIS B 188 PHE 0.026 0.002 PHE B 202 TYR 0.022 0.005 TYR A 96 ARG 0.004 0.001 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.436 Fit side-chains REVERT: A 3 ARG cc_start: 0.5993 (ttt180) cc_final: 0.5750 (ttt-90) REVERT: A 47 ARG cc_start: 0.6227 (ttt-90) cc_final: 0.5936 (ttp80) REVERT: A 135 PHE cc_start: 0.7716 (t80) cc_final: 0.7422 (t80) REVERT: A 137 ARG cc_start: 0.6533 (ttm-80) cc_final: 0.6138 (ttp-170) REVERT: B 3 ARG cc_start: 0.6007 (ttt180) cc_final: 0.5762 (ttt-90) REVERT: B 47 ARG cc_start: 0.6222 (ttt-90) cc_final: 0.5931 (ttp80) REVERT: B 135 PHE cc_start: 0.7738 (t80) cc_final: 0.7445 (t80) REVERT: B 137 ARG cc_start: 0.6552 (ttm-80) cc_final: 0.6154 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 1.3134 time to fit residues: 92.2395 Evaluate side-chains 54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.104277 restraints weight = 4576.783| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.66 r_work: 0.2963 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4192 Z= 0.152 Angle : 0.428 4.809 5730 Z= 0.238 Chirality : 0.037 0.126 682 Planarity : 0.003 0.029 680 Dihedral : 7.399 52.869 978 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.26 % Allowed : 6.61 % Favored : 93.12 % 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: 3.82 (0.35), residues: 512 helix: 2.93 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.52 (0.68), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 78 HIS 0.001 0.000 HIS A 188 PHE 0.016 0.001 PHE A 109 TYR 0.012 0.002 TYR A 96 ARG 0.001 0.000 ARG A 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.505 Fit side-chains REVERT: A 3 ARG cc_start: 0.6254 (ttt180) cc_final: 0.5968 (ttt-90) REVERT: A 135 PHE cc_start: 0.7859 (t80) cc_final: 0.7520 (t80) REVERT: A 137 ARG cc_start: 0.6310 (ttm-80) cc_final: 0.6009 (ttp-170) REVERT: B 3 ARG cc_start: 0.6254 (ttt180) cc_final: 0.5978 (ttt-90) REVERT: B 135 PHE cc_start: 0.7862 (t80) cc_final: 0.7522 (t80) REVERT: B 137 ARG cc_start: 0.6308 (ttm-80) cc_final: 0.6010 (ttp-170) outliers start: 1 outliers final: 2 residues processed: 62 average time/residue: 1.6178 time to fit residues: 103.0585 Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099716 restraints weight = 4536.891| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.67 r_work: 0.3096 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4192 Z= 0.271 Angle : 0.473 5.033 5730 Z= 0.261 Chirality : 0.039 0.140 682 Planarity : 0.003 0.027 680 Dihedral : 7.277 52.262 978 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.26 % Allowed : 9.26 % Favored : 90.48 % 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: 4.06 (0.35), residues: 512 helix: 3.18 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.13 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 78 HIS 0.001 0.000 HIS A 72 PHE 0.017 0.002 PHE B 109 TYR 0.015 0.002 TYR A 96 ARG 0.001 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.341 Fit side-chains REVERT: A 3 ARG cc_start: 0.6431 (ttt180) cc_final: 0.6100 (ttt-90) REVERT: A 51 LYS cc_start: 0.6802 (tttt) cc_final: 0.6535 (tttt) REVERT: A 135 PHE cc_start: 0.7931 (t80) cc_final: 0.7637 (t80) REVERT: A 137 ARG cc_start: 0.6435 (ttm-80) cc_final: 0.6074 (ttp-170) REVERT: B 3 ARG cc_start: 0.6423 (ttt180) cc_final: 0.6082 (ttt-90) REVERT: B 51 LYS cc_start: 0.6793 (tttt) cc_final: 0.6526 (tttt) REVERT: B 135 PHE cc_start: 0.7932 (t80) cc_final: 0.7638 (t80) REVERT: B 137 ARG cc_start: 0.6440 (ttm-80) cc_final: 0.6078 (ttp-170) outliers start: 1 outliers final: 2 residues processed: 66 average time/residue: 1.6236 time to fit residues: 109.9228 Evaluate side-chains 66 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101974 restraints weight = 4526.575| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.66 r_work: 0.2940 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4192 Z= 0.202 Angle : 0.426 5.080 5730 Z= 0.236 Chirality : 0.037 0.130 682 Planarity : 0.002 0.025 680 Dihedral : 7.067 53.799 978 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % 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: 4.56 (0.36), residues: 512 helix: 3.49 (0.23), residues: 412 sheet: None (None), residues: 0 loop : 0.82 (0.71), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 78 HIS 0.000 0.000 HIS A 98 PHE 0.016 0.001 PHE B 109 TYR 0.012 0.002 TYR A 96 ARG 0.001 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.453 Fit side-chains REVERT: A 3 ARG cc_start: 0.6327 (ttt180) cc_final: 0.5992 (ttt-90) REVERT: A 51 LYS cc_start: 0.6601 (tttt) cc_final: 0.6360 (tttt) REVERT: A 135 PHE cc_start: 0.7814 (t80) cc_final: 0.7516 (t80) REVERT: A 137 ARG cc_start: 0.6264 (ttm-80) cc_final: 0.5929 (ttp-170) REVERT: B 3 ARG cc_start: 0.6351 (ttt180) cc_final: 0.6010 (ttt-90) REVERT: B 51 LYS cc_start: 0.6595 (tttt) cc_final: 0.6355 (tttt) REVERT: B 135 PHE cc_start: 0.7814 (t80) cc_final: 0.7509 (t80) REVERT: B 137 ARG cc_start: 0.6251 (ttm-80) cc_final: 0.5919 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 1.6561 time to fit residues: 105.4487 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 0.0970 chunk 1 optimal weight: 0.0370 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.101393 restraints weight = 4634.725| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.67 r_work: 0.2932 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4192 Z= 0.211 Angle : 0.431 5.107 5730 Z= 0.237 Chirality : 0.037 0.131 682 Planarity : 0.002 0.023 680 Dihedral : 7.004 55.442 978 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.59 (0.36), residues: 512 helix: 3.52 (0.23), residues: 412 sheet: None (None), residues: 0 loop : 0.77 (0.71), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 PHE 0.015 0.001 PHE A 109 TYR 0.011 0.001 TYR A 96 ARG 0.002 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.425 Fit side-chains REVERT: A 3 ARG cc_start: 0.6374 (ttt180) cc_final: 0.6036 (ttt-90) REVERT: A 51 LYS cc_start: 0.6641 (tttt) cc_final: 0.6410 (tttt) REVERT: A 135 PHE cc_start: 0.7806 (t80) cc_final: 0.7515 (t80) REVERT: A 137 ARG cc_start: 0.6259 (ttm-80) cc_final: 0.5918 (ttp-170) REVERT: B 3 ARG cc_start: 0.6380 (ttt180) cc_final: 0.6045 (ttt-90) REVERT: B 51 LYS cc_start: 0.6637 (tttt) cc_final: 0.6406 (tttt) REVERT: B 135 PHE cc_start: 0.7806 (t80) cc_final: 0.7513 (t80) REVERT: B 137 ARG cc_start: 0.6244 (ttm-80) cc_final: 0.5904 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 1.6507 time to fit residues: 105.0780 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.098229 restraints weight = 4584.250| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.64 r_work: 0.2900 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4192 Z= 0.307 Angle : 0.484 5.162 5730 Z= 0.265 Chirality : 0.039 0.143 682 Planarity : 0.002 0.023 680 Dihedral : 7.195 55.373 978 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.53 % Allowed : 12.17 % Favored : 87.30 % 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: 4.35 (0.36), residues: 512 helix: 3.35 (0.23), residues: 412 sheet: None (None), residues: 0 loop : 0.69 (0.70), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.001 0.000 HIS A 72 PHE 0.016 0.002 PHE B 109 TYR 0.012 0.002 TYR A 96 ARG 0.002 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.458 Fit side-chains REVERT: A 3 ARG cc_start: 0.6419 (ttt180) cc_final: 0.6035 (ttt-90) REVERT: A 47 ARG cc_start: 0.6473 (ttt-90) cc_final: 0.6045 (ttp80) REVERT: A 135 PHE cc_start: 0.7857 (t80) cc_final: 0.7546 (t80) REVERT: A 137 ARG cc_start: 0.6307 (ttm-80) cc_final: 0.5946 (ttp-170) REVERT: B 3 ARG cc_start: 0.6432 (ttt180) cc_final: 0.6102 (ttt-90) REVERT: B 47 ARG cc_start: 0.6474 (ttt-90) cc_final: 0.6047 (ttp80) REVERT: B 135 PHE cc_start: 0.7859 (t80) cc_final: 0.7549 (t80) REVERT: B 137 ARG cc_start: 0.6300 (ttm-80) cc_final: 0.5942 (ttp-170) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 1.6872 time to fit residues: 107.4679 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097740 restraints weight = 4660.896| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.67 r_work: 0.2889 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4192 Z= 0.348 Angle : 0.509 5.183 5730 Z= 0.277 Chirality : 0.040 0.146 682 Planarity : 0.003 0.023 680 Dihedral : 7.396 55.149 978 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.53 % Allowed : 12.17 % Favored : 87.30 % 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: 4.12 (0.36), residues: 512 helix: 3.21 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 0.45 (0.69), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.001 0.000 HIS A 98 PHE 0.016 0.002 PHE A 109 TYR 0.012 0.002 TYR A 96 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.408 Fit side-chains REVERT: A 3 ARG cc_start: 0.6438 (ttt180) cc_final: 0.6067 (ttt-90) REVERT: A 47 ARG cc_start: 0.6579 (ttt-90) cc_final: 0.6148 (ttp80) REVERT: A 135 PHE cc_start: 0.7868 (t80) cc_final: 0.7568 (t80) REVERT: A 137 ARG cc_start: 0.6343 (ttm-80) cc_final: 0.5972 (ttp-170) REVERT: B 3 ARG cc_start: 0.6445 (ttt180) cc_final: 0.6127 (ttt-90) REVERT: B 47 ARG cc_start: 0.6574 (ttt-90) cc_final: 0.6145 (ttp80) REVERT: B 135 PHE cc_start: 0.7865 (t80) cc_final: 0.7567 (t80) REVERT: B 137 ARG cc_start: 0.6332 (ttm-80) cc_final: 0.5963 (ttp-170) outliers start: 2 outliers final: 4 residues processed: 62 average time/residue: 1.6868 time to fit residues: 107.3999 Evaluate side-chains 66 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 219 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.0470 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.104330 restraints weight = 4374.426| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.62 r_work: 0.2976 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 4192 Z= 0.138 Angle : 0.395 5.036 5730 Z= 0.216 Chirality : 0.035 0.119 682 Planarity : 0.002 0.021 680 Dihedral : 6.915 58.262 978 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.70 (0.36), residues: 512 helix: 3.59 (0.24), residues: 414 sheet: None (None), residues: 0 loop : 0.76 (0.68), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.001 0.000 HIS B 188 PHE 0.014 0.001 PHE B 109 TYR 0.010 0.001 TYR B 113 ARG 0.001 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.399 Fit side-chains REVERT: A 3 ARG cc_start: 0.6290 (ttt180) cc_final: 0.5930 (ttt-90) REVERT: A 135 PHE cc_start: 0.7781 (t80) cc_final: 0.7474 (t80) REVERT: A 137 ARG cc_start: 0.6196 (ttm-80) cc_final: 0.5854 (ttp-170) REVERT: B 3 ARG cc_start: 0.6322 (ttt180) cc_final: 0.6017 (ttt-90) REVERT: B 135 PHE cc_start: 0.7783 (t80) cc_final: 0.7474 (t80) REVERT: B 137 ARG cc_start: 0.6190 (ttm-80) cc_final: 0.5849 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 59 average time/residue: 1.5905 time to fit residues: 96.4102 Evaluate side-chains 61 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.102547 restraints weight = 4461.669| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.65 r_work: 0.2948 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4192 Z= 0.188 Angle : 0.421 5.126 5730 Z= 0.230 Chirality : 0.036 0.127 682 Planarity : 0.002 0.021 680 Dihedral : 6.930 59.948 978 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % 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: 4.66 (0.36), residues: 512 helix: 3.56 (0.24), residues: 414 sheet: None (None), residues: 0 loop : 0.77 (0.67), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 78 HIS 0.000 0.000 HIS A 98 PHE 0.014 0.001 PHE A 109 TYR 0.010 0.001 TYR A 96 ARG 0.002 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.346 Fit side-chains REVERT: A 3 ARG cc_start: 0.6364 (ttt180) cc_final: 0.5998 (ttt-90) REVERT: A 135 PHE cc_start: 0.7830 (t80) cc_final: 0.7504 (t80) REVERT: A 137 ARG cc_start: 0.6260 (ttm-80) cc_final: 0.5904 (ttp-170) REVERT: B 3 ARG cc_start: 0.6389 (ttt180) cc_final: 0.6080 (ttt-90) REVERT: B 135 PHE cc_start: 0.7830 (t80) cc_final: 0.7507 (t80) REVERT: B 137 ARG cc_start: 0.6252 (ttm-80) cc_final: 0.5898 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 1.6771 time to fit residues: 106.6319 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.137529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104276 restraints weight = 4504.005| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.66 r_work: 0.2974 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4192 Z= 0.153 Angle : 0.399 5.093 5730 Z= 0.218 Chirality : 0.035 0.120 682 Planarity : 0.002 0.020 680 Dihedral : 6.730 57.820 978 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.26 % Allowed : 11.90 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.76 (0.36), residues: 512 helix: 3.63 (0.24), residues: 414 sheet: None (None), residues: 0 loop : 0.80 (0.66), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.000 0.000 HIS A 98 PHE 0.014 0.001 PHE A 109 TYR 0.010 0.001 TYR A 96 ARG 0.003 0.000 ARG A 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.424 Fit side-chains REVERT: A 3 ARG cc_start: 0.6282 (ttt180) cc_final: 0.5922 (ttt-90) REVERT: A 135 PHE cc_start: 0.7787 (t80) cc_final: 0.7456 (t80) REVERT: A 137 ARG cc_start: 0.6135 (ttm-80) cc_final: 0.5790 (ttp-170) REVERT: B 3 ARG cc_start: 0.6339 (ttt180) cc_final: 0.6035 (ttt-90) REVERT: B 135 PHE cc_start: 0.7785 (t80) cc_final: 0.7456 (t80) REVERT: B 137 ARG cc_start: 0.6130 (ttm-80) cc_final: 0.5786 (ttp-170) outliers start: 1 outliers final: 2 residues processed: 57 average time/residue: 1.6771 time to fit residues: 98.4648 Evaluate side-chains 58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 48 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.132134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099135 restraints weight = 4532.732| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.63 r_work: 0.2909 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4192 Z= 0.294 Angle : 0.483 5.216 5730 Z= 0.262 Chirality : 0.039 0.140 682 Planarity : 0.002 0.022 680 Dihedral : 7.195 59.360 978 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % 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: 4.39 (0.36), residues: 512 helix: 3.36 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 0.73 (0.70), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 PHE 0.015 0.002 PHE B 109 TYR 0.011 0.002 TYR A 96 ARG 0.002 0.000 ARG A 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3861.75 seconds wall clock time: 68 minutes 58.13 seconds (4138.13 seconds total)