Starting phenix.real_space_refine on Mon Jan 13 21:33:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1n_35928/01_2025/8j1n_35928.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1n_35928/01_2025/8j1n_35928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j1n_35928/01_2025/8j1n_35928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1n_35928/01_2025/8j1n_35928.map" model { file = "/net/cci-nas-00/data/ceres_data/8j1n_35928/01_2025/8j1n_35928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1n_35928/01_2025/8j1n_35928.cif" } resolution = 2.51 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= 0.146 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 4 5.49 5 S 18 5.16 5 C 2106 2.51 5 N 545 2.21 5 O 619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3292 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2180 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'CDL': 1, 'DNF': 1, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 102 Time building chain proxies: 2.94, per 1000 atoms: 0.89 Number of scatterers: 3292 At special positions: 0 Unit cell: (66.72, 68.388, 110.922, 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 18 16.00 P 4 15.00 O 619 8.00 N 545 7.00 C 2106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 417.3 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 3 sheets defined 62.6% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 11 through 43 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 76 through 107 removed outlier: 4.129A pdb=" N PHE A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 143 removed outlier: 3.512A pdb=" N LYS A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.603A pdb=" N LYS A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 205 Processing helix chain 'A' and resid 210 through 242 removed outlier: 3.839A pdb=" N HIS A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.655A pdb=" N LYS A 268 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 297 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.727A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.727A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 648 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: 0.96 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 517 1.30 - 1.43: 891 1.43 - 1.56: 1920 1.56 - 1.69: 8 1.69 - 1.81: 27 Bond restraints: 3363 Sorted by residual: bond pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.457 -0.123 1.10e-02 8.26e+03 1.26e+02 bond pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.442 -0.108 1.10e-02 8.26e+03 9.61e+01 bond pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.458 -0.116 1.50e-02 4.44e+03 5.93e+01 bond pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.445 -0.103 1.50e-02 4.44e+03 4.74e+01 bond pdb=" C21 PC1 A 403 " pdb=" O21 PC1 A 403 " ideal model delta sigma weight residual 1.331 1.457 -0.126 2.00e-02 2.50e+03 3.96e+01 ... (remaining 3358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 4345 1.95 - 3.90: 144 3.90 - 5.85: 55 5.85 - 7.80: 6 7.80 - 9.75: 9 Bond angle restraints: 4559 Sorted by residual: angle pdb=" C51 CDL A 402 " pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.79 -9.46 1.32e+00 5.72e-01 5.12e+01 angle pdb=" C11 CDL A 402 " pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.58 -9.25 1.32e+00 5.72e-01 4.90e+01 angle pdb=" C71 CDL A 402 " pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 111.64 121.39 -9.75 1.65e+00 3.69e-01 3.51e+01 angle pdb=" C31 CDL A 402 " pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 111.64 120.78 -9.14 1.65e+00 3.69e-01 3.08e+01 angle pdb=" OB6 CDL A 402 " pdb=" CB5 CDL A 402 " pdb=" OB7 CDL A 402 " ideal model delta sigma weight residual 123.92 118.75 5.17 1.00e+00 9.92e-01 2.65e+01 ... (remaining 4554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.92: 1835 20.92 - 41.84: 122 41.84 - 62.75: 34 62.75 - 83.67: 4 83.67 - 104.59: 4 Dihedral angle restraints: 1999 sinusoidal: 816 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ARG B 72 " pdb=" C ARG B 72 " pdb=" N ASP B 73 " pdb=" CA ASP B 73 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA5 CDL A 402 " pdb=" CA4 CDL A 402 " pdb=" OA6 CDL A 402 " pdb=" CA6 CDL A 402 " ideal model delta sinusoidal sigma weight residual 168.24 63.65 104.59 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" CA TRP B 111 " pdb=" C TRP B 111 " pdb=" N GLY B 112 " pdb=" CA GLY B 112 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 337 0.045 - 0.090: 132 0.090 - 0.135: 33 0.135 - 0.180: 3 0.180 - 0.225: 1 Chirality restraints: 506 Sorted by residual: chirality pdb=" CB ILE A 116 " pdb=" CA ILE A 116 " pdb=" CG1 ILE A 116 " pdb=" CG2 ILE A 116 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA VAL A 211 " pdb=" N VAL A 211 " pdb=" C VAL A 211 " pdb=" CB VAL A 211 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CG LEU A 90 " pdb=" CB LEU A 90 " pdb=" CD1 LEU A 90 " pdb=" CD2 LEU A 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 503 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 101 " 0.025 2.00e-02 2.50e+03 3.82e-02 2.55e+01 pdb=" CG PHE B 101 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 PHE B 101 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 PHE B 101 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE B 101 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 101 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 101 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 27 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO B 28 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 96 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C ASP A 96 " 0.023 2.00e-02 2.50e+03 pdb=" O ASP A 96 " -0.009 2.00e-02 2.50e+03 pdb=" N THR A 97 " -0.008 2.00e-02 2.50e+03 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 501 2.76 - 3.29: 3101 3.29 - 3.83: 5992 3.83 - 4.36: 6913 4.36 - 4.90: 11952 Nonbonded interactions: 28459 Sorted by model distance: nonbonded pdb=" O TRP A 173 " pdb=" OG1 THR A 176 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR A 30 " pdb=" NH1 ARG A 276 " model vdw 2.233 3.120 nonbonded pdb=" O GLY A 130 " pdb=" OG1 THR A 133 " model vdw 2.300 3.040 nonbonded pdb=" O ALA A 63 " pdb=" OG1 THR A 67 " model vdw 2.342 3.040 nonbonded pdb=" OE2 GLU B 6 " pdb=" N CYS B 96 " model vdw 2.353 3.120 ... (remaining 28454 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: 0.910 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.230 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:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.009 0.126 3363 Z= 0.609 Angle : 1.010 9.745 4559 Z= 0.523 Chirality : 0.049 0.225 506 Planarity : 0.005 0.038 569 Dihedral : 15.984 104.588 1242 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 1.72 (0.39), residues: 410 helix: 1.87 (0.32), residues: 223 sheet: -0.02 (0.64), residues: 59 loop : 0.60 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 56 HIS 0.004 0.001 HIS A 214 PHE 0.086 0.004 PHE B 101 TYR 0.020 0.002 TYR A 157 ARG 0.008 0.001 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.553 Fit side-chains REVERT: A 157 TYR cc_start: 0.7543 (m-80) cc_final: 0.6787 (t80) REVERT: A 169 LEU cc_start: 0.8127 (mm) cc_final: 0.7893 (mt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 1.0037 time to fit residues: 71.6706 Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.0060 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.181711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132795 restraints weight = 3331.264| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.73 r_work: 0.3357 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3363 Z= 0.190 Angle : 0.553 6.671 4559 Z= 0.287 Chirality : 0.041 0.250 506 Planarity : 0.004 0.033 569 Dihedral : 12.915 90.680 535 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.48 % Allowed : 10.65 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.39), residues: 410 helix: 2.58 (0.32), residues: 223 sheet: 0.01 (0.65), residues: 54 loop : 0.34 (0.51), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 PHE 0.026 0.002 PHE B 101 TYR 0.010 0.001 TYR A 157 ARG 0.002 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.293 Fit side-chains REVERT: A 150 LYS cc_start: 0.8368 (tptp) cc_final: 0.8078 (tttm) REVERT: A 157 TYR cc_start: 0.7959 (m-80) cc_final: 0.7018 (t80) REVERT: A 169 LEU cc_start: 0.8362 (mm) cc_final: 0.8047 (mt) REVERT: B 71 SER cc_start: 0.8747 (t) cc_final: 0.8381 (t) REVERT: B 78 THR cc_start: 0.9187 (m) cc_final: 0.8878 (t) REVERT: B 83 MET cc_start: 0.8357 (mtp) cc_final: 0.8057 (mtp) REVERT: B 95 TYR cc_start: 0.8357 (m-80) cc_final: 0.7932 (m-80) REVERT: B 119 VAL cc_start: 0.7746 (OUTLIER) cc_final: 0.7492 (p) outliers start: 5 outliers final: 1 residues processed: 61 average time/residue: 1.0356 time to fit residues: 65.4487 Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.181040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131703 restraints weight = 3261.632| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.72 r_work: 0.3329 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3363 Z= 0.207 Angle : 0.524 6.518 4559 Z= 0.271 Chirality : 0.040 0.188 506 Planarity : 0.004 0.030 569 Dihedral : 12.132 81.341 535 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.37 % Allowed : 12.13 % Favored : 85.50 % 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: 2.61 (0.39), residues: 410 helix: 2.84 (0.32), residues: 223 sheet: 0.44 (0.64), residues: 54 loop : 0.39 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 111 HIS 0.003 0.001 HIS B 59 PHE 0.014 0.002 PHE B 101 TYR 0.012 0.001 TYR A 157 ARG 0.002 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.363 Fit side-chains REVERT: A 150 LYS cc_start: 0.8381 (tptp) cc_final: 0.8130 (tttm) REVERT: A 157 TYR cc_start: 0.7935 (m-80) cc_final: 0.7073 (t80) REVERT: A 169 LEU cc_start: 0.8388 (mm) cc_final: 0.8066 (mt) REVERT: A 187 ASN cc_start: 0.8593 (t0) cc_final: 0.7842 (m-40) REVERT: B 71 SER cc_start: 0.8735 (t) cc_final: 0.8184 (p) REVERT: B 83 MET cc_start: 0.8294 (mtp) cc_final: 0.7828 (mtp) REVERT: B 95 TYR cc_start: 0.8482 (m-80) cc_final: 0.8144 (m-80) outliers start: 8 outliers final: 2 residues processed: 62 average time/residue: 0.9852 time to fit residues: 63.4320 Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain B residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 33 optimal weight: 0.0040 chunk 25 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.182463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.133374 restraints weight = 3319.601| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.74 r_work: 0.3357 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3363 Z= 0.159 Angle : 0.496 6.370 4559 Z= 0.252 Chirality : 0.040 0.229 506 Planarity : 0.004 0.029 569 Dihedral : 11.797 79.459 535 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.78 % Allowed : 13.61 % Favored : 84.62 % 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: 2.97 (0.40), residues: 410 helix: 3.13 (0.32), residues: 223 sheet: 0.65 (0.64), residues: 54 loop : 0.54 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 PHE 0.007 0.001 PHE A 128 TYR 0.010 0.001 TYR A 194 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.373 Fit side-chains REVERT: A 150 LYS cc_start: 0.8388 (tptp) cc_final: 0.8147 (tttm) REVERT: A 157 TYR cc_start: 0.7884 (m-80) cc_final: 0.7034 (t80) REVERT: A 169 LEU cc_start: 0.8328 (mm) cc_final: 0.8027 (mt) REVERT: A 187 ASN cc_start: 0.8526 (t0) cc_final: 0.7809 (m-40) REVERT: B 71 SER cc_start: 0.8636 (t) cc_final: 0.8202 (p) REVERT: B 83 MET cc_start: 0.8260 (mtp) cc_final: 0.8052 (mtp) REVERT: B 95 TYR cc_start: 0.8420 (m-80) cc_final: 0.8116 (m-80) outliers start: 6 outliers final: 1 residues processed: 62 average time/residue: 1.1036 time to fit residues: 70.7453 Evaluate side-chains 56 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 0.0170 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.181693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132362 restraints weight = 3349.243| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.76 r_work: 0.3361 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3363 Z= 0.172 Angle : 0.509 6.330 4559 Z= 0.257 Chirality : 0.040 0.246 506 Planarity : 0.004 0.028 569 Dihedral : 11.660 78.382 535 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.07 % Allowed : 14.79 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.07 (0.40), residues: 410 helix: 3.20 (0.31), residues: 223 sheet: 0.78 (0.65), residues: 54 loop : 0.56 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.003 0.001 HIS B 59 PHE 0.008 0.001 PHE A 128 TYR 0.010 0.001 TYR A 157 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.339 Fit side-chains REVERT: A 116 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7568 (mp) REVERT: A 150 LYS cc_start: 0.8384 (tptp) cc_final: 0.8113 (tttm) REVERT: A 157 TYR cc_start: 0.7905 (m-80) cc_final: 0.7034 (t80) REVERT: A 169 LEU cc_start: 0.8290 (mm) cc_final: 0.7983 (mt) REVERT: A 187 ASN cc_start: 0.8512 (t0) cc_final: 0.7762 (m-40) REVERT: B 71 SER cc_start: 0.8591 (t) cc_final: 0.8138 (p) REVERT: B 83 MET cc_start: 0.8243 (mtp) cc_final: 0.7963 (mtp) REVERT: B 95 TYR cc_start: 0.8386 (m-80) cc_final: 0.8049 (m-80) outliers start: 7 outliers final: 4 residues processed: 64 average time/residue: 1.0122 time to fit residues: 67.1748 Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.0060 chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.180749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.131134 restraints weight = 3394.524| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.77 r_work: 0.3344 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3363 Z= 0.202 Angle : 0.524 6.851 4559 Z= 0.265 Chirality : 0.041 0.269 506 Planarity : 0.004 0.029 569 Dihedral : 11.663 78.663 535 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.78 % Allowed : 15.68 % Favored : 82.54 % 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: 3.09 (0.40), residues: 410 helix: 3.21 (0.31), residues: 223 sheet: 0.82 (0.65), residues: 54 loop : 0.58 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 56 HIS 0.002 0.001 HIS B 35 PHE 0.014 0.002 PHE A 285 TYR 0.012 0.001 TYR A 157 ARG 0.002 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.288 Fit side-chains REVERT: A 116 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7582 (mp) REVERT: A 150 LYS cc_start: 0.8392 (tptp) cc_final: 0.8118 (tttm) REVERT: A 157 TYR cc_start: 0.7964 (m-80) cc_final: 0.7067 (t80) REVERT: A 169 LEU cc_start: 0.8342 (mm) cc_final: 0.8020 (mt) REVERT: A 187 ASN cc_start: 0.8525 (t0) cc_final: 0.7762 (m-40) REVERT: B 71 SER cc_start: 0.8614 (t) cc_final: 0.8163 (p) REVERT: B 83 MET cc_start: 0.8251 (mtp) cc_final: 0.8022 (mtp) REVERT: B 95 TYR cc_start: 0.8462 (m-80) cc_final: 0.8067 (m-80) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 1.0056 time to fit residues: 67.8009 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.0050 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 0.0370 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.4672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.181603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.132412 restraints weight = 3262.882| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.72 r_work: 0.3355 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3363 Z= 0.179 Angle : 0.529 11.830 4559 Z= 0.264 Chirality : 0.041 0.324 506 Planarity : 0.004 0.029 569 Dihedral : 11.509 78.433 535 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.07 % Allowed : 16.86 % Favored : 81.07 % 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: 3.19 (0.40), residues: 410 helix: 3.31 (0.31), residues: 222 sheet: 0.90 (0.65), residues: 54 loop : 0.58 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.002 0.001 HIS B 35 PHE 0.008 0.001 PHE A 128 TYR 0.010 0.001 TYR A 157 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.372 Fit side-chains REVERT: A 150 LYS cc_start: 0.8384 (tptp) cc_final: 0.8119 (tttm) REVERT: A 157 TYR cc_start: 0.7895 (m-80) cc_final: 0.7020 (t80) REVERT: A 169 LEU cc_start: 0.8271 (mm) cc_final: 0.7977 (mt) REVERT: A 187 ASN cc_start: 0.8486 (t0) cc_final: 0.7729 (m-40) REVERT: A 206 ILE cc_start: 0.5962 (mp) cc_final: 0.5527 (mm) REVERT: B 71 SER cc_start: 0.8598 (t) cc_final: 0.8188 (p) REVERT: B 83 MET cc_start: 0.8251 (mtp) cc_final: 0.7904 (mtp) REVERT: B 95 TYR cc_start: 0.8447 (m-80) cc_final: 0.8066 (m-80) outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 0.9566 time to fit residues: 64.5661 Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.180155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.130081 restraints weight = 3254.547| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.75 r_work: 0.3339 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3363 Z= 0.201 Angle : 0.541 10.475 4559 Z= 0.272 Chirality : 0.042 0.343 506 Planarity : 0.004 0.029 569 Dihedral : 11.535 77.095 535 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.37 % Allowed : 16.27 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.40), residues: 410 helix: 3.24 (0.31), residues: 222 sheet: 0.94 (0.65), residues: 54 loop : 0.56 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 56 HIS 0.002 0.001 HIS B 59 PHE 0.017 0.002 PHE A 285 TYR 0.012 0.001 TYR A 157 ARG 0.003 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.378 Fit side-chains REVERT: A 150 LYS cc_start: 0.8388 (tptp) cc_final: 0.8124 (tttm) REVERT: A 157 TYR cc_start: 0.7947 (m-80) cc_final: 0.7055 (t80) REVERT: A 169 LEU cc_start: 0.8312 (mm) cc_final: 0.7994 (mt) REVERT: A 187 ASN cc_start: 0.8513 (t0) cc_final: 0.7758 (m-40) REVERT: B 71 SER cc_start: 0.8593 (t) cc_final: 0.8165 (p) REVERT: B 83 MET cc_start: 0.8262 (mtp) cc_final: 0.7981 (mtp) REVERT: B 95 TYR cc_start: 0.8470 (m-80) cc_final: 0.8064 (m-80) outliers start: 8 outliers final: 5 residues processed: 64 average time/residue: 0.9431 time to fit residues: 62.7115 Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.180014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130064 restraints weight = 3294.141| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.75 r_work: 0.3333 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3363 Z= 0.200 Angle : 0.545 11.655 4559 Z= 0.272 Chirality : 0.042 0.356 506 Planarity : 0.004 0.031 569 Dihedral : 11.584 74.555 535 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.78 % Allowed : 16.57 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.15 (0.40), residues: 410 helix: 3.24 (0.31), residues: 222 sheet: 0.99 (0.65), residues: 54 loop : 0.59 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.002 0.001 HIS B 35 PHE 0.009 0.001 PHE A 128 TYR 0.012 0.001 TYR A 157 ARG 0.003 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.373 Fit side-chains REVERT: A 150 LYS cc_start: 0.8353 (tptp) cc_final: 0.8094 (tttm) REVERT: A 157 TYR cc_start: 0.7928 (m-80) cc_final: 0.7047 (t80) REVERT: A 169 LEU cc_start: 0.8342 (mm) cc_final: 0.8013 (mt) REVERT: A 187 ASN cc_start: 0.8511 (t0) cc_final: 0.7753 (m-40) REVERT: A 206 ILE cc_start: 0.6271 (mp) cc_final: 0.5884 (mm) REVERT: B 71 SER cc_start: 0.8600 (t) cc_final: 0.8182 (p) REVERT: B 83 MET cc_start: 0.8261 (mtp) cc_final: 0.7956 (mtp) REVERT: B 95 TYR cc_start: 0.8495 (m-80) cc_final: 0.8052 (m-80) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 0.9718 time to fit residues: 64.5157 Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.179480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129460 restraints weight = 3214.477| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.74 r_work: 0.3321 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3363 Z= 0.211 Angle : 0.547 10.708 4559 Z= 0.275 Chirality : 0.042 0.335 506 Planarity : 0.004 0.030 569 Dihedral : 11.588 73.969 535 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.48 % Allowed : 17.16 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.39), residues: 410 helix: 3.21 (0.31), residues: 222 sheet: 0.98 (0.65), residues: 54 loop : 0.57 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 56 HIS 0.003 0.001 HIS B 35 PHE 0.011 0.001 PHE A 223 TYR 0.012 0.001 TYR A 157 ARG 0.002 0.000 ARG A 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.383 Fit side-chains REVERT: A 150 LYS cc_start: 0.8344 (tptp) cc_final: 0.8085 (tttm) REVERT: A 157 TYR cc_start: 0.7942 (m-80) cc_final: 0.7028 (t80) REVERT: A 169 LEU cc_start: 0.8340 (mm) cc_final: 0.8014 (mt) REVERT: A 206 ILE cc_start: 0.6301 (mp) cc_final: 0.5907 (mm) REVERT: B 71 SER cc_start: 0.8593 (t) cc_final: 0.8155 (p) REVERT: B 83 MET cc_start: 0.8247 (mtp) cc_final: 0.7892 (mtp) REVERT: B 95 TYR cc_start: 0.8503 (m-80) cc_final: 0.8081 (m-80) outliers start: 5 outliers final: 5 residues processed: 63 average time/residue: 0.9562 time to fit residues: 62.5360 Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.179878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130145 restraints weight = 3235.049| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.74 r_work: 0.3331 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3363 Z= 0.191 Angle : 0.540 11.346 4559 Z= 0.269 Chirality : 0.042 0.350 506 Planarity : 0.004 0.031 569 Dihedral : 11.512 73.071 535 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.07 % Allowed : 16.86 % Favored : 81.07 % 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: 3.15 (0.40), residues: 410 helix: 3.25 (0.31), residues: 222 sheet: 0.96 (0.65), residues: 54 loop : 0.59 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.002 0.001 HIS B 35 PHE 0.009 0.001 PHE A 128 TYR 0.011 0.001 TYR A 157 ARG 0.002 0.000 ARG B 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3264.34 seconds wall clock time: 58 minutes 29.11 seconds (3509.11 seconds total)