Starting phenix.real_space_refine on Thu Mar 6 00:32:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hbw_34645/03_2025/8hbw_34645.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbw_34645/03_2025/8hbw_34645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hbw_34645/03_2025/8hbw_34645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbw_34645/03_2025/8hbw_34645.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbw_34645/03_2025/8hbw_34645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbw_34645/03_2025/8hbw_34645.cif" } resolution = 2.57 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= 0.003 sd= 0.159 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 7 5.49 5 S 18 5.16 5 C 2109 2.51 5 N 548 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3309 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2179 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 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: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {'ATP': 1, 'CDL': 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: 3.21, per 1000 atoms: 0.97 Number of scatterers: 3309 At special positions: 0 Unit cell: (65.052, 71.724, 111.756, 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 7 15.00 O 627 8.00 N 548 7.00 C 2109 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: 1.33 Conformation dependent library (CDL) restraints added in 407.8 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: 15 helices and 3 sheets defined 62.3% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 11 through 42 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 76 through 94 removed outlier: 4.367A pdb=" N SER A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 111 through 143 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 155 through 167 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.629A pdb=" N LYS A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 204 Processing helix chain 'A' and resid 210 through 242 removed outlier: 4.224A 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 Processing helix chain 'A' and resid 269 through 298 removed outlier: 3.609A pdb=" N SER A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) 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: 6.892A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.486A 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: 6.892A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 627 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: 0.93 Time building geometry restraints manager: 1.20 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: 547 1.32 - 1.44: 902 1.44 - 1.56: 1893 1.56 - 1.68: 13 1.68 - 1.81: 27 Bond restraints: 3382 Sorted by residual: bond pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.446 -0.112 1.10e-02 8.26e+03 1.03e+02 bond pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.454 -0.112 1.50e-02 4.44e+03 5.57e+01 bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.43e+01 bond pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.449 -0.107 1.50e-02 4.44e+03 5.10e+01 ... (remaining 3377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 4506 3.41 - 6.82: 70 6.82 - 10.22: 14 10.22 - 13.63: 1 13.63 - 17.04: 1 Bond angle restraints: 4592 Sorted by residual: angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 122.83 17.04 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP A 401 " pdb=" O3A ATP A 401 " pdb=" PB ATP A 401 " ideal model delta sigma weight residual 136.83 124.25 12.58 1.00e+00 1.00e+00 1.58e+02 angle pdb=" C5 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N3 ATP A 401 " ideal model delta sigma weight residual 126.80 119.46 7.34 1.00e+00 1.00e+00 5.39e+01 angle pdb=" C11 CDL A 402 " pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.23 -8.90 1.32e+00 5.72e-01 4.53e+01 angle pdb=" N3 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 127.04 134.51 -7.47 1.15e+00 7.59e-01 4.24e+01 ... (remaining 4587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 1792 17.12 - 34.24: 156 34.24 - 51.36: 64 51.36 - 68.49: 14 68.49 - 85.61: 6 Dihedral angle restraints: 2032 sinusoidal: 849 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ALA A 208 " pdb=" C ALA A 208 " pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta harmonic sigma weight residual -180.00 -162.45 -17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 209 " pdb=" C ASP A 209 " pdb=" N ASP A 210 " pdb=" CA ASP A 210 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB GLU A 100 " pdb=" CG GLU A 100 " pdb=" CD GLU A 100 " pdb=" OE1 GLU A 100 " ideal model delta sinusoidal sigma weight residual 0.00 85.61 -85.61 1 3.00e+01 1.11e-03 9.85e+00 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 331 0.043 - 0.086: 138 0.086 - 0.129: 33 0.129 - 0.172: 5 0.172 - 0.214: 3 Chirality restraints: 510 Sorted by residual: chirality pdb=" CA LYS A 66 " pdb=" N LYS A 66 " pdb=" C LYS A 66 " pdb=" CB LYS A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU A 261 " pdb=" N GLU A 261 " pdb=" C GLU A 261 " pdb=" CB GLU A 261 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA ARG A 238 " pdb=" N ARG A 238 " pdb=" C ARG A 238 " pdb=" CB ARG A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 507 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 9 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO A 10 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 84 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C GLN A 84 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN A 84 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE A 85 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 101 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C PHE B 101 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE B 101 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY B 102 " -0.010 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 360 2.74 - 3.28: 3189 3.28 - 3.82: 5979 3.82 - 4.36: 7174 4.36 - 4.90: 12102 Nonbonded interactions: 28804 Sorted by model distance: nonbonded pdb=" OG1 THR A 103 " pdb=" O THR A 108 " model vdw 2.199 3.040 nonbonded pdb=" OE2 GLU A 45 " pdb=" OH TYR A 247 " model vdw 2.266 3.040 nonbonded pdb=" O LYS A 292 " pdb=" OG SER A 296 " model vdw 2.276 3.040 nonbonded pdb=" O GLY A 130 " pdb=" OG1 THR A 133 " model vdw 2.320 3.040 nonbonded pdb=" O TRP A 173 " pdb=" OG1 THR A 176 " model vdw 2.323 3.040 ... (remaining 28799 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: 1.470 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.680 Find NCS groups from input model: 0.030 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:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 0.010 0.124 3382 Z= 0.670 Angle : 1.053 17.042 4592 Z= 0.645 Chirality : 0.050 0.214 510 Planarity : 0.005 0.057 567 Dihedral : 16.265 85.607 1275 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.39), residues: 410 helix: 1.83 (0.32), residues: 221 sheet: -0.32 (0.61), residues: 60 loop : 0.59 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 173 HIS 0.003 0.001 HIS B 124 PHE 0.018 0.003 PHE A 223 TYR 0.014 0.002 TYR A 157 ARG 0.021 0.002 ARG B 104 *********************** 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 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.338 Fit side-chains REVERT: A 55 LYS cc_start: 0.8108 (tttp) cc_final: 0.7810 (tptp) REVERT: A 161 ARG cc_start: 0.7447 (ttt180) cc_final: 0.6715 (mtt90) REVERT: A 206 ILE cc_start: 0.6885 (mm) cc_final: 0.6564 (mp) REVERT: A 248 LYS cc_start: 0.8664 (ptmm) cc_final: 0.8426 (ptmt) REVERT: A 293 ARG cc_start: 0.6520 (ptm-80) cc_final: 0.6132 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 1.4162 time to fit residues: 89.9664 Evaluate side-chains 53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.133669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.119003 restraints weight = 3557.466| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 0.93 r_work: 0.3204 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3382 Z= 0.220 Angle : 0.542 6.815 4592 Z= 0.286 Chirality : 0.040 0.141 510 Planarity : 0.005 0.051 567 Dihedral : 13.766 78.621 569 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.48 % Allowed : 9.20 % Favored : 89.32 % 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: 2.43 (0.40), residues: 410 helix: 2.64 (0.32), residues: 221 sheet: 0.04 (0.64), residues: 54 loop : 0.65 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.002 0.001 HIS A 147 PHE 0.010 0.002 PHE A 223 TYR 0.008 0.001 TYR A 74 ARG 0.004 0.001 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 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.460 Fit side-chains REVERT: A 55 LYS cc_start: 0.8328 (tttp) cc_final: 0.7829 (tptp) REVERT: A 117 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7622 (tt) REVERT: A 161 ARG cc_start: 0.7984 (ttt180) cc_final: 0.6617 (mtt90) REVERT: A 206 ILE cc_start: 0.6792 (mm) cc_final: 0.6406 (mp) REVERT: A 293 ARG cc_start: 0.6389 (ptm-80) cc_final: 0.6002 (tmt-80) outliers start: 5 outliers final: 0 residues processed: 61 average time/residue: 1.4667 time to fit residues: 92.0825 Evaluate side-chains 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.129812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115677 restraints weight = 3585.355| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 0.86 r_work: 0.3170 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 3382 Z= 0.362 Angle : 0.612 7.516 4592 Z= 0.319 Chirality : 0.044 0.142 510 Planarity : 0.005 0.046 567 Dihedral : 13.814 76.254 569 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.08 % Allowed : 12.46 % Favored : 85.46 % 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: 2.34 (0.40), residues: 410 helix: 2.62 (0.32), residues: 221 sheet: -0.13 (0.64), residues: 54 loop : 0.55 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 HIS 0.003 0.001 HIS B 124 PHE 0.018 0.003 PHE A 223 TYR 0.011 0.001 TYR A 157 ARG 0.006 0.001 ARG B 72 *********************** 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 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.331 Fit side-chains REVERT: A 55 LYS cc_start: 0.8355 (tttp) cc_final: 0.7899 (tptp) REVERT: A 57 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8201 (t) REVERT: A 117 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7697 (tt) REVERT: A 161 ARG cc_start: 0.7986 (ttt180) cc_final: 0.6622 (mtt90) REVERT: A 206 ILE cc_start: 0.6919 (mm) cc_final: 0.6534 (mp) REVERT: A 293 ARG cc_start: 0.6445 (ptm-80) cc_final: 0.6062 (tmt-80) outliers start: 7 outliers final: 2 residues processed: 59 average time/residue: 1.2687 time to fit residues: 76.9520 Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 0.0270 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.134315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.120380 restraints weight = 3636.795| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 0.93 r_work: 0.3202 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3382 Z= 0.211 Angle : 0.534 7.973 4592 Z= 0.276 Chirality : 0.040 0.141 510 Planarity : 0.005 0.043 567 Dihedral : 12.827 72.736 569 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.37 % Allowed : 13.06 % Favored : 84.57 % 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: 2.65 (0.40), residues: 410 helix: 2.91 (0.32), residues: 221 sheet: 0.01 (0.65), residues: 54 loop : 0.62 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.001 0.001 HIS A 145 PHE 0.010 0.001 PHE A 223 TYR 0.009 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 *********************** 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 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.332 Fit side-chains REVERT: A 55 LYS cc_start: 0.8350 (tttp) cc_final: 0.7838 (tptp) REVERT: A 57 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8181 (t) REVERT: A 117 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7609 (tt) REVERT: A 161 ARG cc_start: 0.8004 (ttt180) cc_final: 0.6675 (mpt-90) REVERT: A 206 ILE cc_start: 0.6736 (mm) cc_final: 0.6368 (mp) REVERT: A 293 ARG cc_start: 0.6463 (ptm-80) cc_final: 0.6093 (tmt-80) outliers start: 8 outliers final: 1 residues processed: 60 average time/residue: 1.3000 time to fit residues: 80.1600 Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.136734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.122099 restraints weight = 3577.948| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 0.91 r_work: 0.3241 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3382 Z= 0.169 Angle : 0.504 8.462 4592 Z= 0.259 Chirality : 0.039 0.128 510 Planarity : 0.004 0.041 567 Dihedral : 11.942 69.576 569 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.37 % Allowed : 12.46 % Favored : 85.16 % 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: 2.87 (0.40), residues: 410 helix: 3.10 (0.32), residues: 221 sheet: 0.16 (0.66), residues: 54 loop : 0.66 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 280 HIS 0.001 0.000 HIS A 145 PHE 0.007 0.001 PHE A 223 TYR 0.007 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 *********************** 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 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.381 Fit side-chains REVERT: A 55 LYS cc_start: 0.8297 (tttp) cc_final: 0.7779 (tptp) REVERT: A 57 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8139 (t) REVERT: A 70 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6484 (mtp-110) REVERT: A 117 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7579 (tt) REVERT: A 161 ARG cc_start: 0.8000 (ttt180) cc_final: 0.6577 (mtt90) REVERT: A 206 ILE cc_start: 0.6395 (mm) cc_final: 0.6057 (mp) REVERT: A 293 ARG cc_start: 0.6402 (ptm-80) cc_final: 0.6036 (tmt-80) outliers start: 8 outliers final: 2 residues processed: 65 average time/residue: 1.2761 time to fit residues: 85.2877 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 : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 190 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.6980 chunk 33 optimal weight: 0.0270 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.121457 restraints weight = 3730.353| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 0.89 r_work: 0.3231 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3382 Z= 0.183 Angle : 0.514 8.309 4592 Z= 0.265 Chirality : 0.039 0.125 510 Planarity : 0.004 0.039 567 Dihedral : 11.821 70.107 569 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.37 % Allowed : 14.84 % Favored : 82.79 % 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: 3.11 (0.32), residues: 222 sheet: 0.32 (0.68), residues: 54 loop : 0.77 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 HIS 0.001 0.000 HIS A 145 PHE 0.012 0.002 PHE A 285 TYR 0.008 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 *********************** 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 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.349 Fit side-chains REVERT: A 53 ARG cc_start: 0.7648 (tmt170) cc_final: 0.7405 (mmm160) REVERT: A 55 LYS cc_start: 0.8321 (tttp) cc_final: 0.7842 (tptp) REVERT: A 57 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8164 (t) REVERT: A 70 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6578 (mtp-110) REVERT: A 117 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7657 (tt) REVERT: A 161 ARG cc_start: 0.8014 (ttt180) cc_final: 0.6689 (mtt90) REVERT: A 206 ILE cc_start: 0.6539 (mm) cc_final: 0.6209 (mp) REVERT: A 293 ARG cc_start: 0.6462 (ptm-80) cc_final: 0.6093 (tmt-80) outliers start: 8 outliers final: 3 residues processed: 65 average time/residue: 1.3075 time to fit residues: 87.3211 Evaluate side-chains 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.136043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.120393 restraints weight = 3710.050| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.06 r_work: 0.3230 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3382 Z= 0.229 Angle : 0.551 8.191 4592 Z= 0.284 Chirality : 0.041 0.131 510 Planarity : 0.005 0.038 567 Dihedral : 12.134 71.698 569 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.08 % Allowed : 15.43 % Favored : 82.49 % 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: 2.84 (0.40), residues: 410 helix: 3.02 (0.32), residues: 222 sheet: 0.09 (0.66), residues: 54 loop : 0.76 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 103 HIS 0.002 0.001 HIS A 147 PHE 0.013 0.002 PHE B 101 TYR 0.010 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 *********************** 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 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.341 Fit side-chains REVERT: A 53 ARG cc_start: 0.7639 (tmt170) cc_final: 0.7413 (mmm160) REVERT: A 55 LYS cc_start: 0.8376 (tttp) cc_final: 0.7901 (tptp) REVERT: A 70 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6699 (mtp-110) REVERT: A 117 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7693 (tt) REVERT: A 161 ARG cc_start: 0.8079 (ttt180) cc_final: 0.6721 (mtt90) REVERT: A 206 ILE cc_start: 0.6617 (mm) cc_final: 0.6288 (mp) REVERT: A 293 ARG cc_start: 0.6500 (ptm-80) cc_final: 0.6137 (tmt-80) outliers start: 7 outliers final: 3 residues processed: 63 average time/residue: 1.3032 time to fit residues: 84.4721 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 : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.137130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.121616 restraints weight = 3690.914| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.04 r_work: 0.3245 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3382 Z= 0.201 Angle : 0.534 8.470 4592 Z= 0.275 Chirality : 0.040 0.127 510 Planarity : 0.004 0.037 567 Dihedral : 11.998 71.611 569 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.08 % Allowed : 15.43 % Favored : 82.49 % 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: 2.89 (0.40), residues: 410 helix: 3.10 (0.32), residues: 222 sheet: 0.12 (0.67), residues: 54 loop : 0.72 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 111 HIS 0.001 0.001 HIS A 147 PHE 0.010 0.001 PHE A 223 TYR 0.008 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 *********************** 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 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.334 Fit side-chains REVERT: A 53 ARG cc_start: 0.7651 (tmt170) cc_final: 0.7443 (mmm160) REVERT: A 55 LYS cc_start: 0.8377 (tttp) cc_final: 0.7910 (tptp) REVERT: A 70 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6686 (mtp-110) REVERT: A 117 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7673 (tt) REVERT: A 161 ARG cc_start: 0.8059 (ttt180) cc_final: 0.6717 (mtt90) REVERT: A 206 ILE cc_start: 0.6539 (mm) cc_final: 0.6208 (mp) REVERT: A 293 ARG cc_start: 0.6514 (ptm-80) cc_final: 0.6154 (tmt-80) outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 1.3334 time to fit residues: 84.8248 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 : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.0070 chunk 35 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.138019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.122527 restraints weight = 3691.580| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.04 r_work: 0.3267 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3382 Z= 0.184 Angle : 0.527 8.698 4592 Z= 0.270 Chirality : 0.039 0.127 510 Planarity : 0.004 0.037 567 Dihedral : 11.774 71.313 569 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.37 % Allowed : 15.73 % Favored : 81.90 % 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: 2.94 (0.40), residues: 410 helix: 3.14 (0.32), residues: 222 sheet: 0.11 (0.67), residues: 54 loop : 0.75 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 111 HIS 0.001 0.000 HIS A 145 PHE 0.013 0.002 PHE A 285 TYR 0.008 0.001 TYR A 157 ARG 0.004 0.000 ARG A 238 *********************** 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 68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.504 Fit side-chains REVERT: A 55 LYS cc_start: 0.8351 (tttp) cc_final: 0.7878 (tptp) REVERT: A 70 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6654 (mtp-110) REVERT: A 117 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7683 (tt) REVERT: A 161 ARG cc_start: 0.8046 (ttt180) cc_final: 0.6690 (mtt90) REVERT: A 206 ILE cc_start: 0.6502 (mm) cc_final: 0.6174 (mp) REVERT: A 293 ARG cc_start: 0.6489 (ptm-80) cc_final: 0.6129 (tmt-80) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 2.1127 time to fit residues: 140.6869 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 : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.137042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121422 restraints weight = 3699.591| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.06 r_work: 0.3252 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3382 Z= 0.215 Angle : 0.543 8.666 4592 Z= 0.279 Chirality : 0.040 0.126 510 Planarity : 0.004 0.037 567 Dihedral : 11.861 71.284 569 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.08 % Allowed : 15.43 % Favored : 82.49 % 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: 2.91 (0.40), residues: 410 helix: 3.10 (0.32), residues: 222 sheet: 0.09 (0.68), residues: 54 loop : 0.78 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 HIS 0.001 0.001 HIS A 147 PHE 0.010 0.002 PHE A 223 TYR 0.009 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 ********************** 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 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.565 Fit side-chains REVERT: A 55 LYS cc_start: 0.8390 (tttp) cc_final: 0.7906 (tptp) REVERT: A 70 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6688 (mtp-110) REVERT: A 117 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7680 (tt) REVERT: A 161 ARG cc_start: 0.8067 (ttt180) cc_final: 0.6721 (mtt90) REVERT: A 206 ILE cc_start: 0.6542 (mm) cc_final: 0.6321 (mp) REVERT: A 293 ARG cc_start: 0.6483 (ptm-80) cc_final: 0.6116 (tmt-80) outliers start: 7 outliers final: 4 residues processed: 61 average time/residue: 1.8987 time to fit residues: 118.7355 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.136468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.120754 restraints weight = 3717.221| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.07 r_work: 0.3236 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3382 Z= 0.231 Angle : 0.551 8.621 4592 Z= 0.283 Chirality : 0.040 0.128 510 Planarity : 0.004 0.037 567 Dihedral : 11.972 71.509 569 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.78 % Allowed : 16.32 % Favored : 81.90 % 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: 2.86 (0.40), residues: 410 helix: 3.05 (0.32), residues: 222 sheet: 0.08 (0.68), residues: 54 loop : 0.77 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 57 HIS 0.002 0.001 HIS A 147 PHE 0.011 0.002 PHE A 223 TYR 0.009 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.25 seconds wall clock time: 60 minutes 59.39 seconds (3659.39 seconds total)