Starting phenix.real_space_refine on Tue Aug 4 14:57:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ov0_70885/08_2026/9ov0_70885.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ov0_70885/08_2026/9ov0_70885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ov0_70885/08_2026/9ov0_70885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ov0_70885/08_2026/9ov0_70885.map" model { file = "/net/cci-nas-00/data/ceres_data/9ov0_70885/08_2026/9ov0_70885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ov0_70885/08_2026/9ov0_70885.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 16 5.16 5 C 2750 2.51 5 N 666 2.21 5 O 690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4125 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2020 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 15, 'TRANS': 249} Chain breaks: 1 Chain: "A" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2020 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 15, 'TRANS': 249} Chain breaks: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {' K': 1, 'LBN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' K': 2, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 1.22, per 1000 atoms: 0.30 Number of scatterers: 4125 At special positions: 0 Unit cell: (68.06, 77.08, 96.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 16 16.00 O 690 8.00 N 666 7.00 C 2750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS A 53 " 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: 0.39 Conformation dependent library (CDL) restraints added in 151.2 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 988 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 77.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'B' and resid 6 through 51 removed outlier: 4.149A pdb=" N ALA B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 13 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 55 through 70 removed outlier: 3.545A pdb=" N GLY B 70 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 116 through 152 Proline residue: B 132 - end of helix removed outlier: 3.914A pdb=" N VAL B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 185 Processing helix chain 'B' and resid 185 through 196 removed outlier: 3.690A pdb=" N ALA B 189 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 213 Processing helix chain 'B' and resid 230 through 264 Processing helix chain 'B' and resid 265 through 270 removed outlier: 3.626A pdb=" N ILE B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 51 removed outlier: 3.999A pdb=" N ALA A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A 13 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.706A pdb=" N LEU A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.867A pdb=" N VAL A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.599A pdb=" N LEU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 152 removed outlier: 4.203A pdb=" N VAL A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 185 Processing helix chain 'A' and resid 186 through 196 Processing helix chain 'A' and resid 200 through 213 Processing helix chain 'A' and resid 230 through 263 removed outlier: 4.009A pdb=" N HIS A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 921 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: 0.46 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 708 1.33 - 1.45: 1090 1.45 - 1.57: 2408 1.57 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 4228 Sorted by residual: bond pdb=" CE1 TYR A 109 " pdb=" CZ TYR A 109 " ideal model delta sigma weight residual 1.378 1.350 0.028 2.40e-02 1.74e+03 1.38e+00 bond pdb=" CA GLY A 110 " pdb=" C GLY A 110 " ideal model delta sigma weight residual 1.514 1.498 0.016 1.39e-02 5.18e+03 1.33e+00 bond pdb=" CD1 TYR A 109 " pdb=" CE1 TYR A 109 " ideal model delta sigma weight residual 1.382 1.354 0.028 3.00e-02 1.11e+03 8.75e-01 bond pdb=" CD1 TYR B 109 " pdb=" CE1 TYR B 109 " ideal model delta sigma weight residual 1.382 1.355 0.027 3.00e-02 1.11e+03 7.99e-01 bond pdb=" C TYR A 109 " pdb=" N GLY A 110 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.66e-02 3.63e+03 7.35e-01 ... (remaining 4223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 5562 1.58 - 3.16: 169 3.16 - 4.73: 20 4.73 - 6.31: 12 6.31 - 7.89: 5 Bond angle restraints: 5768 Sorted by residual: angle pdb=" C SER B 213 " pdb=" N THR B 214 " pdb=" CA THR B 214 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.70e+00 angle pdb=" N THR B 214 " pdb=" CA THR B 214 " pdb=" C THR B 214 " ideal model delta sigma weight residual 110.80 116.14 -5.34 2.13e+00 2.20e-01 6.28e+00 angle pdb=" N GLY B 130 " pdb=" CA GLY B 130 " pdb=" C GLY B 130 " ideal model delta sigma weight residual 113.18 118.65 -5.47 2.37e+00 1.78e-01 5.32e+00 angle pdb=" CA TRP A 91 " pdb=" CB TRP A 91 " pdb=" CG TRP A 91 " ideal model delta sigma weight residual 113.60 117.84 -4.24 1.90e+00 2.77e-01 4.99e+00 angle pdb=" CA GLY A 70 " pdb=" C GLY A 70 " pdb=" N ARG A 71 " ideal model delta sigma weight residual 114.62 117.38 -2.76 1.26e+00 6.30e-01 4.80e+00 ... (remaining 5763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 2320 24.09 - 48.17: 136 48.17 - 72.26: 10 72.26 - 96.34: 2 96.34 - 120.43: 3 Dihedral angle restraints: 2471 sinusoidal: 939 harmonic: 1532 Sorted by residual: dihedral pdb=" CA SER B 213 " pdb=" C SER B 213 " pdb=" N THR B 214 " pdb=" CA THR B 214 " ideal model delta harmonic sigma weight residual 180.00 155.85 24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" C10 LBN B 302 " pdb=" C4 LBN B 302 " pdb=" C7 LBN B 302 " pdb=" C33 LBN B 302 " ideal model delta sinusoidal sigma weight residual 179.81 59.38 120.43 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" CA THR B 106 " pdb=" C THR B 106 " pdb=" N VAL B 107 " pdb=" CA VAL B 107 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 2468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 397 0.028 - 0.055: 189 0.055 - 0.083: 71 0.083 - 0.111: 25 0.111 - 0.139: 10 Chirality restraints: 692 Sorted by residual: chirality pdb=" CA THR B 106 " pdb=" N THR B 106 " pdb=" C THR B 106 " pdb=" CB THR B 106 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA THR B 214 " pdb=" N THR B 214 " pdb=" C THR B 214 " pdb=" CB THR B 214 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CB VAL A 107 " pdb=" CA VAL A 107 " pdb=" CG1 VAL A 107 " pdb=" CG2 VAL A 107 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 689 not shown) Planarity restraints: 702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 109 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C TYR A 109 " -0.025 2.00e-02 2.50e+03 pdb=" O TYR A 109 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY A 110 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 91 " 0.012 2.00e-02 2.50e+03 7.67e-03 1.47e+00 pdb=" CG TRP A 91 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 91 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 91 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 91 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 91 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 91 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 91 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 91 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 91 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 221 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO A 222 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 222 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 222 " 0.016 5.00e-02 4.00e+02 ... (remaining 699 not shown) Histogram of nonbonded interaction distances: 2.48 - 3.01: 2422 3.01 - 3.54: 5620 3.54 - 4.08: 6596 4.08 - 4.61: 10302 4.61 - 5.14: 13004 Nonbonded interactions: 37944 Sorted by model distance: nonbonded pdb=" O5 LBN B 302 " pdb=" O7 LBN B 302 " model vdw 2.479 2.432 nonbonded pdb=" O VAL B 107 " pdb=" K K A 302 " model vdw 2.484 2.850 nonbonded pdb=" O ILE B 215 " pdb=" K K A 301 " model vdw 2.497 2.850 nonbonded pdb=" N THR B 112 " pdb=" OG1 THR B 112 " model vdw 2.521 2.496 nonbonded pdb=" O THR B 214 " pdb=" K K B 301 " model vdw 2.558 2.850 ... (remaining 37939 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 301) selection = (chain 'B' and resid 4 through 301) } 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 group one per residue 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.800 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4229 Z= 0.177 Angle : 0.691 7.888 5770 Z= 0.341 Chirality : 0.039 0.139 692 Planarity : 0.004 0.030 702 Dihedral : 14.677 120.426 1480 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.83 % Allowed : 9.90 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.38), residues: 522 helix: 1.49 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -1.56 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.016 0.002 TYR A 17 PHE 0.012 0.001 PHE B 209 TRP 0.021 0.001 TRP A 91 HIS 0.007 0.001 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 4228) covalent geometry : angle 0.69063 / 0.34 ( 5768) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 0.58319 / 0.28 ( 2) hydrogen bonds : bond 0.09499 / 6.62 ( 307) hydrogen bonds : angle 4.78124 / 3.21 ( 921) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: B 46 GLN cc_start: 0.9042 (pt0) cc_final: 0.8713 (pt0) REVERT: B 53 CYS cc_start: 0.7890 (OUTLIER) cc_final: 0.6760 (t) REVERT: B 62 PHE cc_start: 0.9381 (t80) cc_final: 0.9173 (t80) REVERT: B 135 MET cc_start: 0.7045 (tmm) cc_final: 0.5666 (mmt) REVERT: B 201 PHE cc_start: 0.7563 (t80) cc_final: 0.7209 (t80) REVERT: B 206 TYR cc_start: 0.9211 (t80) cc_final: 0.8870 (t80) REVERT: B 224 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 246 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7127 (mt) REVERT: B 257 ARG cc_start: 0.7924 (ttt-90) cc_final: 0.7680 (ttp-170) REVERT: B 263 HIS cc_start: 0.8272 (t-90) cc_final: 0.8043 (t-90) REVERT: A 46 GLN cc_start: 0.8934 (pt0) cc_final: 0.8378 (pt0) REVERT: A 49 GLN cc_start: 0.9048 (pp30) cc_final: 0.8796 (pp30) REVERT: A 64 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8677 (tm-30) REVERT: A 65 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8359 (mmm160) REVERT: A 159 MET cc_start: 0.6674 (pmm) cc_final: 0.6157 (pmm) REVERT: A 254 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7808 (tm-30) REVERT: A 255 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8397 (p) REVERT: A 257 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7973 (ttp-170) outliers start: 20 outliers final: 9 residues processed: 152 average time/residue: 0.0613 time to fit residues: 11.5648 Evaluate side-chains 115 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.0020 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 8.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 HIS B 172 HIS A 151 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.180630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139878 restraints weight = 6352.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143384 restraints weight = 3753.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145666 restraints weight = 2754.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.146902 restraints weight = 2308.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147519 restraints weight = 2094.472| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4229 Z= 0.136 Angle : 0.744 11.128 5770 Z= 0.341 Chirality : 0.042 0.370 692 Planarity : 0.004 0.030 702 Dihedral : 13.142 108.364 662 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.56 % Allowed : 20.53 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.39), residues: 522 helix: 1.52 (0.26), residues: 396 sheet: None (None), residues: 0 loop : -1.28 (0.62), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 44 TYR 0.012 0.001 TYR A 17 PHE 0.011 0.001 PHE A 209 TRP 0.024 0.001 TRP A 156 HIS 0.008 0.002 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 4228) covalent geometry : angle 0.74378 / 0.34 ( 5768) SS BOND : bond 0.00011 / 0.01 ( 1) SS BOND : angle 0.32134 / 0.13 ( 2) hydrogen bonds : bond 0.03855 / 2.64 ( 307) hydrogen bonds : angle 3.98732 / 2.80 ( 921) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: B 46 GLN cc_start: 0.8899 (pt0) cc_final: 0.8427 (pm20) REVERT: B 53 CYS cc_start: 0.8048 (OUTLIER) cc_final: 0.6654 (t) REVERT: B 135 MET cc_start: 0.7042 (tmm) cc_final: 0.5470 (mmt) REVERT: B 212 LEU cc_start: 0.8497 (mt) cc_final: 0.8199 (mp) REVERT: B 224 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7716 (mm-30) REVERT: B 246 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7036 (mt) REVERT: B 257 ARG cc_start: 0.8137 (ttt-90) cc_final: 0.7672 (ttp-170) REVERT: A 29 GLU cc_start: 0.6848 (pp20) cc_final: 0.6525 (pp20) REVERT: A 46 GLN cc_start: 0.8923 (pt0) cc_final: 0.8514 (pt0) REVERT: A 64 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8811 (tm-30) REVERT: A 65 ARG cc_start: 0.8724 (tpp80) cc_final: 0.8128 (mmm160) REVERT: A 159 MET cc_start: 0.6331 (pmm) cc_final: 0.5990 (pmm) REVERT: A 254 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8032 (tm-30) outliers start: 23 outliers final: 16 residues processed: 116 average time/residue: 0.0441 time to fit residues: 6.9169 Evaluate side-chains 113 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 256 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 41 optimal weight: 0.0070 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 HIS ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS A 172 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.182243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.142130 restraints weight = 6227.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.145633 restraints weight = 3701.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147776 restraints weight = 2715.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149293 restraints weight = 2276.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.149828 restraints weight = 2046.533| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4229 Z= 0.129 Angle : 0.734 12.452 5770 Z= 0.337 Chirality : 0.039 0.146 692 Planarity : 0.004 0.030 702 Dihedral : 13.074 105.595 658 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 6.52 % Allowed : 21.26 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.38), residues: 522 helix: 1.34 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.71 (0.62), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 166 TYR 0.013 0.001 TYR A 17 PHE 0.009 0.001 PHE A 209 TRP 0.026 0.001 TRP A 156 HIS 0.009 0.002 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 4228) covalent geometry : angle 0.73418 / 0.34 ( 5768) SS BOND : bond 0.00044 / 0.03 ( 1) SS BOND : angle 0.20870 / 0.10 ( 2) hydrogen bonds : bond 0.03531 / 2.40 ( 307) hydrogen bonds : angle 3.86775 / 2.75 ( 921) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: B 46 GLN cc_start: 0.8979 (pt0) cc_final: 0.8602 (pm20) REVERT: B 53 CYS cc_start: 0.7903 (OUTLIER) cc_final: 0.6633 (t) REVERT: B 135 MET cc_start: 0.6964 (tmm) cc_final: 0.5380 (mmt) REVERT: B 257 ARG cc_start: 0.8061 (ttt-90) cc_final: 0.7737 (ttp-170) REVERT: A 29 GLU cc_start: 0.6545 (pp20) cc_final: 0.5803 (pp20) REVERT: A 33 GLU cc_start: 0.7860 (pm20) cc_final: 0.7494 (pm20) REVERT: A 46 GLN cc_start: 0.8791 (pt0) cc_final: 0.8571 (pt0) REVERT: A 64 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8774 (tm-30) REVERT: A 65 ARG cc_start: 0.8776 (tpp80) cc_final: 0.8141 (mmm160) REVERT: A 159 MET cc_start: 0.6165 (pmm) cc_final: 0.5955 (pmm) REVERT: A 254 GLN cc_start: 0.8615 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 255 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8424 (p) outliers start: 27 outliers final: 18 residues processed: 117 average time/residue: 0.0468 time to fit residues: 7.1763 Evaluate side-chains 115 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 21 optimal weight: 0.0870 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS A 263 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.182429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.142446 restraints weight = 6210.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146025 restraints weight = 3732.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.148365 restraints weight = 2739.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149714 restraints weight = 2270.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.150730 restraints weight = 2043.925| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4229 Z= 0.127 Angle : 0.724 13.599 5770 Z= 0.329 Chirality : 0.039 0.147 692 Planarity : 0.004 0.031 702 Dihedral : 13.028 105.386 656 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 6.76 % Allowed : 22.71 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.38), residues: 522 helix: 1.37 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.81 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.013 0.001 TYR A 17 PHE 0.016 0.001 PHE A 62 TRP 0.030 0.001 TRP A 156 HIS 0.009 0.002 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 4228) covalent geometry : angle 0.72441 / 0.33 ( 5768) SS BOND : bond 0.00006 / 0.00 ( 1) SS BOND : angle 0.16543 / 0.07 ( 2) hydrogen bonds : bond 0.03317 / 2.27 ( 307) hydrogen bonds : angle 3.80219 / 2.71 ( 921) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: B 46 GLN cc_start: 0.9038 (pt0) cc_final: 0.8628 (pm20) REVERT: B 53 CYS cc_start: 0.7805 (OUTLIER) cc_final: 0.6487 (t) REVERT: B 105 THR cc_start: 0.9115 (t) cc_final: 0.8875 (m) REVERT: B 135 MET cc_start: 0.6963 (tmm) cc_final: 0.5368 (mmt) REVERT: B 257 ARG cc_start: 0.8034 (ttt-90) cc_final: 0.7789 (ttp-170) REVERT: A 29 GLU cc_start: 0.6471 (pp20) cc_final: 0.5827 (pp20) REVERT: A 64 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8807 (tm-30) REVERT: A 254 GLN cc_start: 0.8608 (tm-30) cc_final: 0.7953 (tm-30) REVERT: A 255 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8450 (p) outliers start: 28 outliers final: 22 residues processed: 123 average time/residue: 0.0497 time to fit residues: 7.9754 Evaluate side-chains 122 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS A 172 HIS A 263 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.179432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140162 restraints weight = 6252.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143495 restraints weight = 3680.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.145880 restraints weight = 2705.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146997 restraints weight = 2242.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148129 restraints weight = 2025.428| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4229 Z= 0.158 Angle : 0.755 10.376 5770 Z= 0.351 Chirality : 0.041 0.152 692 Planarity : 0.004 0.031 702 Dihedral : 13.210 107.907 656 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 7.49 % Allowed : 24.40 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.39), residues: 522 helix: 1.27 (0.27), residues: 410 sheet: None (None), residues: 0 loop : -1.80 (0.64), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 65 TYR 0.016 0.002 TYR B 241 PHE 0.013 0.002 PHE A 209 TRP 0.031 0.001 TRP A 156 HIS 0.008 0.002 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 4228) covalent geometry : angle 0.75493 / 0.35 ( 5768) SS BOND : bond 0.00041 / 0.03 ( 1) SS BOND : angle 0.15779 / 0.07 ( 2) hydrogen bonds : bond 0.03431 / 2.37 ( 307) hydrogen bonds : angle 3.85331 / 2.74 ( 921) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 GLN cc_start: 0.9064 (pt0) cc_final: 0.8651 (pm20) REVERT: B 53 CYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7422 (p) REVERT: B 105 THR cc_start: 0.9180 (t) cc_final: 0.8963 (m) REVERT: B 135 MET cc_start: 0.7054 (tmm) cc_final: 0.5401 (mmt) REVERT: B 212 LEU cc_start: 0.8490 (mt) cc_final: 0.8153 (mp) REVERT: B 257 ARG cc_start: 0.8100 (ttt-90) cc_final: 0.7755 (ttp-170) REVERT: A 254 GLN cc_start: 0.8692 (tm-30) cc_final: 0.7997 (tm-30) REVERT: A 255 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8445 (p) outliers start: 31 outliers final: 22 residues processed: 122 average time/residue: 0.0427 time to fit residues: 6.9499 Evaluate side-chains 121 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS A 46 GLN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS A 263 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.180643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141145 restraints weight = 6372.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144795 restraints weight = 3751.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147206 restraints weight = 2723.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148293 restraints weight = 2249.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149331 restraints weight = 2036.170| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4229 Z= 0.134 Angle : 0.743 9.943 5770 Z= 0.345 Chirality : 0.040 0.150 692 Planarity : 0.004 0.030 702 Dihedral : 13.095 106.118 655 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 7.49 % Allowed : 26.81 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.39), residues: 522 helix: 1.30 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -1.89 (0.64), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 65 TYR 0.013 0.001 TYR B 241 PHE 0.009 0.001 PHE A 209 TRP 0.031 0.001 TRP A 156 HIS 0.008 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 4228) covalent geometry : angle 0.74287 / 0.34 ( 5768) SS BOND : bond 0.00038 / 0.02 ( 1) SS BOND : angle 0.11677 / 0.05 ( 2) hydrogen bonds : bond 0.03340 / 2.31 ( 307) hydrogen bonds : angle 3.77634 / 2.68 ( 921) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 CYS cc_start: 0.7655 (OUTLIER) cc_final: 0.6385 (t) REVERT: B 105 THR cc_start: 0.9167 (t) cc_final: 0.8947 (m) REVERT: B 135 MET cc_start: 0.7032 (tmm) cc_final: 0.5341 (mmt) REVERT: B 212 LEU cc_start: 0.8454 (mt) cc_final: 0.8114 (mp) REVERT: B 257 ARG cc_start: 0.8034 (ttt-90) cc_final: 0.7808 (ttp-170) REVERT: A 254 GLN cc_start: 0.8649 (tm-30) cc_final: 0.7962 (tm-30) REVERT: A 255 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8446 (p) outliers start: 31 outliers final: 25 residues processed: 122 average time/residue: 0.0360 time to fit residues: 5.9102 Evaluate side-chains 126 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 269 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 0.0370 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 33 optimal weight: 0.0670 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS A 46 GLN A 151 HIS A 172 HIS A 263 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.181742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142304 restraints weight = 6363.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145882 restraints weight = 3733.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148128 restraints weight = 2721.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149665 restraints weight = 2265.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.150156 restraints weight = 2019.968| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4229 Z= 0.131 Angle : 0.770 10.496 5770 Z= 0.351 Chirality : 0.040 0.149 692 Planarity : 0.004 0.032 702 Dihedral : 13.149 111.357 655 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 7.25 % Allowed : 28.74 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.39), residues: 522 helix: 1.35 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -1.96 (0.63), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 65 TYR 0.014 0.001 TYR B 241 PHE 0.018 0.001 PHE B 93 TRP 0.033 0.001 TRP A 156 HIS 0.010 0.002 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4228) covalent geometry : angle 0.76976 / 0.35 ( 5768) SS BOND : bond 0.00039 / 0.02 ( 1) SS BOND : angle 0.09415 / 0.04 ( 2) hydrogen bonds : bond 0.03303 / 2.28 ( 307) hydrogen bonds : angle 3.72323 / 2.65 ( 921) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 CYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7301 (p) REVERT: B 105 THR cc_start: 0.9162 (t) cc_final: 0.8927 (m) REVERT: B 135 MET cc_start: 0.7001 (tmm) cc_final: 0.5332 (mmt) REVERT: B 257 ARG cc_start: 0.8030 (ttt-90) cc_final: 0.7591 (ttp-170) REVERT: A 33 GLU cc_start: 0.7869 (pm20) cc_final: 0.7660 (pm20) outliers start: 30 outliers final: 23 residues processed: 121 average time/residue: 0.0379 time to fit residues: 6.0572 Evaluate side-chains 121 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 269 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 44 optimal weight: 0.2980 chunk 41 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 0.0030 chunk 10 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS A 263 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.183503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144786 restraints weight = 6275.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148622 restraints weight = 3702.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.151003 restraints weight = 2671.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.152612 restraints weight = 2195.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.153012 restraints weight = 1944.200| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4229 Z= 0.131 Angle : 0.800 16.116 5770 Z= 0.364 Chirality : 0.040 0.163 692 Planarity : 0.004 0.035 702 Dihedral : 12.536 112.002 653 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 6.52 % Allowed : 30.43 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.39), residues: 522 helix: 1.33 (0.27), residues: 410 sheet: None (None), residues: 0 loop : -2.04 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 65 TYR 0.013 0.001 TYR A 17 PHE 0.009 0.001 PHE B 62 TRP 0.033 0.001 TRP A 156 HIS 0.008 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 4228) covalent geometry : angle 0.79982 / 0.36 ( 5768) SS BOND : bond 0.00058 / 0.04 ( 1) SS BOND : angle 0.10497 / 0.05 ( 2) hydrogen bonds : bond 0.03313 / 2.30 ( 307) hydrogen bonds : angle 3.74876 / 2.69 ( 921) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: B 53 CYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7203 (p) REVERT: B 105 THR cc_start: 0.9128 (t) cc_final: 0.8908 (m) REVERT: B 135 MET cc_start: 0.6922 (tmm) cc_final: 0.5311 (mmt) REVERT: B 257 ARG cc_start: 0.8019 (ttt-90) cc_final: 0.7733 (ttp-170) REVERT: A 267 GLU cc_start: 0.8239 (mp0) cc_final: 0.7339 (tp30) outliers start: 27 outliers final: 20 residues processed: 121 average time/residue: 0.0464 time to fit residues: 7.2884 Evaluate side-chains 119 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 269 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 35 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 HIS A 46 GLN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS A 263 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.182572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144199 restraints weight = 6340.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.147773 restraints weight = 3713.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.150353 restraints weight = 2691.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.151607 restraints weight = 2199.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.152696 restraints weight = 1962.292| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4229 Z= 0.142 Angle : 0.789 10.311 5770 Z= 0.372 Chirality : 0.041 0.165 692 Planarity : 0.004 0.033 702 Dihedral : 12.435 107.341 653 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 6.76 % Allowed : 30.43 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.39), residues: 522 helix: 1.34 (0.27), residues: 410 sheet: None (None), residues: 0 loop : -2.10 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 65 TYR 0.014 0.001 TYR B 241 PHE 0.025 0.002 PHE A 62 TRP 0.033 0.001 TRP A 156 HIS 0.008 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 4228) covalent geometry : angle 0.78910 / 0.37 ( 5768) SS BOND : bond 0.00073 / 0.05 ( 1) SS BOND : angle 0.07843 / 0.04 ( 2) hydrogen bonds : bond 0.03355 / 2.33 ( 307) hydrogen bonds : angle 3.76741 / 2.70 ( 921) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: B 53 CYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6260 (t) REVERT: B 105 THR cc_start: 0.9141 (t) cc_final: 0.8941 (m) REVERT: B 126 PHE cc_start: 0.8661 (t80) cc_final: 0.8442 (t80) REVERT: B 135 MET cc_start: 0.6976 (tmm) cc_final: 0.5343 (mmt) REVERT: B 257 ARG cc_start: 0.8053 (ttt-90) cc_final: 0.7720 (ttp-170) REVERT: B 267 GLU cc_start: 0.8289 (pm20) cc_final: 0.7954 (pp20) outliers start: 28 outliers final: 22 residues processed: 117 average time/residue: 0.0541 time to fit residues: 8.3280 Evaluate side-chains 122 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 269 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 46 GLN B 151 HIS A 151 HIS A 263 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.177092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.137546 restraints weight = 6172.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140953 restraints weight = 3695.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142697 restraints weight = 2724.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.144428 restraints weight = 2315.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144785 restraints weight = 2074.144| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4229 Z= 0.192 Angle : 0.828 9.966 5770 Z= 0.403 Chirality : 0.044 0.160 692 Planarity : 0.004 0.031 702 Dihedral : 12.949 108.656 653 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 7.00 % Allowed : 30.43 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.39), residues: 522 helix: 1.18 (0.27), residues: 408 sheet: None (None), residues: 0 loop : -2.23 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 65 TYR 0.019 0.002 TYR A 241 PHE 0.017 0.002 PHE A 209 TRP 0.027 0.001 TRP A 156 HIS 0.006 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 4228) covalent geometry : angle 0.82838 / 0.40 ( 5768) SS BOND : bond 0.00131 / 0.08 ( 1) SS BOND : angle 0.08077 / 0.03 ( 2) hydrogen bonds : bond 0.03939 / 2.75 ( 307) hydrogen bonds : angle 3.99111 / 2.88 ( 921) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: B 46 GLN cc_start: 0.9338 (pt0) cc_final: 0.9081 (pt0) REVERT: B 53 CYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7099 (p) REVERT: B 126 PHE cc_start: 0.8771 (t80) cc_final: 0.8527 (t80) REVERT: B 135 MET cc_start: 0.7153 (tmm) cc_final: 0.5932 (mmt) REVERT: B 246 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7229 (mt) REVERT: B 257 ARG cc_start: 0.8107 (ttt-90) cc_final: 0.7855 (ttp-170) REVERT: B 267 GLU cc_start: 0.8391 (pm20) cc_final: 0.7985 (pp20) REVERT: A 71 ARG cc_start: 0.7037 (ptm160) cc_final: 0.6606 (mtp180) REVERT: A 254 GLN cc_start: 0.8886 (tp40) cc_final: 0.8638 (tp40) REVERT: A 263 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.8016 (p90) outliers start: 29 outliers final: 23 residues processed: 123 average time/residue: 0.0485 time to fit residues: 7.9381 Evaluate side-chains 129 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 269 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 HIS A 46 GLN A 151 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.179229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141353 restraints weight = 6255.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144762 restraints weight = 3654.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147118 restraints weight = 2669.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.148464 restraints weight = 2201.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148847 restraints weight = 1967.725| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4229 Z= 0.162 Angle : 0.816 10.485 5770 Z= 0.392 Chirality : 0.043 0.175 692 Planarity : 0.004 0.031 702 Dihedral : 12.965 107.339 653 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 7.00 % Allowed : 30.43 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.39), residues: 522 helix: 1.24 (0.27), residues: 406 sheet: None (None), residues: 0 loop : -2.34 (0.63), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 65 TYR 0.013 0.002 TYR A 241 PHE 0.023 0.002 PHE A 62 TRP 0.027 0.001 TRP A 156 HIS 0.005 0.001 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 4228) covalent geometry : angle 0.81656 / 0.39 ( 5768) SS BOND : bond 0.00058 / 0.04 ( 1) SS BOND : angle 0.18947 / 0.08 ( 2) hydrogen bonds : bond 0.03616 / 2.50 ( 307) hydrogen bonds : angle 3.88674 / 2.81 ( 921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 742.85 seconds wall clock time: 13 minutes 27.97 seconds (807.97 seconds total)