Starting phenix.real_space_refine on Tue Mar 3 11:04:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo3_33335/03_2026/7xo3_33335.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo3_33335/03_2026/7xo3_33335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xo3_33335/03_2026/7xo3_33335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo3_33335/03_2026/7xo3_33335.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xo3_33335/03_2026/7xo3_33335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo3_33335/03_2026/7xo3_33335.map" } resolution = 2.6 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= 0.001 sd= 0.004 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: 3 Type Number sf(0) Gaussians C 1626 2.51 5 N 450 2.21 5 O 522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2598 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Restraints were copied for chains: A, E, C, F, D Time building chain proxies: 0.43, per 1000 atoms: 0.17 Number of scatterers: 2598 At special positions: 0 Unit cell: (79.5, 117.66, 32.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 522 8.00 N 450 7.00 C 1626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.15 Conformation dependent library (CDL) restraints added in 70.4 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 37 through 42 removed outlier: 6.386A pdb=" N LEU B 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLY E 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 37 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL F 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR B 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER F 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY B 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 48 through 57 removed outlier: 6.293A pdb=" N VAL B 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL E 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLY B 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N THR E 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ALA B 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N ALA E 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N VAL B 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N HIS F 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 61 through 67 removed outlier: 6.057A pdb=" N GLU B 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR F 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL F 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASN B 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 71 through 72 removed outlier: 6.466A pdb=" N VAL B 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 75 through 79 removed outlier: 5.994A pdb=" N THR B 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA E 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL B 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 82 through 83 removed outlier: 6.362A pdb=" N VAL B 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.898A pdb=" N SER B 87 " --> pdb=" O ILE E 88 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 42 removed outlier: 6.433A pdb=" N LEU A 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLY C 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A 40 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 48 through 57 removed outlier: 8.988A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N GLY C 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N HIS A 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N ALA C 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL A 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL C 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR A 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU C 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA A 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N HIS D 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 61 through 67 removed outlier: 6.050A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR D 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL D 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN A 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 removed outlier: 6.445A pdb=" N VAL A 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 79 removed outlier: 6.033A pdb=" N THR A 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA C 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.374A pdb=" N VAL A 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.889A pdb=" N SER A 87 " --> pdb=" O ILE C 88 " (cutoff:3.500A) 43 hydrogen bonds defined for protein. 129 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: 0.28 Time building geometry restraints manager: 0.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 456 1.29 - 1.35: 407 1.35 - 1.42: 103 1.42 - 1.48: 426 1.48 - 1.55: 1218 Bond restraints: 2610 Sorted by residual: bond pdb=" C GLY B 67 " pdb=" O GLY B 67 " ideal model delta sigma weight residual 1.233 1.227 0.006 6.90e-03 2.10e+04 7.30e-01 bond pdb=" C GLY E 67 " pdb=" O GLY E 67 " ideal model delta sigma weight residual 1.233 1.227 0.006 6.90e-03 2.10e+04 6.58e-01 bond pdb=" C GLY C 67 " pdb=" O GLY C 67 " ideal model delta sigma weight residual 1.233 1.227 0.005 6.90e-03 2.10e+04 6.26e-01 bond pdb=" C GLY A 67 " pdb=" O GLY A 67 " ideal model delta sigma weight residual 1.233 1.227 0.005 6.90e-03 2.10e+04 6.24e-01 bond pdb=" C GLY D 67 " pdb=" O GLY D 67 " ideal model delta sigma weight residual 1.233 1.227 0.005 6.90e-03 2.10e+04 5.82e-01 ... (remaining 2605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.36: 2602 0.36 - 0.72: 604 0.72 - 1.08: 232 1.08 - 1.44: 54 1.44 - 1.80: 36 Bond angle restraints: 3528 Sorted by residual: angle pdb=" CA GLY C 84 " pdb=" C GLY C 84 " pdb=" N ALA C 85 " ideal model delta sigma weight residual 115.25 116.89 -1.64 1.43e+00 4.89e-01 1.31e+00 angle pdb=" CA GLY B 84 " pdb=" C GLY B 84 " pdb=" N ALA B 85 " ideal model delta sigma weight residual 115.25 116.86 -1.61 1.43e+00 4.89e-01 1.27e+00 angle pdb=" CA GLY F 84 " pdb=" C GLY F 84 " pdb=" N ALA F 85 " ideal model delta sigma weight residual 115.25 116.85 -1.60 1.43e+00 4.89e-01 1.25e+00 angle pdb=" CA GLY D 84 " pdb=" C GLY D 84 " pdb=" N ALA D 85 " ideal model delta sigma weight residual 115.25 116.84 -1.59 1.43e+00 4.89e-01 1.23e+00 angle pdb=" CA GLY A 84 " pdb=" C GLY A 84 " pdb=" N ALA A 85 " ideal model delta sigma weight residual 115.25 116.83 -1.58 1.43e+00 4.89e-01 1.22e+00 ... (remaining 3523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.58: 1314 10.58 - 21.16: 128 21.16 - 31.74: 46 31.74 - 42.32: 12 42.32 - 52.90: 18 Dihedral angle restraints: 1518 sinusoidal: 504 harmonic: 1014 Sorted by residual: dihedral pdb=" CA LEU B 38 " pdb=" CB LEU B 38 " pdb=" CG LEU B 38 " pdb=" CD1 LEU B 38 " ideal model delta sinusoidal sigma weight residual 180.00 139.66 40.34 3 1.50e+01 4.44e-03 7.18e+00 dihedral pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " pdb=" CG LEU A 38 " pdb=" CD1 LEU A 38 " ideal model delta sinusoidal sigma weight residual 180.00 139.68 40.32 3 1.50e+01 4.44e-03 7.18e+00 dihedral pdb=" CA LEU D 38 " pdb=" CB LEU D 38 " pdb=" CG LEU D 38 " pdb=" CD1 LEU D 38 " ideal model delta sinusoidal sigma weight residual 180.00 139.68 40.32 3 1.50e+01 4.44e-03 7.18e+00 ... (remaining 1515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 224 0.026 - 0.051: 118 0.051 - 0.077: 48 0.077 - 0.103: 20 0.103 - 0.129: 52 Chirality restraints: 462 Sorted by residual: chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE D 88 " pdb=" N ILE D 88 " pdb=" C ILE D 88 " pdb=" CB ILE D 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 459 not shown) Planarity restraints: 438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 68 " 0.002 2.00e-02 2.50e+03 4.77e-03 2.28e-01 pdb=" C GLY A 68 " -0.008 2.00e-02 2.50e+03 pdb=" O GLY A 68 " 0.003 2.00e-02 2.50e+03 pdb=" N ALA A 69 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 68 " 0.002 2.00e-02 2.50e+03 4.74e-03 2.25e-01 pdb=" C GLY D 68 " -0.008 2.00e-02 2.50e+03 pdb=" O GLY D 68 " 0.003 2.00e-02 2.50e+03 pdb=" N ALA D 69 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 68 " -0.002 2.00e-02 2.50e+03 4.73e-03 2.24e-01 pdb=" C GLY B 68 " 0.008 2.00e-02 2.50e+03 pdb=" O GLY B 68 " -0.003 2.00e-02 2.50e+03 pdb=" N ALA B 69 " -0.003 2.00e-02 2.50e+03 ... (remaining 435 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 223 2.76 - 3.29: 2264 3.29 - 3.83: 3987 3.83 - 4.36: 4368 4.36 - 4.90: 8731 Nonbonded interactions: 19573 Sorted by model distance: nonbonded pdb=" NE2 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.223 3.120 nonbonded pdb=" NE2 GLN D 62 " pdb=" OG1 THR D 64 " model vdw 2.223 3.120 nonbonded pdb=" NE2 GLN F 62 " pdb=" OG1 THR F 64 " model vdw 2.223 3.120 nonbonded pdb=" NE2 GLN E 62 " pdb=" OG1 THR E 64 " model vdw 2.223 3.120 nonbonded pdb=" NE2 GLN B 62 " pdb=" OG1 THR B 64 " model vdw 2.223 3.120 ... (remaining 19568 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 'B' selection = chain 'A' selection = chain 'E' selection = chain 'C' selection = chain 'F' selection = chain 'D' } 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: 1.520 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.000 Find NCS groups from input model: 0.020 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:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 : 0.002 0.020 2610 Z= 0.109 Angle : 0.408 1.796 3528 Z= 0.248 Chirality : 0.051 0.129 462 Planarity : 0.001 0.005 438 Dihedral : 12.373 52.896 882 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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: -3.31 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR A 39 PHE 0.007 0.002 PHE F 94 HIS 0.001 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 2610) covalent geometry : angle 0.40809 ( 3528) hydrogen bonds : bond 0.14509 ( 43) hydrogen bonds : angle 7.74398 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.109 Fit side-chains REVERT: A 62 GLN cc_start: 0.8271 (tp40) cc_final: 0.8049 (tm130) REVERT: F 97 LYS cc_start: 0.7149 (ttmt) cc_final: 0.6193 (tptt) REVERT: D 97 LYS cc_start: 0.7175 (ttmt) cc_final: 0.6372 (tppt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.7974 time to fit residues: 39.7573 Evaluate side-chains 28 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.131771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.112281 restraints weight = 3635.170| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.89 r_work: 0.3631 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2610 Z= 0.261 Angle : 0.555 5.022 3528 Z= 0.319 Chirality : 0.054 0.137 462 Planarity : 0.003 0.009 438 Dihedral : 5.540 15.634 378 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.75 % Favored : 85.25 % Rotamer: Outliers : 1.52 % Allowed : 15.91 % Favored : 82.58 % 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: -2.52 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR D 39 PHE 0.012 0.003 PHE A 94 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 2610) covalent geometry : angle 0.55537 ( 3528) hydrogen bonds : bond 0.02938 ( 43) hydrogen bonds : angle 5.89861 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.103 Fit side-chains REVERT: C 62 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: F 60 LYS cc_start: 0.7358 (mtpt) cc_final: 0.7059 (mmtm) REVERT: F 97 LYS cc_start: 0.7198 (ttmt) cc_final: 0.6321 (tptt) REVERT: D 97 LYS cc_start: 0.7070 (ttmt) cc_final: 0.6346 (tppt) outliers start: 4 outliers final: 1 residues processed: 36 average time/residue: 0.7722 time to fit residues: 28.3139 Evaluate side-chains 31 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain C residue 62 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.133831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.113171 restraints weight = 3682.558| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.04 r_work: 0.3660 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2610 Z= 0.193 Angle : 0.516 4.570 3528 Z= 0.298 Chirality : 0.052 0.136 462 Planarity : 0.002 0.007 438 Dihedral : 5.367 16.145 378 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 2.27 % Allowed : 17.05 % Favored : 80.68 % 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: -2.29 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR A 39 PHE 0.008 0.002 PHE A 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 2610) covalent geometry : angle 0.51629 ( 3528) hydrogen bonds : bond 0.02677 ( 43) hydrogen bonds : angle 5.51532 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.072 Fit side-chains REVERT: F 97 LYS cc_start: 0.7191 (ttmt) cc_final: 0.6268 (tptt) REVERT: D 97 LYS cc_start: 0.7083 (ttmt) cc_final: 0.6308 (tppt) outliers start: 6 outliers final: 4 residues processed: 31 average time/residue: 0.7566 time to fit residues: 23.9080 Evaluate side-chains 29 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.131219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.110280 restraints weight = 3656.774| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.02 r_work: 0.3621 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 2610 Z= 0.321 Angle : 0.631 5.176 3528 Z= 0.364 Chirality : 0.056 0.139 462 Planarity : 0.003 0.010 438 Dihedral : 6.029 17.877 378 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.57 % Favored : 84.43 % Rotamer: Outliers : 1.89 % Allowed : 19.70 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.27 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.003 TYR D 39 PHE 0.013 0.003 PHE A 94 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00658 ( 2610) covalent geometry : angle 0.63055 ( 3528) hydrogen bonds : bond 0.02892 ( 43) hydrogen bonds : angle 5.58540 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.103 Fit side-chains REVERT: E 97 LYS cc_start: 0.7607 (ttmt) cc_final: 0.6875 (tmtm) REVERT: F 97 LYS cc_start: 0.7184 (ttmt) cc_final: 0.6270 (tptt) REVERT: D 97 LYS cc_start: 0.7087 (ttmt) cc_final: 0.6293 (tptt) outliers start: 5 outliers final: 5 residues processed: 34 average time/residue: 0.7956 time to fit residues: 27.5108 Evaluate side-chains 34 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 chunk 14 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 0.0000 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.139331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.118070 restraints weight = 3532.589| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.02 r_work: 0.3725 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2610 Z= 0.105 Angle : 0.447 3.684 3528 Z= 0.256 Chirality : 0.052 0.140 462 Planarity : 0.001 0.005 438 Dihedral : 4.862 14.891 378 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.89 % Allowed : 20.45 % Favored : 77.65 % 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: -2.04 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR C 39 PHE 0.004 0.001 PHE E 94 HIS 0.001 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 2610) covalent geometry : angle 0.44671 ( 3528) hydrogen bonds : bond 0.01963 ( 43) hydrogen bonds : angle 5.07424 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.110 Fit side-chains REVERT: B 61 GLU cc_start: 0.7835 (mp0) cc_final: 0.7230 (mp0) REVERT: F 97 LYS cc_start: 0.7090 (ttmt) cc_final: 0.6222 (tptt) REVERT: D 97 LYS cc_start: 0.6977 (ttmt) cc_final: 0.6211 (tptt) outliers start: 5 outliers final: 4 residues processed: 31 average time/residue: 0.7176 time to fit residues: 22.6515 Evaluate side-chains 29 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 0.0570 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.136964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.115736 restraints weight = 3545.424| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.97 r_work: 0.3690 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2610 Z= 0.141 Angle : 0.456 3.693 3528 Z= 0.263 Chirality : 0.052 0.138 462 Planarity : 0.002 0.005 438 Dihedral : 5.040 15.730 378 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 1.52 % Allowed : 19.70 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.95 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 39 PHE 0.006 0.002 PHE F 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 2610) covalent geometry : angle 0.45649 ( 3528) hydrogen bonds : bond 0.02066 ( 43) hydrogen bonds : angle 5.05408 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.116 Fit side-chains REVERT: F 97 LYS cc_start: 0.7079 (ttmt) cc_final: 0.6260 (tptt) REVERT: D 97 LYS cc_start: 0.7037 (ttmt) cc_final: 0.6315 (tptt) outliers start: 4 outliers final: 4 residues processed: 27 average time/residue: 0.7502 time to fit residues: 20.6922 Evaluate side-chains 27 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 chunk 4 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.139099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.117732 restraints weight = 3548.613| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.01 r_work: 0.3717 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2610 Z= 0.110 Angle : 0.437 3.461 3528 Z= 0.252 Chirality : 0.051 0.138 462 Planarity : 0.001 0.004 438 Dihedral : 4.786 15.007 378 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 1.52 % Allowed : 19.32 % Favored : 79.17 % 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: -1.90 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 39 PHE 0.005 0.001 PHE B 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 2610) covalent geometry : angle 0.43744 ( 3528) hydrogen bonds : bond 0.01908 ( 43) hydrogen bonds : angle 4.91422 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.115 Fit side-chains REVERT: F 97 LYS cc_start: 0.7089 (ttmt) cc_final: 0.6251 (tptt) REVERT: D 97 LYS cc_start: 0.6938 (ttmt) cc_final: 0.6194 (tppt) outliers start: 4 outliers final: 4 residues processed: 28 average time/residue: 0.7413 time to fit residues: 21.1676 Evaluate side-chains 28 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 30 optimal weight: 0.0270 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 14 optimal weight: 0.4980 chunk 23 optimal weight: 0.0670 chunk 13 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.138826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.117440 restraints weight = 3599.747| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.01 r_work: 0.3712 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2610 Z= 0.114 Angle : 0.433 3.448 3528 Z= 0.250 Chirality : 0.051 0.138 462 Planarity : 0.001 0.004 438 Dihedral : 4.763 14.802 378 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 1.52 % Allowed : 19.70 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.86 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 39 PHE 0.005 0.001 PHE B 94 HIS 0.001 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 2610) covalent geometry : angle 0.43339 ( 3528) hydrogen bonds : bond 0.01836 ( 43) hydrogen bonds : angle 4.86903 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.082 Fit side-chains REVERT: F 97 LYS cc_start: 0.7090 (ttmt) cc_final: 0.6272 (tptt) REVERT: D 97 LYS cc_start: 0.6944 (ttmt) cc_final: 0.6208 (tppt) outliers start: 4 outliers final: 4 residues processed: 27 average time/residue: 0.7925 time to fit residues: 21.7874 Evaluate side-chains 28 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 24 optimal weight: 0.0870 overall best weight: 3.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.133489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.112351 restraints weight = 3687.381| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.04 r_work: 0.3647 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2610 Z= 0.245 Angle : 0.560 4.030 3528 Z= 0.324 Chirality : 0.054 0.141 462 Planarity : 0.002 0.008 438 Dihedral : 5.637 17.681 378 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.75 % Favored : 85.25 % Rotamer: Outliers : 1.52 % Allowed : 19.32 % Favored : 79.17 % 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: -1.95 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.010 0.003 PHE D 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 2610) covalent geometry : angle 0.56044 ( 3528) hydrogen bonds : bond 0.02320 ( 43) hydrogen bonds : angle 5.22260 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.079 Fit side-chains REVERT: F 97 LYS cc_start: 0.6958 (ttmt) cc_final: 0.6083 (tptt) REVERT: D 97 LYS cc_start: 0.7069 (ttmt) cc_final: 0.6302 (tptt) outliers start: 4 outliers final: 4 residues processed: 27 average time/residue: 0.7709 time to fit residues: 21.2911 Evaluate side-chains 27 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.133841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.112861 restraints weight = 3647.069| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.03 r_work: 0.3654 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2610 Z= 0.235 Angle : 0.563 4.211 3528 Z= 0.325 Chirality : 0.053 0.142 462 Planarity : 0.002 0.008 438 Dihedral : 5.659 17.618 378 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer: Outliers : 1.89 % Allowed : 18.94 % Favored : 79.17 % 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: -2.04 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR D 39 PHE 0.010 0.003 PHE D 94 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 2610) covalent geometry : angle 0.56325 ( 3528) hydrogen bonds : bond 0.02342 ( 43) hydrogen bonds : angle 5.24071 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.099 Fit side-chains REVERT: F 97 LYS cc_start: 0.6937 (ttmt) cc_final: 0.6069 (tptt) REVERT: D 97 LYS cc_start: 0.7048 (ttmt) cc_final: 0.6278 (tptt) outliers start: 5 outliers final: 5 residues processed: 27 average time/residue: 0.6898 time to fit residues: 19.0256 Evaluate side-chains 27 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 33 optimal weight: 0.0030 overall best weight: 2.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.135932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.115311 restraints weight = 3609.763| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.99 r_work: 0.3686 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2610 Z= 0.153 Angle : 0.484 3.693 3528 Z= 0.278 Chirality : 0.052 0.141 462 Planarity : 0.002 0.006 438 Dihedral : 5.240 16.616 378 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 1.89 % Allowed : 18.94 % Favored : 79.17 % 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: -1.92 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 39 PHE 0.007 0.002 PHE D 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 2610) covalent geometry : angle 0.48356 ( 3528) hydrogen bonds : bond 0.02050 ( 43) hydrogen bonds : angle 5.09340 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1186.07 seconds wall clock time: 20 minutes 51.81 seconds (1251.81 seconds total)