Starting phenix.real_space_refine on Fri Aug 22 19:44:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ehs_28151/08_2025/8ehs_28151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ehs_28151/08_2025/8ehs_28151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ehs_28151/08_2025/8ehs_28151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ehs_28151/08_2025/8ehs_28151.map" model { file = "/net/cci-nas-00/data/ceres_data/8ehs_28151/08_2025/8ehs_28151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ehs_28151/08_2025/8ehs_28151.cif" } resolution = 3.3 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= 0.000 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 4676 2.51 5 N 1253 2.21 5 O 1596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7546 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "A" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "B" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "C" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "D" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "E" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "F" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Time building chain proxies: 1.99, per 1000 atoms: 0.26 Number of scatterers: 7546 At special positions: 0 Unit cell: (85.162, 85.162, 99.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1596 8.00 N 1253 7.00 C 4676 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: 0.50 Conformation dependent library (CDL) restraints added in 398.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 26 sheets defined 3.6% alpha, 54.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'G' and resid 97 through 101 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'D' and resid 97 through 102 removed outlier: 3.622A pdb=" N ASN D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'F' and resid 97 through 102 removed outlier: 3.654A pdb=" N ASN F 102 " --> pdb=" O VAL F 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 8.254A pdb=" N ILE A 29 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR G 6 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU A 31 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG G 8 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N TYR A 33 " --> pdb=" O ARG G 8 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N SER G 10 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE A 136 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A 67 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 8.254A pdb=" N ILE A 29 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR G 6 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU A 31 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG G 8 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N TYR A 33 " --> pdb=" O ARG G 8 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N SER G 10 " --> pdb=" O TYR A 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 15 through 19 removed outlier: 4.385A pdb=" N ILE G 49 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER G 113 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR G 51 " --> pdb=" O VAL G 111 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL G 111 " --> pdb=" O THR G 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 33 through 34 removed outlier: 3.507A pdb=" N SER G 34 " --> pdb=" O ASN G 39 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN G 39 " --> pdb=" O SER G 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 94 through 96 removed outlier: 3.621A pdb=" N GLY G 57 " --> pdb=" O LYS G 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.165A pdb=" N ILE B 29 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A 6 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE B 136 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL B 67 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.165A pdb=" N ILE B 29 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A 6 " --> pdb=" O ILE B 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 15 through 19 removed outlier: 4.587A pdb=" N ILE A 49 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N SER A 113 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR A 51 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL A 111 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 15 through 19 removed outlier: 4.621A pdb=" N ILE C 49 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N SER C 113 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR C 51 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL C 111 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL C 67 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE C 136 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.083A pdb=" N ILE C 29 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR B 6 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU C 31 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG B 8 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE C 136 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL C 67 " --> pdb=" O ILE C 136 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 77 through 84 current: chain 'C' and resid 94 through 96 Processing sheet with id=AB3, first strand: chain 'B' and resid 15 through 19 Processing sheet with id=AB4, first strand: chain 'B' and resid 33 through 34 removed outlier: 3.575A pdb=" N ASN B 39 " --> pdb=" O SER B 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 28 through 31 removed outlier: 8.466A pdb=" N ILE D 29 " --> pdb=" O ASN C 4 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 6 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU D 31 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ARG C 8 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE D 136 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL D 67 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 28 through 31 removed outlier: 8.466A pdb=" N ILE D 29 " --> pdb=" O ASN C 4 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 6 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU D 31 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ARG C 8 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.591A pdb=" N ASN C 39 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 28 through 31 removed outlier: 8.424A pdb=" N ILE E 29 " --> pdb=" O ASN D 4 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR D 6 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU E 31 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG D 8 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE E 136 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL E 67 " --> pdb=" O ILE E 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 28 through 31 removed outlier: 8.424A pdb=" N ILE E 29 " --> pdb=" O ASN D 4 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR D 6 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU E 31 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG D 8 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 15 through 19 removed outlier: 4.482A pdb=" N ILE D 49 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER D 113 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR D 51 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL D 111 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 33 through 34 removed outlier: 3.501A pdb=" N SER D 34 " --> pdb=" O ASN D 39 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN D 39 " --> pdb=" O SER D 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 28 through 30 removed outlier: 8.400A pdb=" N ILE F 29 " --> pdb=" O ASN E 4 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR E 6 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY F 131 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE F 136 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL F 67 " --> pdb=" O ILE F 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 28 through 30 removed outlier: 8.400A pdb=" N ILE F 29 " --> pdb=" O ASN E 4 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR E 6 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY F 131 " --> pdb=" O VAL E 11 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 15 through 19 removed outlier: 4.239A pdb=" N ILE E 49 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER E 113 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR E 51 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL E 111 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 33 through 34 removed outlier: 3.580A pdb=" N ASN E 39 " --> pdb=" O SER E 34 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 15 through 19 removed outlier: 4.370A pdb=" N ILE F 49 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N SER F 113 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR F 51 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL F 111 " --> pdb=" O THR F 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 33 through 34 removed outlier: 3.533A pdb=" N SER F 34 " --> pdb=" O ASN F 39 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN F 39 " --> pdb=" O SER F 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 306 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2506 1.34 - 1.46: 1474 1.46 - 1.58: 3615 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 7637 Sorted by residual: bond pdb=" N VAL G 1 " pdb=" CA VAL G 1 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.39e+00 bond pdb=" N VAL E 1 " pdb=" CA VAL E 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N VAL C 1 " pdb=" CA VAL C 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N VAL B 1 " pdb=" CA VAL B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N VAL F 1 " pdb=" CA VAL F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 ... (remaining 7632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.77: 9658 0.77 - 1.53: 623 1.53 - 2.30: 73 2.30 - 3.06: 14 3.06 - 3.83: 41 Bond angle restraints: 10409 Sorted by residual: angle pdb=" C ASP A 93 " pdb=" CA ASP A 93 " pdb=" CB ASP A 93 " ideal model delta sigma weight residual 109.54 112.42 -2.88 1.84e+00 2.95e-01 2.45e+00 angle pdb=" N MET E 72 " pdb=" CA MET E 72 " pdb=" C MET E 72 " ideal model delta sigma weight residual 111.36 113.00 -1.64 1.09e+00 8.42e-01 2.27e+00 angle pdb=" N MET D 72 " pdb=" CA MET D 72 " pdb=" C MET D 72 " ideal model delta sigma weight residual 111.36 112.98 -1.62 1.09e+00 8.42e-01 2.20e+00 angle pdb=" N MET G 72 " pdb=" CA MET G 72 " pdb=" C MET G 72 " ideal model delta sigma weight residual 111.36 112.97 -1.61 1.09e+00 8.42e-01 2.18e+00 angle pdb=" CA GLN A 124 " pdb=" C GLN A 124 " pdb=" N GLY A 125 " ideal model delta sigma weight residual 114.90 116.86 -1.96 1.37e+00 5.33e-01 2.04e+00 ... (remaining 10404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4342 17.95 - 35.90: 264 35.90 - 53.85: 42 53.85 - 71.80: 19 71.80 - 89.75: 16 Dihedral angle restraints: 4683 sinusoidal: 1750 harmonic: 2933 Sorted by residual: dihedral pdb=" CA ASP C 99 " pdb=" CB ASP C 99 " pdb=" CG ASP C 99 " pdb=" OD1 ASP C 99 " ideal model delta sinusoidal sigma weight residual -30.00 -91.71 61.71 1 2.00e+01 2.50e-03 1.26e+01 dihedral pdb=" CB GLU E 95 " pdb=" CG GLU E 95 " pdb=" CD GLU E 95 " pdb=" OE1 GLU E 95 " ideal model delta sinusoidal sigma weight residual 0.00 89.75 -89.75 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU D 129 " pdb=" CG GLU D 129 " pdb=" CD GLU D 129 " pdb=" OE1 GLU D 129 " ideal model delta sinusoidal sigma weight residual 0.00 89.38 -89.38 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 758 0.029 - 0.057: 386 0.057 - 0.086: 38 0.086 - 0.114: 111 0.114 - 0.143: 30 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA VAL D 1 " pdb=" N VAL D 1 " pdb=" C VAL D 1 " pdb=" CB VAL D 1 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA VAL B 1 " pdb=" N VAL B 1 " pdb=" C VAL B 1 " pdb=" CB VAL B 1 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA VAL E 1 " pdb=" N VAL E 1 " pdb=" C VAL E 1 " pdb=" CB VAL E 1 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 1320 not shown) Planarity restraints: 1337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 142 " 0.023 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C THR E 142 " -0.080 2.00e-02 2.50e+03 pdb=" O THR E 142 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN E 143 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 142 " 0.023 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C THR B 142 " -0.080 2.00e-02 2.50e+03 pdb=" O THR B 142 " 0.030 2.00e-02 2.50e+03 pdb=" N GLN B 143 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 142 " -0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C THR C 142 " 0.079 2.00e-02 2.50e+03 pdb=" O THR C 142 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN C 143 " -0.026 2.00e-02 2.50e+03 ... (remaining 1334 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 101 2.65 - 3.21: 6867 3.21 - 3.77: 10358 3.77 - 4.34: 15566 4.34 - 4.90: 26430 Nonbonded interactions: 59322 Sorted by model distance: nonbonded pdb=" OG SER G 63 " pdb=" OG SER G 138 " model vdw 2.082 3.040 nonbonded pdb=" OG SER D 63 " pdb=" OG SER D 138 " model vdw 2.090 3.040 nonbonded pdb=" OG SER F 63 " pdb=" OG SER F 138 " model vdw 2.117 3.040 nonbonded pdb=" OG SER E 63 " pdb=" OG SER E 138 " model vdw 2.122 3.040 nonbonded pdb=" OG SER B 63 " pdb=" OG SER B 138 " model vdw 2.146 3.040 ... (remaining 59317 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.120 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 0.035 7637 Z= 0.135 Angle : 0.471 3.830 10409 Z= 0.263 Chirality : 0.044 0.143 1323 Planarity : 0.004 0.047 1337 Dihedral : 14.122 89.752 2779 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 1.50 (0.27), residues: 1001 helix: None (None), residues: 0 sheet: 0.86 (0.24), residues: 406 loop : 1.29 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 8 TYR 0.004 0.001 TYR C 133 PHE 0.004 0.001 PHE E 96 HIS 0.002 0.000 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 7637) covalent geometry : angle 0.47127 (10409) hydrogen bonds : bond 0.25447 ( 261) hydrogen bonds : angle 10.46862 ( 762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.208 Fit side-chains REVERT: G 14 LYS cc_start: 0.7176 (mttm) cc_final: 0.6912 (mtpt) REVERT: A 87 LYS cc_start: 0.8506 (ptpp) cc_final: 0.8190 (ptpt) REVERT: A 137 ILE cc_start: 0.8445 (mm) cc_final: 0.8228 (mt) REVERT: C 39 ASN cc_start: 0.8608 (t0) cc_final: 0.8216 (t0) REVERT: C 126 THR cc_start: 0.7962 (m) cc_final: 0.7426 (p) REVERT: C 141 MET cc_start: 0.8911 (ttp) cc_final: 0.8470 (mtm) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0799 time to fit residues: 12.8610 Evaluate side-chains 92 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.0010 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN B 115 GLN D 38 ASN D 115 GLN E 38 ASN E 115 GLN F 115 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.115650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.108672 restraints weight = 8730.279| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 0.80 r_work: 0.3036 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7637 Z= 0.198 Angle : 0.618 5.662 10409 Z= 0.331 Chirality : 0.050 0.172 1323 Planarity : 0.004 0.030 1337 Dihedral : 7.255 74.593 1043 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.35 % Allowed : 5.40 % Favored : 93.25 % 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 aren not related in a simple way. whole: 1.02 (0.26), residues: 1001 helix: None (None), residues: 0 sheet: 0.84 (0.25), residues: 378 loop : 0.71 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 8 TYR 0.009 0.002 TYR A 133 PHE 0.012 0.001 PHE D 40 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 7637) covalent geometry : angle 0.61807 (10409) hydrogen bonds : bond 0.04236 ( 261) hydrogen bonds : angle 5.77668 ( 762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.305 Fit side-chains REVERT: G 39 ASN cc_start: 0.8826 (t0) cc_final: 0.8548 (t0) REVERT: G 69 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8538 (t) REVERT: A 3 LYS cc_start: 0.8305 (mmtt) cc_final: 0.8022 (mmmt) REVERT: C 52 ASN cc_start: 0.7708 (t0) cc_final: 0.7508 (t0) REVERT: C 126 THR cc_start: 0.8208 (m) cc_final: 0.7772 (p) REVERT: D 105 THR cc_start: 0.8364 (p) cc_final: 0.8156 (p) REVERT: E 69 SER cc_start: 0.8758 (t) cc_final: 0.8377 (p) outliers start: 12 outliers final: 10 residues processed: 108 average time/residue: 0.0940 time to fit residues: 13.8693 Evaluate side-chains 99 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain F residue 106 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 120 HIS A 143 GLN D 4 ASN E 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.106885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.099273 restraints weight = 9071.189| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 0.91 r_work: 0.2892 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 7637 Z= 0.286 Angle : 0.701 7.457 10409 Z= 0.372 Chirality : 0.053 0.165 1323 Planarity : 0.004 0.040 1337 Dihedral : 7.389 86.866 1043 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.59 % Allowed : 10.91 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.25), residues: 1001 helix: -3.89 (0.38), residues: 42 sheet: 0.82 (0.26), residues: 336 loop : 0.12 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 8 TYR 0.008 0.002 TYR G 33 PHE 0.014 0.002 PHE D 40 HIS 0.004 0.001 HIS F 120 Details of bonding type rmsd covalent geometry : bond 0.00728 ( 7637) covalent geometry : angle 0.70107 (10409) hydrogen bonds : bond 0.04127 ( 261) hydrogen bonds : angle 5.92566 ( 762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.259 Fit side-chains REVERT: G 44 SER cc_start: 0.8354 (m) cc_final: 0.8126 (t) REVERT: A 118 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8162 (m) REVERT: A 142 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8137 (p) REVERT: C 126 THR cc_start: 0.8444 (m) cc_final: 0.7984 (p) REVERT: E 69 SER cc_start: 0.8810 (t) cc_final: 0.8492 (p) REVERT: E 122 ASP cc_start: 0.8649 (t0) cc_final: 0.8338 (t0) REVERT: F 24 SER cc_start: 0.8739 (p) cc_final: 0.8314 (t) REVERT: F 129 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7569 (mp0) outliers start: 23 outliers final: 17 residues processed: 113 average time/residue: 0.0778 time to fit residues: 12.4637 Evaluate side-chains 107 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain F residue 106 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 66 optimal weight: 0.0020 chunk 71 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.116205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.109183 restraints weight = 8871.963| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 0.80 r_work: 0.3023 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7637 Z= 0.102 Angle : 0.478 3.876 10409 Z= 0.258 Chirality : 0.045 0.147 1323 Planarity : 0.003 0.028 1337 Dihedral : 6.207 87.993 1043 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.04 % Allowed : 13.84 % Favored : 83.13 % 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 aren not related in a simple way. whole: 0.42 (0.25), residues: 1001 helix: -3.65 (0.46), residues: 42 sheet: 0.45 (0.25), residues: 371 loop : 0.63 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 8 TYR 0.005 0.001 TYR A 133 PHE 0.005 0.001 PHE E 96 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7637) covalent geometry : angle 0.47809 (10409) hydrogen bonds : bond 0.02780 ( 261) hydrogen bonds : angle 5.21702 ( 762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.289 Fit side-chains REVERT: G 6 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8526 (m) REVERT: G 14 LYS cc_start: 0.7216 (mttm) cc_final: 0.6585 (mtpt) REVERT: C 126 THR cc_start: 0.8306 (m) cc_final: 0.7837 (p) REVERT: C 141 MET cc_start: 0.9002 (ttp) cc_final: 0.8439 (mtm) REVERT: D 105 THR cc_start: 0.8284 (p) cc_final: 0.8083 (p) REVERT: E 6 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8622 (m) REVERT: E 56 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7929 (mtpt) REVERT: E 69 SER cc_start: 0.8791 (t) cc_final: 0.8512 (p) REVERT: F 87 LYS cc_start: 0.8198 (ptpp) cc_final: 0.7723 (ptpt) REVERT: F 129 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7230 (mp0) outliers start: 27 outliers final: 19 residues processed: 106 average time/residue: 0.0731 time to fit residues: 11.3202 Evaluate side-chains 105 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 6 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN B 50 HIS F 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.106416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.098720 restraints weight = 9174.887| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 0.90 r_work: 0.2884 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 7637 Z= 0.287 Angle : 0.671 6.793 10409 Z= 0.355 Chirality : 0.052 0.163 1323 Planarity : 0.004 0.039 1337 Dihedral : 6.658 68.013 1043 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.95 % Allowed : 13.16 % Favored : 81.89 % 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 aren not related in a simple way. whole: -0.09 (0.25), residues: 1001 helix: -3.76 (0.42), residues: 42 sheet: 0.53 (0.26), residues: 329 loop : -0.05 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 8 TYR 0.008 0.002 TYR F 133 PHE 0.011 0.002 PHE D 40 HIS 0.004 0.001 HIS F 120 Details of bonding type rmsd covalent geometry : bond 0.00731 ( 7637) covalent geometry : angle 0.67116 (10409) hydrogen bonds : bond 0.03577 ( 261) hydrogen bonds : angle 5.67050 ( 762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 93 time to evaluate : 0.249 Fit side-chains REVERT: G 44 SER cc_start: 0.8331 (m) cc_final: 0.8092 (t) REVERT: A 72 MET cc_start: 0.7875 (mmm) cc_final: 0.7497 (mmm) REVERT: C 126 THR cc_start: 0.8459 (m) cc_final: 0.8034 (p) REVERT: E 69 SER cc_start: 0.8824 (t) cc_final: 0.8568 (p) REVERT: E 122 ASP cc_start: 0.8640 (t0) cc_final: 0.8327 (t0) REVERT: F 24 SER cc_start: 0.8758 (p) cc_final: 0.8300 (t) REVERT: F 129 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7563 (mp0) outliers start: 44 outliers final: 35 residues processed: 124 average time/residue: 0.0734 time to fit residues: 13.0980 Evaluate side-chains 124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 8 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.3108 r_free = 0.3108 target = 0.110451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.101872 restraints weight = 9016.156| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.03 r_work: 0.2906 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7637 Z= 0.143 Angle : 0.519 4.652 10409 Z= 0.278 Chirality : 0.046 0.147 1323 Planarity : 0.003 0.034 1337 Dihedral : 5.957 56.590 1043 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 4.16 % Allowed : 14.85 % Favored : 80.99 % 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 aren not related in a simple way. whole: -0.00 (0.25), residues: 1001 helix: -3.65 (0.45), residues: 42 sheet: 0.49 (0.27), residues: 322 loop : 0.08 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 8 TYR 0.006 0.001 TYR G 133 PHE 0.006 0.001 PHE E 96 HIS 0.002 0.001 HIS F 120 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7637) covalent geometry : angle 0.51881 (10409) hydrogen bonds : bond 0.02863 ( 261) hydrogen bonds : angle 5.31484 ( 762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 0.345 Fit side-chains REVERT: G 44 SER cc_start: 0.8273 (m) cc_final: 0.8026 (t) REVERT: A 72 MET cc_start: 0.7927 (mmm) cc_final: 0.7586 (mmm) REVERT: A 118 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.7962 (m) REVERT: C 126 THR cc_start: 0.8422 (m) cc_final: 0.8012 (p) REVERT: D 39 ASN cc_start: 0.9082 (t0) cc_final: 0.8808 (t0) REVERT: E 69 SER cc_start: 0.8867 (t) cc_final: 0.8605 (p) REVERT: E 122 ASP cc_start: 0.8648 (t0) cc_final: 0.8305 (t0) REVERT: E 126 THR cc_start: 0.8161 (t) cc_final: 0.7956 (p) REVERT: F 87 LYS cc_start: 0.8236 (ptpp) cc_final: 0.7734 (ptpt) REVERT: F 129 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7364 (mp0) outliers start: 37 outliers final: 28 residues processed: 116 average time/residue: 0.0756 time to fit residues: 12.8434 Evaluate side-chains 121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 19 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3154 r_free = 0.3154 target = 0.113775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.106432 restraints weight = 8835.259| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 0.85 r_work: 0.2991 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7637 Z= 0.139 Angle : 0.509 4.535 10409 Z= 0.272 Chirality : 0.046 0.149 1323 Planarity : 0.003 0.034 1337 Dihedral : 5.598 46.292 1043 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.39 % Allowed : 14.96 % Favored : 80.65 % 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 aren not related in a simple way. whole: 0.08 (0.25), residues: 1001 helix: -3.60 (0.46), residues: 42 sheet: 0.51 (0.27), residues: 322 loop : 0.16 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 8 TYR 0.005 0.001 TYR G 133 PHE 0.006 0.001 PHE E 96 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 7637) covalent geometry : angle 0.50904 (10409) hydrogen bonds : bond 0.02830 ( 261) hydrogen bonds : angle 5.17561 ( 762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 89 time to evaluate : 0.296 Fit side-chains REVERT: G 14 LYS cc_start: 0.7236 (mttm) cc_final: 0.6677 (mtpt) REVERT: G 44 SER cc_start: 0.8293 (m) cc_final: 0.8071 (t) REVERT: G 118 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7966 (m) REVERT: A 72 MET cc_start: 0.7862 (mmm) cc_final: 0.7460 (mmm) REVERT: A 118 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.7946 (m) REVERT: C 126 THR cc_start: 0.8443 (m) cc_final: 0.8077 (p) REVERT: E 69 SER cc_start: 0.8828 (t) cc_final: 0.8584 (p) REVERT: F 129 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7288 (mp0) outliers start: 39 outliers final: 34 residues processed: 116 average time/residue: 0.0751 time to fit residues: 12.6869 Evaluate side-chains 124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 70 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3164 r_free = 0.3164 target = 0.114540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.107232 restraints weight = 8871.844| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 0.84 r_work: 0.3005 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7637 Z= 0.130 Angle : 0.499 4.680 10409 Z= 0.266 Chirality : 0.045 0.147 1323 Planarity : 0.003 0.032 1337 Dihedral : 5.324 40.457 1043 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 4.27 % Allowed : 15.64 % Favored : 80.09 % 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 aren not related in a simple way. whole: 0.16 (0.25), residues: 1001 helix: -3.53 (0.48), residues: 42 sheet: 0.53 (0.27), residues: 322 loop : 0.24 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 8 TYR 0.005 0.001 TYR G 133 PHE 0.006 0.001 PHE E 96 HIS 0.002 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7637) covalent geometry : angle 0.49946 (10409) hydrogen bonds : bond 0.02708 ( 261) hydrogen bonds : angle 5.09877 ( 762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 0.290 Fit side-chains REVERT: G 14 LYS cc_start: 0.7266 (mttm) cc_final: 0.6712 (mtpt) REVERT: G 118 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7976 (m) REVERT: A 118 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.7931 (m) REVERT: C 126 THR cc_start: 0.8465 (m) cc_final: 0.8091 (p) REVERT: E 32 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8612 (p) REVERT: E 69 SER cc_start: 0.8832 (t) cc_final: 0.8595 (p) REVERT: F 129 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7269 (mp0) outliers start: 38 outliers final: 31 residues processed: 120 average time/residue: 0.0748 time to fit residues: 12.9125 Evaluate side-chains 124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 12 optimal weight: 0.0970 chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.113808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.106446 restraints weight = 8738.042| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 0.86 r_work: 0.2981 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7637 Z= 0.151 Angle : 0.525 5.636 10409 Z= 0.279 Chirality : 0.046 0.147 1323 Planarity : 0.003 0.032 1337 Dihedral : 5.368 34.361 1043 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.27 % Allowed : 15.97 % Favored : 79.75 % 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 aren not related in a simple way. whole: 0.11 (0.26), residues: 1001 helix: -3.55 (0.48), residues: 42 sheet: 0.48 (0.27), residues: 322 loop : 0.22 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 8 TYR 0.005 0.001 TYR G 133 PHE 0.006 0.001 PHE E 96 HIS 0.002 0.001 HIS F 120 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 7637) covalent geometry : angle 0.52541 (10409) hydrogen bonds : bond 0.02816 ( 261) hydrogen bonds : angle 5.16981 ( 762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.308 Fit side-chains REVERT: G 14 LYS cc_start: 0.7288 (mttm) cc_final: 0.6617 (mtpt) REVERT: A 72 MET cc_start: 0.7862 (mmm) cc_final: 0.7501 (mmm) REVERT: A 118 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.7990 (m) REVERT: C 126 THR cc_start: 0.8482 (m) cc_final: 0.8102 (p) REVERT: E 32 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8689 (p) REVERT: E 69 SER cc_start: 0.8853 (t) cc_final: 0.8602 (p) REVERT: F 129 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7363 (mp0) outliers start: 38 outliers final: 33 residues processed: 116 average time/residue: 0.0786 time to fit residues: 12.9527 Evaluate side-chains 123 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 96 optimal weight: 0.0980 chunk 2 optimal weight: 6.9990 chunk 44 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 41 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 66 optimal weight: 0.0980 overall best weight: 0.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.120917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.113886 restraints weight = 8707.872| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 0.82 r_work: 0.3094 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7637 Z= 0.075 Angle : 0.434 4.618 10409 Z= 0.232 Chirality : 0.043 0.137 1323 Planarity : 0.003 0.026 1337 Dihedral : 4.395 22.424 1043 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.36 % Allowed : 17.89 % Favored : 79.75 % 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 aren not related in a simple way. whole: 0.23 (0.26), residues: 1001 helix: -3.48 (0.49), residues: 42 sheet: 0.32 (0.26), residues: 364 loop : 0.48 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 8 TYR 0.003 0.000 TYR C 33 PHE 0.007 0.001 PHE E 96 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00174 ( 7637) covalent geometry : angle 0.43383 (10409) hydrogen bonds : bond 0.02278 ( 261) hydrogen bonds : angle 4.69151 ( 762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.294 Fit side-chains REVERT: G 14 LYS cc_start: 0.7238 (mttm) cc_final: 0.6551 (mtpt) REVERT: A 118 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8025 (m) REVERT: C 52 ASN cc_start: 0.7793 (t0) cc_final: 0.7431 (t0) REVERT: C 126 THR cc_start: 0.8363 (m) cc_final: 0.8045 (p) REVERT: C 141 MET cc_start: 0.8959 (ttp) cc_final: 0.8434 (mtm) REVERT: E 6 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8594 (m) REVERT: E 32 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8813 (p) REVERT: F 129 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7210 (mp0) outliers start: 21 outliers final: 16 residues processed: 107 average time/residue: 0.0705 time to fit residues: 11.1635 Evaluate side-chains 111 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 106 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.116329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.108957 restraints weight = 8649.224| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 0.85 r_work: 0.3024 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7637 Z= 0.117 Angle : 0.481 4.274 10409 Z= 0.255 Chirality : 0.045 0.143 1323 Planarity : 0.003 0.026 1337 Dihedral : 4.673 20.130 1043 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.59 % Allowed : 17.77 % Favored : 79.64 % 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 aren not related in a simple way. whole: 0.40 (0.26), residues: 1001 helix: -3.44 (0.50), residues: 42 sheet: 0.33 (0.26), residues: 357 loop : 0.67 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 8 TYR 0.004 0.001 TYR G 133 PHE 0.005 0.001 PHE E 96 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7637) covalent geometry : angle 0.48082 (10409) hydrogen bonds : bond 0.02632 ( 261) hydrogen bonds : angle 4.82006 ( 762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1632.26 seconds wall clock time: 28 minutes 55.47 seconds (1735.47 seconds total)