Starting phenix.real_space_refine on Wed Aug 5 11:12:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3t_46547/08_2026/9d3t_46547.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3t_46547/08_2026/9d3t_46547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d3t_46547/08_2026/9d3t_46547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3t_46547/08_2026/9d3t_46547.map" model { file = "/net/cci-nas-00/data/ceres_data/9d3t_46547/08_2026/9d3t_46547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3t_46547/08_2026/9d3t_46547.cif" } resolution = 2.8 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= 0.002 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 200 5.49 5 S 14 5.16 5 C 5441 2.51 5 N 1801 2.21 5 O 2193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9649 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 744 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 772 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 672 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 85} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 755 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 683 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 88} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 685 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 2059 Classifications: {'DNA': 100} Link IDs: {'rna3p': 99} Chain: "J" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 2041 Classifications: {'DNA': 100} Link IDs: {'rna3p': 99} Time building chain proxies: 2.40, per 1000 atoms: 0.25 Number of scatterers: 9649 At special positions: 0 Unit cell: (116.875, 77.605, 116.875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 200 15.00 O 2193 8.00 N 1801 7.00 C 5441 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: 1.16 Conformation dependent library (CDL) restraints added in 223.1 milliseconds 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 73.2% alpha, 2.8% beta 97 base pairs and 182 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.056A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.873A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.503A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.530A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.570A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 53 through 72 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.530A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 58 through 84 removed outlier: 3.821A pdb=" N MET D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.627A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.500A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.696A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.541A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.705A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 51 Processing helix chain 'G' and resid 53 through 73 removed outlier: 3.653A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.703A pdb=" N LYS H 43 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.724A pdb=" N SER H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SER H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 116 removed outlier: 3.517A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.095A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.255A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.386A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.168A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 349 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 255 hydrogen bonds 510 hydrogen bond angles 0 basepair planarities 97 basepair parallelities 182 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1977 1.33 - 1.45: 3109 1.45 - 1.57: 4710 1.57 - 1.69: 398 1.69 - 1.81: 26 Bond restraints: 10220 Sorted by residual: bond pdb=" C3' DC J -1 " pdb=" C2' DC J -1 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DC I -22 " pdb=" C2' DC I -22 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" CA ALA C 60 " pdb=" C ALA C 60 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.40e-02 5.10e+03 1.10e+01 bond pdb=" C3' DC I 43 " pdb=" C2' DC I 43 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DC I 41 " pdb=" C2' DC I 41 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 ... (remaining 10215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 13938 1.90 - 3.80: 684 3.80 - 5.70: 36 5.70 - 7.60: 7 7.60 - 9.51: 4 Bond angle restraints: 14669 Sorted by residual: angle pdb=" N ARG D 92 " pdb=" CA ARG D 92 " pdb=" C ARG D 92 " ideal model delta sigma weight residual 113.18 105.72 7.46 1.33e+00 5.65e-01 3.15e+01 angle pdb=" N ALA C 52 " pdb=" CA ALA C 52 " pdb=" C ALA C 52 " ideal model delta sigma weight residual 114.09 105.99 8.10 1.55e+00 4.16e-01 2.73e+01 angle pdb=" N GLY F 28 " pdb=" CA GLY F 28 " pdb=" C GLY F 28 " ideal model delta sigma weight residual 115.32 108.85 6.47 1.31e+00 5.83e-01 2.44e+01 angle pdb=" N ALA G 52 " pdb=" CA ALA G 52 " pdb=" C ALA G 52 " ideal model delta sigma weight residual 114.16 106.95 7.21 1.48e+00 4.57e-01 2.37e+01 angle pdb=" N SER C 19 " pdb=" CA SER C 19 " pdb=" C SER C 19 " ideal model delta sigma weight residual 113.88 108.21 5.67 1.23e+00 6.61e-01 2.12e+01 ... (remaining 14664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.09: 4023 27.09 - 54.19: 1326 54.19 - 81.28: 240 81.28 - 108.37: 5 108.37 - 135.47: 1 Dihedral angle restraints: 5595 sinusoidal: 3533 harmonic: 2062 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 84.53 135.47 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" CG ARG C 35 " pdb=" CD ARG C 35 " pdb=" NE ARG C 35 " pdb=" CZ ARG C 35 " ideal model delta sinusoidal sigma weight residual 90.00 41.04 48.96 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 5592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 728 0.029 - 0.057: 573 0.057 - 0.086: 255 0.086 - 0.114: 97 0.114 - 0.143: 35 Chirality restraints: 1688 Sorted by residual: chirality pdb=" CA GLN A 125 " pdb=" N GLN A 125 " pdb=" C GLN A 125 " pdb=" CB GLN A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" C4' DT I 17 " pdb=" C5' DT I 17 " pdb=" O4' DT I 17 " pdb=" C3' DT I 17 " both_signs ideal model delta sigma weight residual False -2.53 -2.39 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA PRO E 66 " pdb=" N PRO E 66 " pdb=" C PRO E 66 " pdb=" CB PRO E 66 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 1685 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO D 103 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 17 " 0.032 2.00e-02 2.50e+03 1.55e-02 6.04e+00 pdb=" N1 DT I 17 " -0.033 2.00e-02 2.50e+03 pdb=" C2 DT I 17 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 17 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT I 17 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I 17 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT I 17 " 0.013 2.00e-02 2.50e+03 pdb=" C5 DT I 17 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 17 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DT I 17 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 70 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C PHE D 70 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE D 70 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU D 71 " 0.012 2.00e-02 2.50e+03 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 605 2.71 - 3.26: 8411 3.26 - 3.81: 18269 3.81 - 4.35: 23315 4.35 - 4.90: 33907 Nonbonded interactions: 84507 Sorted by model distance: nonbonded pdb=" OG SER H 36 " pdb=" OG SER H 38 " model vdw 2.164 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.188 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.227 3.040 nonbonded pdb=" O HIS B 75 " pdb=" NH2 ARG D 92 " model vdw 2.229 3.120 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.260 3.040 ... (remaining 84502 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 'E' and (resid 43 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 134)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 18 and (name N or name CA or name C or name O or name CB \ )) or resid 19 through 31 or (resid 32 and (name N or name CA or name C or name \ O or name CB )) or resid 33 through 70 or (resid 71 through 72 and (name N or na \ me CA or name C or name O or name CB )) or resid 73 through 74 or (resid 75 and \ (name N or name CA or name C or name O or name CB )) or resid 76 through 109 or \ (resid 110 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 18 through 98 or (resid 99 and (name N or name CA or name \ C or name O or name CB )) or resid 100 through 110)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 36 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB )) or resid 72 through 115 or (resid 116 through 117 and \ (name N or name CA or name C or name O or name CB )) or resid 118 through 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.530 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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 : 0.007 0.048 10220 Z= 0.582 Angle : 0.877 9.505 14669 Z= 0.707 Chirality : 0.048 0.143 1688 Planarity : 0.006 0.062 1166 Dihedral : 28.864 135.467 4267 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.03 % Allowed : 35.55 % Favored : 60.42 % 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: -1.59 (0.31), residues: 698 helix: -0.77 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -1.46 (0.43), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 35 TYR 0.014 0.003 TYR D 83 PHE 0.022 0.003 PHE E 67 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.58 (10220) covalent geometry : angle 0.87692 / 0.71 (14669) hydrogen bonds : bond 0.14595 / 9.12 ( 604) hydrogen bonds : angle 5.74101 / 4.09 ( 1548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.301 Fit side-chains REVERT: A 64 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7776 (mtmm) REVERT: C 94 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7983 (m-40) REVERT: G 64 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: G 99 LYS cc_start: 0.7593 (mttp) cc_final: 0.7240 (mtpp) outliers start: 23 outliers final: 17 residues processed: 128 average time/residue: 0.5979 time to fit residues: 80.5625 Evaluate side-chains 126 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.225977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.180988 restraints weight = 10705.969| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 1.04 r_work: 0.4115 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4001 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10220 Z= 0.145 Angle : 0.653 7.886 14669 Z= 0.376 Chirality : 0.044 0.231 1688 Planarity : 0.005 0.055 1166 Dihedral : 30.455 134.735 2985 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 6.30 % Allowed : 32.05 % Favored : 61.65 % 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: -0.62 (0.31), residues: 698 helix: -0.07 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.14 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 95 TYR 0.013 0.001 TYR G 50 PHE 0.019 0.002 PHE E 67 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.15 (10220) covalent geometry : angle 0.65326 / 0.38 (14669) hydrogen bonds : bond 0.04572 / 3.07 ( 604) hydrogen bonds : angle 3.58658 / 2.48 ( 1548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.245 Fit side-chains REVERT: B 93 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7279 (mt0) REVERT: E 59 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6540 (mm-30) REVERT: F 92 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.6680 (ttm-80) REVERT: G 64 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: G 99 LYS cc_start: 0.7546 (mttp) cc_final: 0.7229 (mtpp) REVERT: H 47 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6812 (tm-30) REVERT: H 62 MET cc_start: 0.8007 (mmt) cc_final: 0.7711 (mmt) outliers start: 36 outliers final: 11 residues processed: 131 average time/residue: 0.5997 time to fit residues: 82.6831 Evaluate side-chains 117 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 41 optimal weight: 0.0030 chunk 70 optimal weight: 30.0000 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS C 73 ASN C 94 ASN C 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.223923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.179500 restraints weight = 10746.701| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 1.02 r_work: 0.4107 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3991 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10220 Z= 0.143 Angle : 0.614 7.727 14669 Z= 0.357 Chirality : 0.043 0.207 1688 Planarity : 0.004 0.053 1166 Dihedral : 30.384 134.932 2966 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.95 % Allowed : 30.65 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.31), residues: 698 helix: 0.36 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.04 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 95 TYR 0.011 0.002 TYR A 54 PHE 0.017 0.002 PHE E 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (10220) covalent geometry : angle 0.61413 / 0.36 (14669) hydrogen bonds : bond 0.04452 / 2.96 ( 604) hydrogen bonds : angle 3.29556 / 2.27 ( 1548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.272 Fit side-chains REVERT: A 49 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6146 (ptp-110) REVERT: B 93 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7302 (mt0) REVERT: E 59 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6710 (mm-30) REVERT: E 94 GLU cc_start: 0.7545 (tp30) cc_final: 0.7242 (tp30) REVERT: F 92 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.6620 (ttm-80) REVERT: G 56 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: G 95 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.6550 (tmtt) REVERT: G 99 LYS cc_start: 0.7531 (mttp) cc_final: 0.7282 (mtpp) outliers start: 34 outliers final: 14 residues processed: 124 average time/residue: 0.7145 time to fit residues: 93.3910 Evaluate side-chains 119 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 50.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN C 104 GLN F 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.223355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.178667 restraints weight = 10756.891| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 1.02 r_work: 0.4105 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3990 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10220 Z= 0.152 Angle : 0.615 7.017 14669 Z= 0.355 Chirality : 0.043 0.214 1688 Planarity : 0.005 0.052 1166 Dihedral : 30.378 134.314 2960 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 6.13 % Allowed : 29.60 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.31), residues: 698 helix: 0.53 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.00 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 35 TYR 0.011 0.002 TYR A 54 PHE 0.017 0.002 PHE E 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (10220) covalent geometry : angle 0.61467 / 0.35 (14669) hydrogen bonds : bond 0.04318 / 2.89 ( 604) hydrogen bonds : angle 3.21645 / 2.21 ( 1548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.260 Fit side-chains REVERT: A 49 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6086 (ptp-110) REVERT: A 59 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7284 (pm20) REVERT: A 105 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7847 (mp0) REVERT: B 93 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7274 (mt0) REVERT: C 71 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6660 (tmm-80) REVERT: E 59 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6682 (mm-30) REVERT: F 92 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.6626 (ttm-80) REVERT: G 56 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: G 64 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: G 95 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.6483 (tmtt) REVERT: G 99 LYS cc_start: 0.7543 (mttp) cc_final: 0.7214 (mtpp) outliers start: 35 outliers final: 19 residues processed: 123 average time/residue: 0.7662 time to fit residues: 99.2949 Evaluate side-chains 125 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 60 optimal weight: 0.2980 chunk 2 optimal weight: 0.3980 chunk 80 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 94 ASN C 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.224813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.180449 restraints weight = 10837.558| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.01 r_work: 0.4131 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4019 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10220 Z= 0.131 Angle : 0.596 7.090 14669 Z= 0.346 Chirality : 0.042 0.218 1688 Planarity : 0.004 0.050 1166 Dihedral : 30.380 134.812 2960 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.60 % Allowed : 30.47 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.32), residues: 698 helix: 0.69 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.91 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 95 TYR 0.021 0.002 TYR D 83 PHE 0.017 0.001 PHE E 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 (10220) covalent geometry : angle 0.59649 / 0.35 (14669) hydrogen bonds : bond 0.04021 / 2.70 ( 604) hydrogen bonds : angle 3.13185 / 2.15 ( 1548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.277 Fit side-chains REVERT: A 49 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6082 (ptp-110) REVERT: A 59 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7256 (pm20) REVERT: B 93 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7289 (mt0) REVERT: B 95 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7457 (ptp-110) REVERT: C 71 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6628 (tmm-80) REVERT: E 59 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6684 (mm-30) REVERT: F 92 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.6630 (ttm-80) REVERT: G 56 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: G 64 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: G 95 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.6520 (tmtt) REVERT: G 99 LYS cc_start: 0.7582 (mttp) cc_final: 0.7284 (mtpp) outliers start: 32 outliers final: 15 residues processed: 120 average time/residue: 0.7527 time to fit residues: 95.0705 Evaluate side-chains 123 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 11 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 53 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 94 ASN C 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.225674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.181283 restraints weight = 10788.328| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 1.03 r_work: 0.4133 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4019 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10220 Z= 0.130 Angle : 0.595 7.362 14669 Z= 0.345 Chirality : 0.042 0.212 1688 Planarity : 0.004 0.049 1166 Dihedral : 30.361 135.020 2960 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.60 % Allowed : 30.82 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.31), residues: 698 helix: 0.85 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.85 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 35 TYR 0.011 0.001 TYR A 54 PHE 0.016 0.001 PHE E 67 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 (10220) covalent geometry : angle 0.59532 / 0.35 (14669) hydrogen bonds : bond 0.03915 / 2.64 ( 604) hydrogen bonds : angle 3.04768 / 2.09 ( 1548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 49 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6120 (ptp-110) REVERT: A 59 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7264 (pm20) REVERT: B 95 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7333 (ptp-110) REVERT: C 71 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6623 (tmm-80) REVERT: E 59 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6649 (mm-30) REVERT: F 92 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.6635 (ttm-80) REVERT: G 56 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: G 64 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: G 95 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.6531 (tmtt) REVERT: G 99 LYS cc_start: 0.7570 (mttp) cc_final: 0.7287 (mtpp) outliers start: 32 outliers final: 16 residues processed: 120 average time/residue: 0.6993 time to fit residues: 88.4902 Evaluate side-chains 123 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 50.0000 chunk 84 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 94 ASN C 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.224490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.179112 restraints weight = 10711.886| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 1.03 r_work: 0.4109 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3996 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10220 Z= 0.165 Angle : 0.618 7.007 14669 Z= 0.355 Chirality : 0.043 0.217 1688 Planarity : 0.004 0.049 1166 Dihedral : 30.332 133.828 2957 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 6.30 % Allowed : 29.77 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.31), residues: 698 helix: 0.75 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.96 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 45 TYR 0.013 0.002 TYR A 54 PHE 0.014 0.002 PHE E 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (10220) covalent geometry : angle 0.61800 / 0.35 (14669) hydrogen bonds : bond 0.04702 / 3.13 ( 604) hydrogen bonds : angle 3.16014 / 2.18 ( 1548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 49 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6194 (ptp-110) REVERT: B 95 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7481 (ptp-110) REVERT: C 61 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7668 (tp30) REVERT: C 71 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6593 (tmm-80) REVERT: E 59 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6706 (mm-30) REVERT: F 92 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.6649 (ttm-80) REVERT: G 56 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: G 64 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: G 95 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.6581 (tmtt) REVERT: G 99 LYS cc_start: 0.7556 (mttp) cc_final: 0.7197 (mtpp) outliers start: 36 outliers final: 17 residues processed: 123 average time/residue: 0.7100 time to fit residues: 92.0356 Evaluate side-chains 124 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 71 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 77 optimal weight: 50.0000 chunk 66 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 94 ASN C 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.225409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.180739 restraints weight = 10695.377| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 1.02 r_work: 0.4120 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4004 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10220 Z= 0.144 Angle : 0.609 7.376 14669 Z= 0.351 Chirality : 0.042 0.220 1688 Planarity : 0.004 0.049 1166 Dihedral : 30.355 134.218 2957 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.08 % Allowed : 31.52 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.32), residues: 698 helix: 0.87 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.93 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 35 TYR 0.013 0.002 TYR A 54 PHE 0.015 0.002 PHE E 67 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (10220) covalent geometry : angle 0.60932 / 0.35 (14669) hydrogen bonds : bond 0.04317 / 2.88 ( 604) hydrogen bonds : angle 3.12373 / 2.17 ( 1548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 49 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6183 (ptp-110) REVERT: C 61 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: C 71 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6586 (tmm-80) REVERT: E 59 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6698 (mm-30) REVERT: F 92 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.6640 (ttm-80) REVERT: G 56 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: G 64 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7290 (tm-30) REVERT: G 95 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.6597 (tmtt) REVERT: G 99 LYS cc_start: 0.7558 (mttp) cc_final: 0.7206 (mtpp) outliers start: 29 outliers final: 16 residues processed: 120 average time/residue: 0.6915 time to fit residues: 87.6327 Evaluate side-chains 124 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 81 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 76 optimal weight: 50.0000 chunk 49 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.222815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.178097 restraints weight = 10596.346| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 1.03 r_work: 0.4110 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3996 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10220 Z= 0.162 Angle : 0.615 7.948 14669 Z= 0.353 Chirality : 0.043 0.213 1688 Planarity : 0.004 0.048 1166 Dihedral : 30.383 134.864 2953 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.90 % Allowed : 31.00 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.31), residues: 698 helix: 0.82 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.96 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 45 TYR 0.012 0.002 TYR A 54 PHE 0.014 0.002 PHE E 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (10220) covalent geometry : angle 0.61540 / 0.35 (14669) hydrogen bonds : bond 0.04401 / 2.95 ( 604) hydrogen bonds : angle 3.14093 / 2.19 ( 1548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.263 Fit side-chains REVERT: A 49 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6179 (ptp-110) REVERT: B 93 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7264 (mt0) REVERT: C 71 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6580 (tmm-80) REVERT: E 59 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6716 (mm-30) REVERT: F 92 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.6657 (ttm-80) REVERT: G 56 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: G 64 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: G 95 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.6639 (tmtt) REVERT: G 99 LYS cc_start: 0.7547 (mttp) cc_final: 0.7197 (mtpp) outliers start: 28 outliers final: 17 residues processed: 118 average time/residue: 0.6869 time to fit residues: 85.4059 Evaluate side-chains 123 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 64 optimal weight: 0.0000 chunk 55 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.0170 chunk 59 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.4624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 94 ASN F 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.224483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.180573 restraints weight = 10631.934| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 1.01 r_work: 0.4146 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4035 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10220 Z= 0.130 Angle : 0.608 8.887 14669 Z= 0.350 Chirality : 0.042 0.219 1688 Planarity : 0.004 0.052 1166 Dihedral : 30.388 135.011 2953 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.20 % Allowed : 32.05 % Favored : 63.75 % 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 are not related in a simple way. whole: 0.74 (0.32), residues: 698 helix: 0.96 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.91 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.014 0.002 TYR A 54 PHE 0.018 0.001 PHE E 67 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (10220) covalent geometry : angle 0.60780 / 0.35 (14669) hydrogen bonds : bond 0.04087 / 2.74 ( 604) hydrogen bonds : angle 3.11307 / 2.16 ( 1548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.232 Fit side-chains REVERT: A 49 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6213 (ptp-110) REVERT: C 71 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6498 (tmm-80) REVERT: C 94 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7757 (m-40) REVERT: E 59 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6795 (mm-30) REVERT: F 92 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.6638 (ttm-80) REVERT: G 56 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: G 64 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7199 (tm-30) REVERT: G 95 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.6639 (tmtt) REVERT: G 99 LYS cc_start: 0.7524 (mttp) cc_final: 0.7205 (mtpp) outliers start: 24 outliers final: 14 residues processed: 117 average time/residue: 0.7462 time to fit residues: 91.9394 Evaluate side-chains 122 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 0.0970 chunk 41 optimal weight: 0.0050 chunk 79 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 94 ASN C 104 GLN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.225607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.181988 restraints weight = 10740.513| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 1.02 r_work: 0.4159 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4048 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10220 Z= 0.128 Angle : 0.596 9.041 14669 Z= 0.344 Chirality : 0.042 0.215 1688 Planarity : 0.004 0.048 1166 Dihedral : 30.375 135.550 2953 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.20 % Allowed : 31.87 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.32), residues: 698 helix: 1.07 (0.23), residues: 537 sheet: None (None), residues: 0 loop : -0.81 (0.46), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 88 TYR 0.011 0.001 TYR A 54 PHE 0.017 0.001 PHE E 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.13 (10220) covalent geometry : angle 0.59578 / 0.34 (14669) hydrogen bonds : bond 0.03844 / 2.59 ( 604) hydrogen bonds : angle 3.01081 / 2.10 ( 1548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3389.98 seconds wall clock time: 58 minutes 16.14 seconds (3496.14 seconds total)