Starting phenix.real_space_refine on Fri Feb 6 03:10:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m6x_63666/02_2026/9m6x_63666.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m6x_63666/02_2026/9m6x_63666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m6x_63666/02_2026/9m6x_63666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m6x_63666/02_2026/9m6x_63666.map" model { file = "/net/cci-nas-00/data/ceres_data/9m6x_63666/02_2026/9m6x_63666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m6x_63666/02_2026/9m6x_63666.cif" } resolution = 3.36 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= -0.005 sd= 0.068 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 78 5.16 5 C 14070 2.51 5 N 3678 2.21 5 O 4443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22269 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 921 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "B" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 921 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "C" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 921 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "D" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 921 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "E" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 921 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "F" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 921 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "G" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 921 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 921 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "I" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 921 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "J" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 921 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 921 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "L" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 921 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "M" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1037 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "N" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1037 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "O" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1037 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "P" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1026 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "Q" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1026 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "R" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1026 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "S" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 838 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "T" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 838 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "U" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 838 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "V" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 838 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "W" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 838 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "X" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 838 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Time building chain proxies: 5.48, per 1000 atoms: 0.25 Number of scatterers: 22269 At special positions: 0 Unit cell: (121.2, 118.8, 150, 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 78 16.00 O 4443 8.00 N 3678 7.00 C 14070 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: 1.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5226 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 13 sheets defined 41.4% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 14 through 34 removed outlier: 3.632A pdb=" N ILE A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 50 removed outlier: 3.687A pdb=" N VAL A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 64 removed outlier: 3.547A pdb=" N ASN A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.859A pdb=" N ASP A 88 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU A 89 " --> pdb=" O ASP A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 89' Processing helix chain 'A' and resid 91 through 105 Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 14 through 34 Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.511A pdb=" N VAL B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 64 removed outlier: 3.597A pdb=" N ILE B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 4.074A pdb=" N ASP B 88 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU B 89 " --> pdb=" O ASP B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 89' Processing helix chain 'B' and resid 90 through 106 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 14 through 34 removed outlier: 3.527A pdb=" N ILE C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 50 through 63 removed outlier: 3.531A pdb=" N ILE C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 removed outlier: 4.131A pdb=" N ASP C 88 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU C 89 " --> pdb=" O ASP C 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 85 through 89' Processing helix chain 'C' and resid 90 through 106 Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 14 through 34 removed outlier: 3.620A pdb=" N ILE D 34 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 50 removed outlier: 3.630A pdb=" N VAL D 50 " --> pdb=" O VAL D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 64 removed outlier: 3.595A pdb=" N ASN D 63 " --> pdb=" O LEU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.837A pdb=" N ASP D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU D 89 " --> pdb=" O ASP D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 91 through 105 Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 14 through 34 removed outlier: 3.516A pdb=" N ILE E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 50 through 63 removed outlier: 3.521A pdb=" N ILE E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 4.126A pdb=" N ASP E 88 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU E 89 " --> pdb=" O ASP E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 89' Processing helix chain 'E' and resid 90 through 106 Processing helix chain 'F' and resid 3 through 13 Processing helix chain 'F' and resid 14 through 34 removed outlier: 3.624A pdb=" N ILE F 34 " --> pdb=" O VAL F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 50 removed outlier: 3.626A pdb=" N VAL F 50 " --> pdb=" O VAL F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 64 removed outlier: 3.578A pdb=" N ASN F 63 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.702A pdb=" N ASP F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU F 89 " --> pdb=" O ASP F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 89' Processing helix chain 'F' and resid 91 through 105 Processing helix chain 'G' and resid 3 through 12 Processing helix chain 'G' and resid 14 through 34 removed outlier: 3.516A pdb=" N ILE G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 50 removed outlier: 3.511A pdb=" N VAL G 50 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 64 removed outlier: 3.599A pdb=" N ILE G 54 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 89 removed outlier: 4.055A pdb=" N ASP G 88 " --> pdb=" O SER G 85 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU G 89 " --> pdb=" O ASP G 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 85 through 89' Processing helix chain 'G' and resid 90 through 106 Processing helix chain 'H' and resid 3 through 13 Processing helix chain 'H' and resid 14 through 34 removed outlier: 3.646A pdb=" N ILE H 34 " --> pdb=" O VAL H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 50 removed outlier: 3.627A pdb=" N VAL H 50 " --> pdb=" O VAL H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 64 removed outlier: 3.562A pdb=" N ASN H 63 " --> pdb=" O LEU H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 89 removed outlier: 3.792A pdb=" N ASP H 88 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU H 89 " --> pdb=" O ASP H 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 85 through 89' Processing helix chain 'H' and resid 91 through 105 Processing helix chain 'I' and resid 3 through 12 Processing helix chain 'I' and resid 14 through 34 removed outlier: 3.534A pdb=" N ILE I 34 " --> pdb=" O VAL I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 50 Processing helix chain 'I' and resid 50 through 63 removed outlier: 3.529A pdb=" N ILE I 54 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 89 removed outlier: 4.128A pdb=" N ASP I 88 " --> pdb=" O SER I 85 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU I 89 " --> pdb=" O ASP I 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 85 through 89' Processing helix chain 'I' and resid 90 through 106 Processing helix chain 'J' and resid 3 through 13 Processing helix chain 'J' and resid 14 through 34 removed outlier: 3.627A pdb=" N ILE J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 50 removed outlier: 3.629A pdb=" N VAL J 50 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 64 removed outlier: 3.586A pdb=" N ASN J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 89 removed outlier: 3.825A pdb=" N ASP J 88 " --> pdb=" O SER J 85 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU J 89 " --> pdb=" O ASP J 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 85 through 89' Processing helix chain 'J' and resid 91 through 105 Processing helix chain 'K' and resid 3 through 12 Processing helix chain 'K' and resid 14 through 34 removed outlier: 3.503A pdb=" N ILE K 34 " --> pdb=" O VAL K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 50 Processing helix chain 'K' and resid 50 through 63 removed outlier: 3.524A pdb=" N ILE K 54 " --> pdb=" O VAL K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 89 removed outlier: 4.127A pdb=" N ASP K 88 " --> pdb=" O SER K 85 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU K 89 " --> pdb=" O ASP K 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 85 through 89' Processing helix chain 'K' and resid 90 through 106 Processing helix chain 'L' and resid 3 through 13 Processing helix chain 'L' and resid 14 through 34 removed outlier: 3.606A pdb=" N ILE L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 50 removed outlier: 3.585A pdb=" N VAL L 50 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 64 removed outlier: 3.588A pdb=" N ASN L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.680A pdb=" N ASP L 88 " --> pdb=" O SER L 85 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU L 89 " --> pdb=" O ASP L 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 85 through 89' Processing helix chain 'L' and resid 91 through 105 Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.649A pdb=" N ILE M 9 " --> pdb=" O ARG M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 86 removed outlier: 4.127A pdb=" N VAL M 74 " --> pdb=" O LYS M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 103 Processing helix chain 'N' and resid 4 through 21 removed outlier: 3.693A pdb=" N GLY N 21 " --> pdb=" O CYS N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 86 removed outlier: 4.097A pdb=" N VAL N 74 " --> pdb=" O LYS N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 103 Processing helix chain 'O' and resid 4 through 20 removed outlier: 3.528A pdb=" N ILE O 9 " --> pdb=" O ARG O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 86 removed outlier: 4.082A pdb=" N VAL O 74 " --> pdb=" O LYS O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 103 Processing helix chain 'P' and resid 4 through 20 removed outlier: 3.611A pdb=" N ILE P 9 " --> pdb=" O ARG P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 86 removed outlier: 4.139A pdb=" N VAL P 74 " --> pdb=" O LYS P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 103 Processing helix chain 'Q' and resid 4 through 20 Processing helix chain 'Q' and resid 70 through 86 removed outlier: 4.179A pdb=" N VAL Q 74 " --> pdb=" O LYS Q 70 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 103 Processing helix chain 'R' and resid 4 through 20 Processing helix chain 'R' and resid 70 through 86 removed outlier: 4.149A pdb=" N VAL R 74 " --> pdb=" O LYS R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 103 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 74 removed outlier: 3.769A pdb=" N SER A 79 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 81 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER C 72 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 78 " --> pdb=" O GLN C 75 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 81 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER D 72 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D 79 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER D 81 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER E 72 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU E 78 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER E 81 " --> pdb=" O SER F 72 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER F 72 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER F 79 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER F 81 " --> pdb=" O SER G 72 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER G 72 " --> pdb=" O SER F 81 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU G 78 " --> pdb=" O GLN G 75 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER G 81 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER H 72 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER H 79 " --> pdb=" O SER I 74 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER H 81 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER I 72 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU I 78 " --> pdb=" O GLN I 75 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER I 81 " --> pdb=" O SER J 72 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER J 72 " --> pdb=" O SER I 81 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER J 79 " --> pdb=" O SER K 74 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER J 81 " --> pdb=" O SER K 72 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER K 72 " --> pdb=" O SER J 81 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU K 78 " --> pdb=" O GLN K 75 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER K 81 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER L 72 " --> pdb=" O SER K 81 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER L 79 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER L 81 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER B 72 " --> pdb=" O SER L 81 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 78 " --> pdb=" O GLN B 75 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER B 81 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 72 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 23 through 25 removed outlier: 6.886A pdb=" N THR M 23 " --> pdb=" O VAL M 38 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE M 40 " --> pdb=" O THR M 23 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N TYR M 25 " --> pdb=" O ILE M 40 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N GLY M 42 " --> pdb=" O TYR M 25 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N LEU M 67 " --> pdb=" O PRO M 36 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL M 38 " --> pdb=" O TRP M 65 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP M 65 " --> pdb=" O VAL M 38 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE M 40 " --> pdb=" O SER M 63 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER M 63 " --> pdb=" O ILE M 40 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY M 42 " --> pdb=" O THR M 61 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 54 through 67 current: chain 'M' and resid 117 through 127 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 117 through 127 current: chain 'N' and resid 37 through 49 removed outlier: 5.980A pdb=" N VAL N 38 " --> pdb=" O TRP N 65 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N TRP N 65 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE N 40 " --> pdb=" O SER N 63 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER N 63 " --> pdb=" O ILE N 40 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY N 42 " --> pdb=" O THR N 61 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 54 through 67 current: chain 'N' and resid 94 through 98 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 94 through 98 current: chain 'N' and resid 117 through 128 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 117 through 128 current: chain 'O' and resid 37 through 49 removed outlier: 5.995A pdb=" N VAL O 38 " --> pdb=" O TRP O 65 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TRP O 65 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE O 40 " --> pdb=" O SER O 63 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER O 63 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY O 42 " --> pdb=" O THR O 61 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 54 through 67 current: chain 'O' and resid 94 through 98 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 94 through 98 current: chain 'O' and resid 117 through 128 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 117 through 128 current: chain 'P' and resid 37 through 49 removed outlier: 5.867A pdb=" N VAL P 38 " --> pdb=" O TRP P 65 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N TRP P 65 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ILE P 40 " --> pdb=" O SER P 63 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER P 63 " --> pdb=" O ILE P 40 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY P 42 " --> pdb=" O THR P 61 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 54 through 67 current: chain 'P' and resid 117 through 127 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 117 through 127 current: chain 'Q' and resid 37 through 49 removed outlier: 5.939A pdb=" N VAL Q 38 " --> pdb=" O TRP Q 65 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TRP Q 65 " --> pdb=" O VAL Q 38 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE Q 40 " --> pdb=" O SER Q 63 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER Q 63 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY Q 42 " --> pdb=" O THR Q 61 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 54 through 67 current: chain 'Q' and resid 117 through 127 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 117 through 127 current: chain 'R' and resid 37 through 49 removed outlier: 5.733A pdb=" N VAL R 38 " --> pdb=" O TRP R 65 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TRP R 65 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE R 40 " --> pdb=" O SER R 63 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER R 63 " --> pdb=" O ILE R 40 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY R 42 " --> pdb=" O THR R 61 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 54 through 67 current: chain 'R' and resid 117 through 127 Processing sheet with id=AA3, first strand: chain 'M' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'P' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'Q' and resid 90 through 91 Processing sheet with id=AA6, first strand: chain 'R' and resid 90 through 91 Processing sheet with id=AA7, first strand: chain 'S' and resid 5 through 12 removed outlier: 5.897A pdb=" N VAL S 38 " --> pdb=" O ARG S 61 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ARG S 61 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP S 40 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL S 59 " --> pdb=" O ASP S 40 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY S 42 " --> pdb=" O ALA S 57 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA S 57 " --> pdb=" O GLY S 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN S 55 " --> pdb=" O ASP S 44 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 51 through 62 current: chain 'S' and resid 79 through 87 removed outlier: 6.757A pdb=" N ILE S 96 " --> pdb=" O LEU S 84 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE S 86 " --> pdb=" O SER S 94 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER S 94 " --> pdb=" O PHE S 86 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 93 through 99 current: chain 'T' and resid 30 through 48 removed outlier: 5.938A pdb=" N VAL T 38 " --> pdb=" O ARG T 61 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG T 61 " --> pdb=" O VAL T 38 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASP T 40 " --> pdb=" O VAL T 59 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL T 59 " --> pdb=" O ASP T 40 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY T 42 " --> pdb=" O ALA T 57 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA T 57 " --> pdb=" O GLY T 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 51 through 62 current: chain 'T' and resid 80 through 87 removed outlier: 6.776A pdb=" N ILE T 96 " --> pdb=" O LEU T 84 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE T 86 " --> pdb=" O SER T 94 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER T 94 " --> pdb=" O PHE T 86 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 93 through 99 current: chain 'U' and resid 30 through 48 removed outlier: 5.941A pdb=" N VAL U 38 " --> pdb=" O ARG U 61 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ARG U 61 " --> pdb=" O VAL U 38 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASP U 40 " --> pdb=" O VAL U 59 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL U 59 " --> pdb=" O ASP U 40 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY U 42 " --> pdb=" O ALA U 57 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA U 57 " --> pdb=" O GLY U 42 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN U 55 " --> pdb=" O ASP U 44 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 51 through 62 current: chain 'U' and resid 80 through 87 removed outlier: 6.818A pdb=" N ILE U 96 " --> pdb=" O LEU U 84 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE U 86 " --> pdb=" O SER U 94 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N SER U 94 " --> pdb=" O PHE U 86 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 93 through 99 current: chain 'V' and resid 30 through 40 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 30 through 40 current: chain 'V' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 51 through 55 current: chain 'V' and resid 79 through 87 removed outlier: 6.755A pdb=" N ILE V 96 " --> pdb=" O LEU V 84 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE V 86 " --> pdb=" O SER V 94 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER V 94 " --> pdb=" O PHE V 86 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 93 through 99 current: chain 'W' and resid 30 through 48 removed outlier: 5.956A pdb=" N VAL W 38 " --> pdb=" O ARG W 61 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ARG W 61 " --> pdb=" O VAL W 38 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASP W 40 " --> pdb=" O VAL W 59 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL W 59 " --> pdb=" O ASP W 40 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY W 42 " --> pdb=" O ALA W 57 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA W 57 " --> pdb=" O GLY W 42 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN W 55 " --> pdb=" O ASP W 44 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 51 through 62 current: chain 'W' and resid 80 through 87 removed outlier: 6.758A pdb=" N ILE W 96 " --> pdb=" O LEU W 84 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE W 86 " --> pdb=" O SER W 94 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER W 94 " --> pdb=" O PHE W 86 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 93 through 99 current: chain 'X' and resid 30 through 48 removed outlier: 5.928A pdb=" N VAL X 38 " --> pdb=" O ARG X 61 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ARG X 61 " --> pdb=" O VAL X 38 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP X 40 " --> pdb=" O VAL X 59 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL X 59 " --> pdb=" O ASP X 40 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY X 42 " --> pdb=" O ALA X 57 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA X 57 " --> pdb=" O GLY X 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN X 55 " --> pdb=" O ASP X 44 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 51 through 62 current: chain 'X' and resid 80 through 87 removed outlier: 6.849A pdb=" N ILE X 96 " --> pdb=" O LEU X 84 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE X 86 " --> pdb=" O SER X 94 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER X 94 " --> pdb=" O PHE X 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 15 through 18 removed outlier: 3.599A pdb=" N GLU S 23 " --> pdb=" O ASP S 18 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 15 through 18 removed outlier: 3.615A pdb=" N GLU T 23 " --> pdb=" O ASP T 18 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 15 through 18 removed outlier: 3.648A pdb=" N GLU U 23 " --> pdb=" O ASP U 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'V' and resid 15 through 18 removed outlier: 3.609A pdb=" N GLU V 23 " --> pdb=" O ASP V 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 15 through 18 removed outlier: 3.618A pdb=" N GLU W 23 " --> pdb=" O ASP W 18 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'X' and resid 15 through 18 removed outlier: 3.632A pdb=" N GLU X 23 " --> pdb=" O ASP X 18 " (cutoff:3.500A) 905 hydrogen bonds defined for protein. 2667 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: 3.50 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3880 1.32 - 1.44: 5793 1.44 - 1.56: 12798 1.56 - 1.68: 2 1.68 - 1.81: 138 Bond restraints: 22611 Sorted by residual: bond pdb=" CA TYR R 35 " pdb=" CB TYR R 35 " ideal model delta sigma weight residual 1.530 1.438 0.092 1.58e-02 4.01e+03 3.41e+01 bond pdb=" N PHE O 37 " pdb=" CA PHE O 37 " ideal model delta sigma weight residual 1.455 1.512 -0.057 1.25e-02 6.40e+03 2.08e+01 bond pdb=" CA LYS P 28 " pdb=" C LYS P 28 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.08e-02 8.57e+03 2.04e+01 bond pdb=" N PHE N 37 " pdb=" CA PHE N 37 " ideal model delta sigma weight residual 1.455 1.505 -0.051 1.27e-02 6.20e+03 1.59e+01 bond pdb=" CA PRO P 36 " pdb=" CB PRO P 36 " ideal model delta sigma weight residual 1.536 1.494 0.041 1.05e-02 9.07e+03 1.54e+01 ... (remaining 22606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 30303 2.86 - 5.72: 145 5.72 - 8.57: 34 8.57 - 11.43: 10 11.43 - 14.29: 6 Bond angle restraints: 30498 Sorted by residual: angle pdb=" N PHE O 37 " pdb=" CA PHE O 37 " pdb=" C PHE O 37 " ideal model delta sigma weight residual 108.96 122.76 -13.80 1.49e+00 4.50e-01 8.57e+01 angle pdb=" N PHE N 37 " pdb=" CA PHE N 37 " pdb=" C PHE N 37 " ideal model delta sigma weight residual 109.07 121.93 -12.86 1.52e+00 4.33e-01 7.16e+01 angle pdb=" N PHE P 37 " pdb=" CA PHE P 37 " pdb=" C PHE P 37 " ideal model delta sigma weight residual 109.07 120.84 -11.77 1.52e+00 4.33e-01 6.00e+01 angle pdb=" CA PRO N 36 " pdb=" C PRO N 36 " pdb=" N PHE N 37 " ideal model delta sigma weight residual 116.09 123.10 -7.01 9.20e-01 1.18e+00 5.80e+01 angle pdb=" CA TYR M 35 " pdb=" C TYR M 35 " pdb=" N PRO M 36 " ideal model delta sigma weight residual 117.59 124.80 -7.21 1.03e+00 9.43e-01 4.90e+01 ... (remaining 30493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 12235 16.79 - 33.58: 1194 33.58 - 50.37: 227 50.37 - 67.17: 35 67.17 - 83.96: 19 Dihedral angle restraints: 13710 sinusoidal: 5631 harmonic: 8079 Sorted by residual: dihedral pdb=" C TYR Q 35 " pdb=" N TYR Q 35 " pdb=" CA TYR Q 35 " pdb=" CB TYR Q 35 " ideal model delta harmonic sigma weight residual -122.60 -153.84 31.24 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" N TYR Q 35 " pdb=" C TYR Q 35 " pdb=" CA TYR Q 35 " pdb=" CB TYR Q 35 " ideal model delta harmonic sigma weight residual 122.80 153.58 -30.78 0 2.50e+00 1.60e-01 1.52e+02 dihedral pdb=" N TYR N 35 " pdb=" C TYR N 35 " pdb=" CA TYR N 35 " pdb=" CB TYR N 35 " ideal model delta harmonic sigma weight residual 122.80 153.07 -30.27 0 2.50e+00 1.60e-01 1.47e+02 ... (remaining 13707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 3474 0.283 - 0.565: 9 0.565 - 0.848: 1 0.848 - 1.130: 2 1.130 - 1.413: 3 Chirality restraints: 3489 Sorted by residual: chirality pdb=" CA TYR N 35 " pdb=" N TYR N 35 " pdb=" C TYR N 35 " pdb=" CB TYR N 35 " both_signs ideal model delta sigma weight residual False 2.51 1.10 1.41 2.00e-01 2.50e+01 4.99e+01 chirality pdb=" CA TYR Q 35 " pdb=" N TYR Q 35 " pdb=" C TYR Q 35 " pdb=" CB TYR Q 35 " both_signs ideal model delta sigma weight residual False 2.51 1.21 1.30 2.00e-01 2.50e+01 4.25e+01 chirality pdb=" CA TYR P 35 " pdb=" N TYR P 35 " pdb=" C TYR P 35 " pdb=" CB TYR P 35 " both_signs ideal model delta sigma weight residual False 2.51 1.27 1.24 2.00e-01 2.50e+01 3.84e+01 ... (remaining 3486 not shown) Planarity restraints: 3882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR M 35 " -0.081 5.00e-02 4.00e+02 1.22e-01 2.37e+01 pdb=" N PRO M 36 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO M 36 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO M 36 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR O 35 " -0.076 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO O 36 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO O 36 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO O 36 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR P 35 " 0.044 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO P 36 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO P 36 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO P 36 " 0.042 5.00e-02 4.00e+02 ... (remaining 3879 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1748 2.74 - 3.28: 19806 3.28 - 3.82: 33319 3.82 - 4.36: 36282 4.36 - 4.90: 70390 Nonbonded interactions: 161545 Sorted by model distance: nonbonded pdb=" OE1 GLU H 56 " pdb=" OH TYR H 90 " model vdw 2.200 3.040 nonbonded pdb=" OE1 GLU A 56 " pdb=" OH TYR A 90 " model vdw 2.227 3.040 nonbonded pdb=" OE1 GLU E 56 " pdb=" OH TYR E 90 " model vdw 2.236 3.040 nonbonded pdb=" OE1 GLU K 56 " pdb=" OH TYR K 90 " model vdw 2.236 3.040 nonbonded pdb=" OE1 GLU J 56 " pdb=" OH TYR J 90 " model vdw 2.240 3.040 ... (remaining 161540 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' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 1 through 128) selection = (chain 'N' and resid 1 through 128) selection = (chain 'O' and resid 1 through 128) selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 2.070 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.520 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 22611 Z= 0.219 Angle : 0.610 14.292 30498 Z= 0.370 Chirality : 0.063 1.413 3489 Planarity : 0.004 0.122 3882 Dihedral : 13.713 83.958 8484 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.62 % Favored : 97.27 % Rotamer: Outliers : 0.12 % Allowed : 0.20 % Favored : 99.68 % Cbeta Deviations : 0.27 % 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: 0.81 (0.16), residues: 2715 helix: 2.26 (0.15), residues: 1044 sheet: 1.61 (0.24), residues: 519 loop : -1.74 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 98 TYR 0.042 0.001 TYR R 35 PHE 0.041 0.001 PHE R 37 TRP 0.004 0.001 TRP R 65 HIS 0.002 0.001 HIS V 83 Details of bonding type rmsd covalent geometry : bond 0.00374 (22611) covalent geometry : angle 0.60971 (30498) hydrogen bonds : bond 0.17629 ( 905) hydrogen bonds : angle 5.50471 ( 2667) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 511 time to evaluate : 0.903 Fit side-chains REVERT: A 39 ASP cc_start: 0.8413 (t70) cc_final: 0.8153 (t0) REVERT: A 67 ASN cc_start: 0.8382 (m110) cc_final: 0.8086 (m110) REVERT: D 20 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7384 (tm-30) REVERT: D 39 ASP cc_start: 0.8083 (p0) cc_final: 0.7770 (p0) REVERT: D 67 ASN cc_start: 0.8220 (m-40) cc_final: 0.7953 (m-40) REVERT: F 67 ASN cc_start: 0.8462 (m-40) cc_final: 0.8139 (m-40) REVERT: H 39 ASP cc_start: 0.8371 (t70) cc_final: 0.8123 (t0) REVERT: H 67 ASN cc_start: 0.8342 (m110) cc_final: 0.8039 (m110) REVERT: J 20 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7394 (tm-30) REVERT: N 68 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8708 (tp40) REVERT: Q 2 ILE cc_start: 0.8462 (mt) cc_final: 0.8132 (tt) REVERT: U 40 ASP cc_start: 0.8379 (t70) cc_final: 0.8173 (t0) outliers start: 3 outliers final: 0 residues processed: 513 average time/residue: 0.1796 time to fit residues: 137.0688 Evaluate side-chains 447 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0470 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN L 105 GLN N 114 ASN U 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102712 restraints weight = 31432.181| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.01 r_work: 0.3066 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 22611 Z= 0.114 Angle : 0.453 8.595 30498 Z= 0.252 Chirality : 0.039 0.275 3489 Planarity : 0.004 0.134 3882 Dihedral : 3.849 29.262 3000 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 0.48 % Allowed : 6.99 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.16), residues: 2715 helix: 2.48 (0.15), residues: 1065 sheet: 1.26 (0.22), residues: 600 loop : -1.62 (0.16), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 98 TYR 0.016 0.001 TYR D 55 PHE 0.020 0.001 PHE R 37 TRP 0.003 0.001 TRP R 65 HIS 0.002 0.001 HIS V 83 Details of bonding type rmsd covalent geometry : bond 0.00264 (22611) covalent geometry : angle 0.45261 (30498) hydrogen bonds : bond 0.04757 ( 905) hydrogen bonds : angle 4.19219 ( 2667) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 476 time to evaluate : 0.971 Fit side-chains REVERT: A 39 ASP cc_start: 0.9053 (t70) cc_final: 0.8782 (t0) REVERT: D 20 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7949 (tm-30) REVERT: F 20 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7881 (tm-30) REVERT: F 67 ASN cc_start: 0.8600 (m-40) cc_final: 0.8206 (m-40) REVERT: H 39 ASP cc_start: 0.9008 (t70) cc_final: 0.8729 (t0) REVERT: J 20 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7892 (tm-30) REVERT: L 20 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7906 (tm-30) REVERT: N 68 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8803 (tp40) REVERT: Q 2 ILE cc_start: 0.8661 (mt) cc_final: 0.8163 (tt) REVERT: R 2 ILE cc_start: 0.9250 (mt) cc_final: 0.8920 (mt) REVERT: T 6 GLU cc_start: 0.8775 (tt0) cc_final: 0.8479 (tp30) REVERT: W 6 GLU cc_start: 0.8788 (tt0) cc_final: 0.8493 (tp30) outliers start: 12 outliers final: 6 residues processed: 483 average time/residue: 0.1896 time to fit residues: 134.0468 Evaluate side-chains 440 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 434 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain W residue 65 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 226 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN D 105 GLN H 67 ASN L 105 GLN R 114 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107490 restraints weight = 31928.380| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.97 r_work: 0.3072 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22611 Z= 0.107 Angle : 0.438 7.793 30498 Z= 0.244 Chirality : 0.039 0.250 3489 Planarity : 0.003 0.040 3882 Dihedral : 3.750 27.254 3000 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 0.60 % Allowed : 8.54 % Favored : 90.86 % 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: 1.13 (0.16), residues: 2715 helix: 2.56 (0.15), residues: 1065 sheet: 1.26 (0.22), residues: 597 loop : -1.59 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 98 TYR 0.019 0.001 TYR N 35 PHE 0.017 0.001 PHE R 37 TRP 0.002 0.000 TRP D 97 HIS 0.002 0.001 HIS S 16 Details of bonding type rmsd covalent geometry : bond 0.00246 (22611) covalent geometry : angle 0.43830 (30498) hydrogen bonds : bond 0.04386 ( 905) hydrogen bonds : angle 3.92516 ( 2667) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 455 time to evaluate : 0.930 Fit side-chains REVERT: A 39 ASP cc_start: 0.9032 (t70) cc_final: 0.8753 (t0) REVERT: D 9 MET cc_start: 0.8866 (mmp) cc_final: 0.8534 (mpp) REVERT: D 20 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7936 (tm-30) REVERT: D 68 GLU cc_start: 0.8505 (mp0) cc_final: 0.8285 (mp0) REVERT: E 68 GLU cc_start: 0.8578 (mp0) cc_final: 0.8237 (mp0) REVERT: F 20 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7829 (tm-30) REVERT: F 67 ASN cc_start: 0.8613 (m-40) cc_final: 0.8253 (m-40) REVERT: H 39 ASP cc_start: 0.8921 (t70) cc_final: 0.8578 (t0) REVERT: H 88 ASP cc_start: 0.8767 (m-30) cc_final: 0.8557 (m-30) REVERT: J 9 MET cc_start: 0.8863 (mmp) cc_final: 0.8522 (mpp) REVERT: J 20 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7899 (tm-30) REVERT: L 20 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7820 (tm-30) REVERT: N 68 GLN cc_start: 0.9291 (tm-30) cc_final: 0.8820 (tp40) REVERT: Q 2 ILE cc_start: 0.8673 (mt) cc_final: 0.8159 (tt) REVERT: R 2 ILE cc_start: 0.9239 (mt) cc_final: 0.8906 (mt) REVERT: T 6 GLU cc_start: 0.8785 (tt0) cc_final: 0.8533 (tp30) REVERT: W 6 GLU cc_start: 0.8779 (tt0) cc_final: 0.8524 (tp30) outliers start: 15 outliers final: 11 residues processed: 468 average time/residue: 0.1945 time to fit residues: 132.5733 Evaluate side-chains 450 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 439 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain J residue 8 LYS Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain W residue 65 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 21 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 256 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 GLN K 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107104 restraints weight = 31830.024| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.97 r_work: 0.3068 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 22611 Z= 0.112 Angle : 0.433 7.365 30498 Z= 0.241 Chirality : 0.039 0.223 3489 Planarity : 0.003 0.049 3882 Dihedral : 3.729 29.766 3000 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.91 % Favored : 97.05 % Rotamer: Outliers : 0.75 % Allowed : 10.13 % Favored : 89.11 % 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: 1.18 (0.16), residues: 2715 helix: 2.60 (0.15), residues: 1068 sheet: 1.28 (0.22), residues: 603 loop : -1.61 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 98 TYR 0.018 0.001 TYR P 35 PHE 0.015 0.001 PHE R 37 TRP 0.002 0.000 TRP V 24 HIS 0.003 0.001 HIS S 16 Details of bonding type rmsd covalent geometry : bond 0.00261 (22611) covalent geometry : angle 0.43350 (30498) hydrogen bonds : bond 0.04392 ( 905) hydrogen bonds : angle 3.81435 ( 2667) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 456 time to evaluate : 0.923 Fit side-chains REVERT: A 39 ASP cc_start: 0.9013 (t70) cc_final: 0.8705 (t0) REVERT: D 20 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7955 (tm-30) REVERT: F 20 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7879 (tm-30) REVERT: F 67 ASN cc_start: 0.8583 (m-40) cc_final: 0.8247 (m-40) REVERT: G 9 MET cc_start: 0.8911 (tpp) cc_final: 0.8574 (tpt) REVERT: H 39 ASP cc_start: 0.8913 (t70) cc_final: 0.8563 (t0) REVERT: H 88 ASP cc_start: 0.8712 (m-30) cc_final: 0.8007 (m-30) REVERT: J 20 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7907 (tm-30) REVERT: L 20 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7874 (tm-30) REVERT: R 2 ILE cc_start: 0.9210 (mt) cc_final: 0.8918 (mt) REVERT: R 27 TYR cc_start: 0.8644 (t80) cc_final: 0.8372 (t80) REVERT: T 6 GLU cc_start: 0.8838 (tt0) cc_final: 0.8598 (tp30) REVERT: W 6 GLU cc_start: 0.8867 (tt0) cc_final: 0.8613 (tp30) REVERT: W 45 ARG cc_start: 0.8394 (ttm170) cc_final: 0.8187 (ttt180) outliers start: 19 outliers final: 12 residues processed: 471 average time/residue: 0.1923 time to fit residues: 132.1515 Evaluate side-chains 446 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 434 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain J residue 8 LYS Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain W residue 65 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 76 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 0.0470 chunk 220 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 210 optimal weight: 0.5980 chunk 122 optimal weight: 0.0040 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.6292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110378 restraints weight = 31682.769| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.98 r_work: 0.3106 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22611 Z= 0.082 Angle : 0.401 6.198 30498 Z= 0.224 Chirality : 0.037 0.178 3489 Planarity : 0.002 0.042 3882 Dihedral : 3.506 28.517 3000 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.69 % Favored : 97.27 % Rotamer: Outliers : 0.56 % Allowed : 11.28 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.35 (0.16), residues: 2715 helix: 2.39 (0.15), residues: 1131 sheet: 1.48 (0.22), residues: 606 loop : -1.40 (0.17), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 98 TYR 0.013 0.001 TYR N 35 PHE 0.011 0.001 PHE P 37 TRP 0.003 0.000 TRP S 24 HIS 0.002 0.001 HIS X 16 Details of bonding type rmsd covalent geometry : bond 0.00179 (22611) covalent geometry : angle 0.40100 (30498) hydrogen bonds : bond 0.03349 ( 905) hydrogen bonds : angle 3.63055 ( 2667) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 463 time to evaluate : 0.854 Fit side-chains REVERT: A 39 ASP cc_start: 0.8949 (t70) cc_final: 0.8627 (t0) REVERT: D 20 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7938 (tm-30) REVERT: F 20 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7801 (tm-30) REVERT: F 67 ASN cc_start: 0.8553 (m-40) cc_final: 0.8302 (m-40) REVERT: G 9 MET cc_start: 0.8866 (tpp) cc_final: 0.8514 (tpt) REVERT: G 70 MET cc_start: 0.8829 (mtt) cc_final: 0.8564 (mtm) REVERT: H 39 ASP cc_start: 0.8889 (t70) cc_final: 0.8546 (t0) REVERT: H 88 ASP cc_start: 0.8681 (m-30) cc_final: 0.7990 (m-30) REVERT: J 20 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7897 (tm-30) REVERT: L 20 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7760 (tm-30) REVERT: Q 2 ILE cc_start: 0.8626 (mt) cc_final: 0.8133 (tt) REVERT: S 77 ASP cc_start: 0.8226 (t0) cc_final: 0.8013 (t0) REVERT: T 6 GLU cc_start: 0.8846 (tt0) cc_final: 0.8610 (tp30) REVERT: V 77 ASP cc_start: 0.8206 (t0) cc_final: 0.8000 (t0) REVERT: W 6 GLU cc_start: 0.8850 (tt0) cc_final: 0.8608 (tp30) outliers start: 14 outliers final: 8 residues processed: 473 average time/residue: 0.1892 time to fit residues: 130.9255 Evaluate side-chains 454 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 446 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain O residue 97 SER Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 55 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 236 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 250 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 234 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 245 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108864 restraints weight = 31961.392| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.98 r_work: 0.3082 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22611 Z= 0.095 Angle : 0.411 6.454 30498 Z= 0.228 Chirality : 0.038 0.182 3489 Planarity : 0.003 0.042 3882 Dihedral : 3.514 27.799 3000 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 0.56 % Allowed : 12.48 % Favored : 86.97 % 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: 1.32 (0.16), residues: 2715 helix: 2.40 (0.15), residues: 1131 sheet: 1.46 (0.22), residues: 609 loop : -1.47 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 98 TYR 0.013 0.001 TYR N 35 PHE 0.011 0.001 PHE R 37 TRP 0.003 0.000 TRP S 24 HIS 0.002 0.001 HIS S 16 Details of bonding type rmsd covalent geometry : bond 0.00217 (22611) covalent geometry : angle 0.41056 (30498) hydrogen bonds : bond 0.03828 ( 905) hydrogen bonds : angle 3.56405 ( 2667) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 459 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8915 (t70) cc_final: 0.8603 (t0) REVERT: D 9 MET cc_start: 0.8890 (mmp) cc_final: 0.8658 (tpp) REVERT: D 20 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7981 (tm-30) REVERT: F 20 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7848 (tm-30) REVERT: F 56 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8069 (mt-10) REVERT: F 67 ASN cc_start: 0.8623 (m-40) cc_final: 0.8320 (m-40) REVERT: G 9 MET cc_start: 0.8893 (tpp) cc_final: 0.8526 (tpt) REVERT: H 39 ASP cc_start: 0.8854 (t70) cc_final: 0.8511 (t0) REVERT: H 88 ASP cc_start: 0.8617 (m-30) cc_final: 0.7932 (m-30) REVERT: J 9 MET cc_start: 0.8867 (mmp) cc_final: 0.8633 (tpp) REVERT: J 20 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7963 (tm-30) REVERT: L 56 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7978 (mt-10) REVERT: Q 2 ILE cc_start: 0.8614 (mt) cc_final: 0.8149 (tt) REVERT: R 97 SER cc_start: 0.9056 (t) cc_final: 0.8728 (m) REVERT: T 6 GLU cc_start: 0.8863 (tt0) cc_final: 0.8628 (tp30) REVERT: W 6 GLU cc_start: 0.8868 (tt0) cc_final: 0.8624 (tp30) outliers start: 14 outliers final: 11 residues processed: 470 average time/residue: 0.1855 time to fit residues: 128.3095 Evaluate side-chains 456 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 445 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain O residue 97 SER Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain V residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 119 optimal weight: 6.9990 chunk 254 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 246 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 180 optimal weight: 0.2980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107183 restraints weight = 31738.965| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.99 r_work: 0.3057 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22611 Z= 0.117 Angle : 0.443 6.916 30498 Z= 0.245 Chirality : 0.039 0.208 3489 Planarity : 0.003 0.042 3882 Dihedral : 3.622 26.877 3000 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 0.64 % Allowed : 12.83 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.16), residues: 2715 helix: 2.37 (0.15), residues: 1128 sheet: 1.55 (0.21), residues: 606 loop : -1.46 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 98 TYR 0.016 0.001 TYR N 35 PHE 0.013 0.001 PHE R 37 TRP 0.003 0.000 TRP O 65 HIS 0.003 0.001 HIS S 16 Details of bonding type rmsd covalent geometry : bond 0.00277 (22611) covalent geometry : angle 0.44290 (30498) hydrogen bonds : bond 0.04371 ( 905) hydrogen bonds : angle 3.60452 ( 2667) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 452 time to evaluate : 0.942 Fit side-chains REVERT: A 39 ASP cc_start: 0.8882 (t70) cc_final: 0.8529 (t0) REVERT: D 9 MET cc_start: 0.8909 (mmp) cc_final: 0.8673 (tpp) REVERT: D 20 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7976 (tm-30) REVERT: F 20 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8048 (tm-30) REVERT: F 56 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8198 (mt-10) REVERT: F 67 ASN cc_start: 0.8689 (m-40) cc_final: 0.8338 (m-40) REVERT: G 9 MET cc_start: 0.8948 (tpp) cc_final: 0.8591 (tpt) REVERT: H 39 ASP cc_start: 0.8879 (t70) cc_final: 0.8560 (t0) REVERT: H 88 ASP cc_start: 0.8684 (m-30) cc_final: 0.8017 (m-30) REVERT: J 9 MET cc_start: 0.8898 (mmp) cc_final: 0.8659 (tpp) REVERT: J 20 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7971 (tm-30) REVERT: L 56 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8106 (mt-10) REVERT: Q 97 SER cc_start: 0.9085 (t) cc_final: 0.8756 (m) REVERT: R 97 SER cc_start: 0.9054 (t) cc_final: 0.8733 (m) REVERT: T 6 GLU cc_start: 0.8885 (tt0) cc_final: 0.8642 (tp30) REVERT: W 6 GLU cc_start: 0.8874 (tt0) cc_final: 0.8643 (tp30) REVERT: W 45 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.8023 (ttt180) outliers start: 16 outliers final: 13 residues processed: 463 average time/residue: 0.1922 time to fit residues: 130.2700 Evaluate side-chains 443 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 430 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain J residue 8 LYS Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain O residue 97 SER Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain W residue 65 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 21 optimal weight: 5.9990 chunk 141 optimal weight: 0.3980 chunk 148 optimal weight: 7.9990 chunk 263 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 GLN E 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.104695 restraints weight = 31818.971| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.96 r_work: 0.3024 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22611 Z= 0.156 Angle : 0.487 7.741 30498 Z= 0.269 Chirality : 0.040 0.248 3489 Planarity : 0.003 0.047 3882 Dihedral : 3.851 27.782 3000 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.54 % Rotamer: Outliers : 0.68 % Allowed : 13.39 % Favored : 85.94 % 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: 1.17 (0.16), residues: 2715 helix: 2.62 (0.15), residues: 1065 sheet: 1.33 (0.22), residues: 606 loop : -1.68 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 98 TYR 0.021 0.001 TYR R 35 PHE 0.015 0.001 PHE R 37 TRP 0.005 0.001 TRP P 65 HIS 0.004 0.001 HIS S 16 Details of bonding type rmsd covalent geometry : bond 0.00380 (22611) covalent geometry : angle 0.48677 (30498) hydrogen bonds : bond 0.05264 ( 905) hydrogen bonds : angle 3.73474 ( 2667) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 426 time to evaluate : 0.957 Fit side-chains REVERT: A 39 ASP cc_start: 0.8933 (t70) cc_final: 0.8582 (t0) REVERT: D 9 MET cc_start: 0.8909 (mmp) cc_final: 0.8686 (tpp) REVERT: F 20 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8170 (tm-30) REVERT: F 56 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8286 (mt-10) REVERT: F 67 ASN cc_start: 0.8732 (m-40) cc_final: 0.8334 (m-40) REVERT: G 9 MET cc_start: 0.8964 (tpp) cc_final: 0.8604 (tpt) REVERT: H 39 ASP cc_start: 0.8947 (t70) cc_final: 0.8610 (t0) REVERT: H 88 ASP cc_start: 0.8756 (m-30) cc_final: 0.8131 (m-30) REVERT: Q 27 TYR cc_start: 0.8633 (t80) cc_final: 0.8334 (t80) REVERT: Q 97 SER cc_start: 0.9081 (t) cc_final: 0.8746 (m) REVERT: R 27 TYR cc_start: 0.8650 (t80) cc_final: 0.8444 (t80) REVERT: R 97 SER cc_start: 0.9067 (t) cc_final: 0.8731 (m) REVERT: R 114 ASN cc_start: 0.9016 (m-40) cc_final: 0.8793 (m110) REVERT: T 6 GLU cc_start: 0.8921 (tt0) cc_final: 0.8651 (tp30) REVERT: W 6 GLU cc_start: 0.8914 (tt0) cc_final: 0.8662 (tp30) outliers start: 17 outliers final: 12 residues processed: 438 average time/residue: 0.1923 time to fit residues: 122.8300 Evaluate side-chains 434 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 422 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain O residue 97 SER Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 41 LEU Chi-restraints excluded: chain V residue 30 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 198 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 226 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 231 optimal weight: 0.0980 chunk 237 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.115583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.101753 restraints weight = 31458.053| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.08 r_work: 0.3055 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22611 Z= 0.111 Angle : 0.458 6.785 30498 Z= 0.254 Chirality : 0.038 0.207 3489 Planarity : 0.003 0.039 3882 Dihedral : 3.710 26.101 3000 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 0.52 % Allowed : 14.18 % Favored : 85.30 % 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: 1.17 (0.16), residues: 2715 helix: 2.34 (0.15), residues: 1125 sheet: 1.31 (0.22), residues: 609 loop : -1.55 (0.17), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 98 TYR 0.016 0.001 TYR N 35 PHE 0.013 0.001 PHE R 37 TRP 0.002 0.000 TRP S 24 HIS 0.003 0.001 HIS S 16 Details of bonding type rmsd covalent geometry : bond 0.00259 (22611) covalent geometry : angle 0.45814 (30498) hydrogen bonds : bond 0.04166 ( 905) hydrogen bonds : angle 3.63731 ( 2667) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 434 time to evaluate : 0.975 Fit side-chains REVERT: A 39 ASP cc_start: 0.8912 (t70) cc_final: 0.8564 (t0) REVERT: F 56 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8215 (mt-10) REVERT: F 67 ASN cc_start: 0.8703 (m-40) cc_final: 0.8396 (m-40) REVERT: G 9 MET cc_start: 0.8945 (tpp) cc_final: 0.8586 (tpt) REVERT: H 39 ASP cc_start: 0.8959 (t70) cc_final: 0.8635 (t0) REVERT: H 88 ASP cc_start: 0.8731 (m-30) cc_final: 0.8040 (m-30) REVERT: J 20 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8039 (tm-30) REVERT: Q 27 TYR cc_start: 0.8588 (t80) cc_final: 0.8281 (t80) REVERT: Q 97 SER cc_start: 0.9093 (t) cc_final: 0.8764 (m) REVERT: R 27 TYR cc_start: 0.8628 (t80) cc_final: 0.8335 (t80) REVERT: R 97 SER cc_start: 0.9078 (t) cc_final: 0.8749 (m) REVERT: T 6 GLU cc_start: 0.8912 (tt0) cc_final: 0.8663 (tp30) REVERT: W 6 GLU cc_start: 0.8903 (tt0) cc_final: 0.8664 (tp30) outliers start: 13 outliers final: 12 residues processed: 442 average time/residue: 0.1845 time to fit residues: 119.1213 Evaluate side-chains 440 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 428 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain J residue 8 LYS Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain O residue 97 SER Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 41 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 40 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 249 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.119030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105828 restraints weight = 31956.727| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.96 r_work: 0.3041 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22611 Z= 0.130 Angle : 0.471 7.344 30498 Z= 0.262 Chirality : 0.039 0.225 3489 Planarity : 0.003 0.041 3882 Dihedral : 3.761 25.816 3000 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.65 % Rotamer: Outliers : 0.56 % Allowed : 14.18 % Favored : 85.26 % 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: 1.19 (0.16), residues: 2715 helix: 2.66 (0.15), residues: 1065 sheet: 1.32 (0.22), residues: 603 loop : -1.66 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 45 TYR 0.017 0.001 TYR R 35 PHE 0.013 0.001 PHE R 37 TRP 0.004 0.001 TRP P 65 HIS 0.003 0.001 HIS S 16 Details of bonding type rmsd covalent geometry : bond 0.00312 (22611) covalent geometry : angle 0.47058 (30498) hydrogen bonds : bond 0.04641 ( 905) hydrogen bonds : angle 3.64575 ( 2667) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5430 Ramachandran restraints generated. 2715 Oldfield, 0 Emsley, 2715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 429 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8921 (t70) cc_final: 0.8561 (t0) REVERT: F 41 GLU cc_start: 0.8335 (mp0) cc_final: 0.8111 (mp0) REVERT: F 56 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8219 (mt-10) REVERT: F 67 ASN cc_start: 0.8721 (m-40) cc_final: 0.8359 (m-40) REVERT: G 9 MET cc_start: 0.8944 (tpp) cc_final: 0.8582 (tpt) REVERT: H 39 ASP cc_start: 0.8962 (t70) cc_final: 0.8632 (t0) REVERT: H 88 ASP cc_start: 0.8729 (m-30) cc_final: 0.8031 (m-30) REVERT: J 20 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7985 (tm-30) REVERT: Q 27 TYR cc_start: 0.8609 (t80) cc_final: 0.8309 (t80) REVERT: Q 68 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8917 (tm-30) REVERT: Q 97 SER cc_start: 0.9091 (t) cc_final: 0.8757 (m) REVERT: R 27 TYR cc_start: 0.8627 (t80) cc_final: 0.8335 (t80) REVERT: R 97 SER cc_start: 0.9067 (t) cc_final: 0.8725 (m) REVERT: T 6 GLU cc_start: 0.8910 (tt0) cc_final: 0.8645 (tp30) REVERT: W 6 GLU cc_start: 0.8907 (tt0) cc_final: 0.8659 (tp30) outliers start: 14 outliers final: 13 residues processed: 439 average time/residue: 0.1653 time to fit residues: 107.0824 Evaluate side-chains 431 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 418 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain J residue 8 LYS Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain O residue 97 SER Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain V residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 127 optimal weight: 5.9990 chunk 177 optimal weight: 0.3980 chunk 220 optimal weight: 0.9990 chunk 97 optimal weight: 0.0050 chunk 242 optimal weight: 1.9990 chunk 230 optimal weight: 0.1980 chunk 83 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 255 optimal weight: 3.9990 chunk 53 optimal weight: 0.0670 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 GLN O 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107412 restraints weight = 31145.455| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.00 r_work: 0.3139 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22611 Z= 0.086 Angle : 0.427 6.729 30498 Z= 0.236 Chirality : 0.037 0.140 3489 Planarity : 0.003 0.038 3882 Dihedral : 3.379 22.015 3000 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.43 % Favored : 97.53 % Rotamer: Outliers : 0.28 % Allowed : 14.70 % Favored : 85.02 % 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: 1.43 (0.16), residues: 2715 helix: 2.46 (0.15), residues: 1134 sheet: 1.50 (0.22), residues: 609 loop : -1.38 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 45 TYR 0.007 0.001 TYR N 35 PHE 0.007 0.001 PHE N 37 TRP 0.003 0.000 TRP D 97 HIS 0.003 0.001 HIS T 16 Details of bonding type rmsd covalent geometry : bond 0.00186 (22611) covalent geometry : angle 0.42652 (30498) hydrogen bonds : bond 0.02806 ( 905) hydrogen bonds : angle 3.44618 ( 2667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5163.09 seconds wall clock time: 89 minutes 22.02 seconds (5362.02 seconds total)