Starting phenix.real_space_refine on Wed May 21 10:10:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tsl_41595/05_2025/8tsl_41595.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tsl_41595/05_2025/8tsl_41595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tsl_41595/05_2025/8tsl_41595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tsl_41595/05_2025/8tsl_41595.map" model { file = "/net/cci-nas-00/data/ceres_data/8tsl_41595/05_2025/8tsl_41595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tsl_41595/05_2025/8tsl_41595.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 102 5.16 5 C 13868 2.51 5 N 3682 2.21 5 O 3740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21392 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2039 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 16, 'TRANS': 239} Chain: "D" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2039 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 16, 'TRANS': 239} Chain: "E" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1690 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 197} Chain breaks: 2 Chain: "F" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1642 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain breaks: 2 Chain: "G" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1792 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 8, 'TRANS': 211} Chain breaks: 2 Chain: "H" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1762 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 206} Chain breaks: 2 Chain: "I" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1690 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 197} Chain breaks: 2 Chain: "J" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1642 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain breaks: 2 Chain: "K" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1792 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 8, 'TRANS': 211} Chain breaks: 2 Chain: "L" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1762 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 206} Chain breaks: 2 Chain: "A" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1771 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "B" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1771 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Time building chain proxies: 12.65, per 1000 atoms: 0.59 Number of scatterers: 21392 At special positions: 0 Unit cell: (130.68, 132.84, 152.28, 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 102 16.00 O 3740 8.00 N 3682 7.00 C 13868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 138 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS I 138 " - pdb=" SG CYS J 77 " distance=2.03 Simple disulfide: pdb=" SG CYS J 138 " - pdb=" SG CYS K 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.81 Conformation dependent library (CDL) restraints added in 2.8 seconds 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5028 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 12 sheets defined 65.5% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'C' and resid 15 through 36 removed outlier: 3.602A pdb=" N ILE C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 69 removed outlier: 3.863A pdb=" N TRP C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Proline residue: C 50 - end of helix removed outlier: 3.834A pdb=" N HIS C 53 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER C 62 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 97 removed outlier: 3.540A pdb=" N PHE C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY C 81 " --> pdb=" O PHE C 77 " (cutoff:3.500A) Proline residue: C 84 - end of helix removed outlier: 3.546A pdb=" N GLU C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.557A pdb=" N SER C 101 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 102 " --> pdb=" O ILE C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 102' Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.595A pdb=" N TYR C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 141 removed outlier: 3.953A pdb=" N THR C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 176 removed outlier: 3.622A pdb=" N LEU C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 197 removed outlier: 4.365A pdb=" N ARG C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Proline residue: C 192 - end of helix removed outlier: 4.087A pdb=" N PHE C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 217 through 231 removed outlier: 3.578A pdb=" N HIS C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 263 Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.568A pdb=" N ALA C 268 " --> pdb=" O ARG C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 36 Processing helix chain 'D' and resid 41 through 69 removed outlier: 3.895A pdb=" N TRP D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Proline residue: D 50 - end of helix removed outlier: 3.841A pdb=" N HIS D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER D 62 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 97 removed outlier: 3.514A pdb=" N PHE D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY D 81 " --> pdb=" O PHE D 77 " (cutoff:3.500A) Proline residue: D 84 - end of helix removed outlier: 3.614A pdb=" N GLU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 removed outlier: 3.531A pdb=" N SER D 101 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN D 102 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ARG D 103 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLY D 104 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE D 106 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 141 removed outlier: 3.561A pdb=" N THR D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 176 removed outlier: 3.578A pdb=" N LEU D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 197 removed outlier: 4.471A pdb=" N ARG D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Proline residue: D 192 - end of helix removed outlier: 4.077A pdb=" N PHE D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 210 through 215 Processing helix chain 'D' and resid 217 through 231 removed outlier: 3.572A pdb=" N HIS D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 263 Processing helix chain 'E' and resid 12 through 31 Proline residue: E 22 - end of helix Processing helix chain 'E' and resid 72 through 84 removed outlier: 3.614A pdb=" N THR E 76 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 97 Processing helix chain 'E' and resid 97 through 103 removed outlier: 3.534A pdb=" N GLY E 103 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 129 Processing helix chain 'E' and resid 149 through 177 removed outlier: 3.810A pdb=" N SER E 172 " --> pdb=" O VAL E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 319 removed outlier: 3.798A pdb=" N THR E 318 " --> pdb=" O ILE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 369 Processing helix chain 'F' and resid 6 through 10 removed outlier: 3.737A pdb=" N LEU F 9 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR F 10 " --> pdb=" O SER F 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 6 through 10' Processing helix chain 'F' and resid 11 through 19 Processing helix chain 'F' and resid 19 through 32 Processing helix chain 'F' and resid 73 through 84 removed outlier: 4.015A pdb=" N HIS F 84 " --> pdb=" O GLN F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 97 removed outlier: 3.712A pdb=" N LEU F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 103 Processing helix chain 'F' and resid 118 through 129 Processing helix chain 'F' and resid 149 through 176 removed outlier: 3.791A pdb=" N MET F 175 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 369 removed outlier: 3.672A pdb=" N ASN F 344 " --> pdb=" O ARG F 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 10 through 33 Proline residue: G 22 - end of helix Processing helix chain 'G' and resid 73 through 84 removed outlier: 4.306A pdb=" N HIS G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 97 Processing helix chain 'G' and resid 97 through 102 Processing helix chain 'G' and resid 118 through 129 Processing helix chain 'G' and resid 149 through 180 removed outlier: 4.293A pdb=" N MET G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY G 180 " --> pdb=" O ALA G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 319 Processing helix chain 'G' and resid 340 through 367 Processing helix chain 'H' and resid 11 through 32 removed outlier: 3.885A pdb=" N GLN H 15 " --> pdb=" O ALA H 11 " (cutoff:3.500A) Proline residue: H 22 - end of helix Processing helix chain 'H' and resid 72 through 84 removed outlier: 4.379A pdb=" N HIS H 84 " --> pdb=" O GLN H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 97 Processing helix chain 'H' and resid 97 through 103 Processing helix chain 'H' and resid 118 through 129 Processing helix chain 'H' and resid 149 through 180 removed outlier: 3.682A pdb=" N GLN H 154 " --> pdb=" O PRO H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 317 Processing helix chain 'H' and resid 340 through 367 Processing helix chain 'I' and resid 12 through 31 Proline residue: I 22 - end of helix Processing helix chain 'I' and resid 72 through 84 removed outlier: 3.507A pdb=" N THR I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS I 84 " --> pdb=" O GLN I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 97 Processing helix chain 'I' and resid 97 through 103 removed outlier: 3.534A pdb=" N GLY I 103 " --> pdb=" O ARG I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 129 Processing helix chain 'I' and resid 149 through 177 removed outlier: 3.795A pdb=" N SER I 172 " --> pdb=" O VAL I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 315 through 319 removed outlier: 3.783A pdb=" N THR I 318 " --> pdb=" O ILE I 315 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 369 Processing helix chain 'J' and resid 4 through 9 Processing helix chain 'J' and resid 10 through 19 removed outlier: 3.635A pdb=" N LEU J 14 " --> pdb=" O THR J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 32 Processing helix chain 'J' and resid 73 through 84 removed outlier: 4.029A pdb=" N HIS J 84 " --> pdb=" O GLN J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 97 removed outlier: 3.689A pdb=" N LEU J 89 " --> pdb=" O SER J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 103 Processing helix chain 'J' and resid 118 through 129 Processing helix chain 'J' and resid 149 through 176 removed outlier: 3.798A pdb=" N MET J 175 " --> pdb=" O LEU J 171 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA J 176 " --> pdb=" O SER J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 341 through 369 removed outlier: 3.751A pdb=" N HIS J 369 " --> pdb=" O THR J 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 10 through 33 Proline residue: K 22 - end of helix Processing helix chain 'K' and resid 73 through 84 removed outlier: 4.287A pdb=" N HIS K 84 " --> pdb=" O GLN K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 97 Processing helix chain 'K' and resid 97 through 103 removed outlier: 3.536A pdb=" N GLY K 103 " --> pdb=" O ARG K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 129 Processing helix chain 'K' and resid 149 through 180 removed outlier: 4.295A pdb=" N MET K 175 " --> pdb=" O LEU K 171 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA K 176 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 319 Processing helix chain 'K' and resid 340 through 368 Processing helix chain 'L' and resid 11 through 32 removed outlier: 3.800A pdb=" N GLN L 15 " --> pdb=" O ALA L 11 " (cutoff:3.500A) Proline residue: L 22 - end of helix Processing helix chain 'L' and resid 72 through 84 removed outlier: 4.383A pdb=" N HIS L 84 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 97 Processing helix chain 'L' and resid 97 through 103 Processing helix chain 'L' and resid 118 through 129 Processing helix chain 'L' and resid 149 through 181 removed outlier: 3.692A pdb=" N GLN L 154 " --> pdb=" O PRO L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 Processing helix chain 'L' and resid 340 through 367 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 98 through 114 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 127 through 141 Processing helix chain 'A' and resid 152 through 155 removed outlier: 3.778A pdb=" N VAL A 155 " --> pdb=" O ALA A 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 152 through 155' Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 183 through 191 removed outlier: 3.618A pdb=" N ILE A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 225 Processing helix chain 'B' and resid 43 through 52 Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.546A pdb=" N TYR B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 114 removed outlier: 3.652A pdb=" N GLU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 removed outlier: 4.117A pdb=" N HIS B 118 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 127 through 142 removed outlier: 4.077A pdb=" N PHE B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 removed outlier: 3.631A pdb=" N VAL B 155 " --> pdb=" O ALA B 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 152 through 155' Processing helix chain 'B' and resid 157 through 172 Processing helix chain 'B' and resid 183 through 191 removed outlier: 3.513A pdb=" N ILE B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 225 Processing sheet with id=AA1, first strand: chain 'E' and resid 130 through 135 removed outlier: 3.765A pdb=" N LEU E 140 " --> pdb=" O ASP E 135 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR E 45 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL E 326 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG E 47 " --> pdb=" O LEU E 324 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU E 324 " --> pdb=" O ARG E 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 130 through 134 removed outlier: 6.531A pdb=" N VAL F 43 " --> pdb=" O VAL F 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 130 through 135 removed outlier: 6.377A pdb=" N VAL G 43 " --> pdb=" O VAL G 327 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 130 through 134 removed outlier: 7.032A pdb=" N THR H 45 " --> pdb=" O VAL H 326 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL H 326 " --> pdb=" O THR H 45 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG H 47 " --> pdb=" O LEU H 324 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU H 324 " --> pdb=" O ARG H 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 130 through 135 removed outlier: 3.778A pdb=" N LEU I 140 " --> pdb=" O ASP I 135 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR I 45 " --> pdb=" O VAL I 326 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL I 326 " --> pdb=" O THR I 45 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG I 47 " --> pdb=" O LEU I 324 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU I 324 " --> pdb=" O ARG I 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 130 through 134 removed outlier: 6.539A pdb=" N VAL J 43 " --> pdb=" O VAL J 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 130 through 135 removed outlier: 6.364A pdb=" N VAL K 43 " --> pdb=" O VAL K 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 130 through 134 removed outlier: 6.395A pdb=" N VAL L 43 " --> pdb=" O VAL L 327 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 16 through 28 removed outlier: 6.322A pdb=" N LYS A 9 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 22 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 7 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 24 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG A 5 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE A 26 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU A 3 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A 7 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU A 59 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 68 through 71 removed outlier: 4.836A pdb=" N LEU A 148 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP A 150 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR A 147 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL A 180 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A 149 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY A 35 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A 197 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 37 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 16 through 27 removed outlier: 6.311A pdb=" N ARG B 18 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR B 13 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL B 20 " --> pdb=" O TYR B 11 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N TYR B 11 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ARG B 22 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LYS B 9 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE B 26 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ARG B 5 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 7 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU B 59 " --> pdb=" O LEU B 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 68 through 71 removed outlier: 4.620A pdb=" N LEU B 148 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASP B 150 " --> pdb=" O PRO B 71 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE B 34 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY B 35 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL B 197 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 37 " --> pdb=" O VAL B 197 " (cutoff:3.500A) 1348 hydrogen bonds defined for protein. 3924 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: 6.50 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6803 1.34 - 1.46: 4420 1.46 - 1.58: 10467 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 21858 Sorted by residual: bond pdb=" N VAL F 132 " pdb=" CA VAL F 132 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.20e-02 6.94e+03 8.31e+00 bond pdb=" N VAL H 351 " pdb=" CA VAL H 351 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.01e+00 bond pdb=" N VAL H 350 " pdb=" CA VAL H 350 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.34e+00 bond pdb=" N LEU F 133 " pdb=" CA LEU F 133 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.27e-02 6.20e+03 7.16e+00 bond pdb=" N ASP F 135 " pdb=" CA ASP F 135 " ideal model delta sigma weight residual 1.455 1.488 -0.034 1.27e-02 6.20e+03 6.99e+00 ... (remaining 21853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 28847 1.78 - 3.55: 641 3.55 - 5.33: 93 5.33 - 7.10: 60 7.10 - 8.88: 11 Bond angle restraints: 29652 Sorted by residual: angle pdb=" CB LYS D 33 " pdb=" CG LYS D 33 " pdb=" CD LYS D 33 " ideal model delta sigma weight residual 111.30 119.82 -8.52 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CA LYS D 33 " pdb=" CB LYS D 33 " pdb=" CG LYS D 33 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 angle pdb=" CA ASP K 368 " pdb=" CB ASP K 368 " pdb=" CG ASP K 368 " ideal model delta sigma weight residual 112.60 116.25 -3.65 1.00e+00 1.00e+00 1.33e+01 angle pdb=" CB GLN J 94 " pdb=" CG GLN J 94 " pdb=" CD GLN J 94 " ideal model delta sigma weight residual 112.60 118.39 -5.79 1.70e+00 3.46e-01 1.16e+01 angle pdb=" CB GLN F 94 " pdb=" CG GLN F 94 " pdb=" CD GLN F 94 " ideal model delta sigma weight residual 112.60 118.38 -5.78 1.70e+00 3.46e-01 1.16e+01 ... (remaining 29647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11171 17.99 - 35.98: 1376 35.98 - 53.98: 424 53.98 - 71.97: 82 71.97 - 89.96: 25 Dihedral angle restraints: 13078 sinusoidal: 5318 harmonic: 7760 Sorted by residual: dihedral pdb=" CB CYS F 138 " pdb=" SG CYS F 138 " pdb=" SG CYS G 77 " pdb=" CB CYS G 77 " ideal model delta sinusoidal sigma weight residual -86.00 -174.82 88.82 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS J 138 " pdb=" SG CYS J 138 " pdb=" SG CYS K 77 " pdb=" CB CYS K 77 " ideal model delta sinusoidal sigma weight residual 93.00 179.87 -86.87 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS I 138 " pdb=" SG CYS I 138 " pdb=" SG CYS J 77 " pdb=" CB CYS J 77 " ideal model delta sinusoidal sigma weight residual -86.00 -28.86 -57.14 1 1.00e+01 1.00e-02 4.39e+01 ... (remaining 13075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2650 0.049 - 0.099: 569 0.099 - 0.148: 157 0.148 - 0.198: 27 0.198 - 0.247: 3 Chirality restraints: 3406 Sorted by residual: chirality pdb=" CB ILE C 206 " pdb=" CA ILE C 206 " pdb=" CG1 ILE C 206 " pdb=" CG2 ILE C 206 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB ILE D 206 " pdb=" CA ILE D 206 " pdb=" CG1 ILE D 206 " pdb=" CG2 ILE D 206 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE C 179 " pdb=" CA ILE C 179 " pdb=" CG1 ILE C 179 " pdb=" CG2 ILE C 179 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 9.99e-01 ... (remaining 3403 not shown) Planarity restraints: 3720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 179 " -0.066 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO C 180 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 180 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 180 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG K 367 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C ARG K 367 " -0.058 2.00e-02 2.50e+03 pdb=" O ARG K 367 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP K 368 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 30 " -0.276 9.50e-02 1.11e+02 1.24e-01 9.40e+00 pdb=" NE ARG C 30 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 30 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 30 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 30 " -0.009 2.00e-02 2.50e+03 ... (remaining 3717 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3506 2.76 - 3.30: 19979 3.30 - 3.83: 35844 3.83 - 4.37: 39224 4.37 - 4.90: 69855 Nonbonded interactions: 168408 Sorted by model distance: nonbonded pdb=" NH2 ARG F 47 " pdb=" OH TYR G 78 " model vdw 2.231 3.120 nonbonded pdb=" NH2 ARG J 47 " pdb=" OH TYR K 78 " model vdw 2.234 3.120 nonbonded pdb=" OH TYR H 29 " pdb=" OD1 ASP H 108 " model vdw 2.236 3.040 nonbonded pdb=" O ILE D 54 " pdb=" OG1 THR D 58 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR L 29 " pdb=" OD1 ASP L 108 " model vdw 2.250 3.040 ... (remaining 168403 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 9 through 48 or resid 72 through 176 or resid 321 through \ 369)) selection = (chain 'F' and resid 9 through 369) selection = (chain 'G' and (resid 9 through 48 or resid 72 through 176 or resid 321 through \ 369)) selection = (chain 'H' and (resid 9 through 48 or resid 72 through 176 or resid 321 through \ 369)) selection = (chain 'I' and (resid 9 through 48 or resid 72 through 176 or resid 321 through \ 369)) selection = (chain 'J' and resid 9 through 369) selection = (chain 'K' and (resid 9 through 48 or resid 72 through 176 or resid 321 through \ 369)) selection = (chain 'L' and (resid 9 through 48 or resid 72 through 176 or resid 321 through \ 369)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 45.410 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 0.046 21862 Z= 0.195 Angle : 0.672 8.877 29660 Z= 0.364 Chirality : 0.045 0.247 3406 Planarity : 0.006 0.124 3720 Dihedral : 17.494 89.961 8038 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.47 % Allowed : 27.07 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.17), residues: 2590 helix: 1.35 (0.13), residues: 1566 sheet: 1.28 (0.31), residues: 316 loop : -1.34 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 45 HIS 0.004 0.001 HIS G 369 PHE 0.030 0.001 PHE A 90 TYR 0.028 0.001 TYR G 356 ARG 0.015 0.000 ARG J 13 Details of bonding type rmsd hydrogen bonds : bond 0.11559 ( 1348) hydrogen bonds : angle 5.57389 ( 3924) SS BOND : bond 0.00315 ( 4) SS BOND : angle 2.11807 ( 8) covalent geometry : bond 0.00367 (21858) covalent geometry : angle 0.67145 (29652) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 409 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 16 TRP cc_start: 0.8163 (t-100) cc_final: 0.7806 (t-100) REVERT: L 138 CYS cc_start: 0.8425 (m) cc_final: 0.8161 (m) outliers start: 11 outliers final: 4 residues processed: 414 average time/residue: 0.3465 time to fit residues: 216.4293 Evaluate side-chains 392 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 388 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain E residue 353 CYS Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain A residue 92 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 203 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 236 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 173 HIS F 15 GLN F 169 ASN G 169 ASN H 95 GLN H 169 ASN I 173 HIS J 169 ASN L 48 GLN L 169 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.149831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.094323 restraints weight = 35496.903| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.37 r_work: 0.2925 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21862 Z= 0.129 Angle : 0.534 7.114 29660 Z= 0.270 Chirality : 0.040 0.160 3406 Planarity : 0.004 0.077 3720 Dihedral : 3.893 39.133 2957 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.81 % Allowed : 24.78 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.17), residues: 2590 helix: 1.82 (0.13), residues: 1582 sheet: 1.13 (0.30), residues: 336 loop : -1.22 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 45 HIS 0.004 0.001 HIS L 101 PHE 0.011 0.001 PHE A 90 TYR 0.014 0.001 TYR F 356 ARG 0.008 0.000 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 1348) hydrogen bonds : angle 4.32623 ( 3924) SS BOND : bond 0.00226 ( 4) SS BOND : angle 1.36127 ( 8) covalent geometry : bond 0.00289 (21858) covalent geometry : angle 0.53337 (29652) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 408 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.9025 (mmm160) cc_final: 0.8605 (tpt-90) REVERT: D 33 LYS cc_start: 0.9316 (tppt) cc_final: 0.9110 (tppt) REVERT: D 45 TRP cc_start: 0.7947 (m-90) cc_final: 0.7546 (m-90) REVERT: E 170 GLU cc_start: 0.8482 (tp30) cc_final: 0.8101 (tp30) REVERT: F 15 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7557 (mm110) REVERT: I 170 GLU cc_start: 0.8496 (tp30) cc_final: 0.8132 (tp30) REVERT: J 135 ASP cc_start: 0.8712 (p0) cc_final: 0.8476 (p0) REVERT: J 338 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: L 138 CYS cc_start: 0.8351 (m) cc_final: 0.8107 (m) REVERT: L 363 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8849 (p) REVERT: A 10 TRP cc_start: 0.7255 (p-90) cc_final: 0.6984 (p-90) outliers start: 65 outliers final: 38 residues processed: 440 average time/residue: 0.3282 time to fit residues: 220.5205 Evaluate side-chains 417 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 376 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain E residue 16 TRP Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 16 TRP Chi-restraints excluded: chain I residue 137 ILE Chi-restraints excluded: chain I residue 335 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 338 TYR Chi-restraints excluded: chain J residue 352 CYS Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 92 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 258 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS F 169 ASN ** I 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 HIS J 169 ASN L 173 HIS A 6 ASN A 118 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.147634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.091783 restraints weight = 35404.609| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.33 r_work: 0.2876 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21862 Z= 0.199 Angle : 0.567 9.287 29660 Z= 0.288 Chirality : 0.042 0.203 3406 Planarity : 0.004 0.067 3720 Dihedral : 3.817 33.488 2953 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.88 % Allowed : 23.62 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.17), residues: 2590 helix: 1.83 (0.13), residues: 1584 sheet: 1.08 (0.30), residues: 338 loop : -1.16 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 16 HIS 0.004 0.001 HIS L 101 PHE 0.010 0.001 PHE H 122 TYR 0.014 0.001 TYR E 343 ARG 0.006 0.000 ARG K 47 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 1348) hydrogen bonds : angle 4.27034 ( 3924) SS BOND : bond 0.00120 ( 4) SS BOND : angle 1.71493 ( 8) covalent geometry : bond 0.00474 (21858) covalent geometry : angle 0.56604 (29652) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 387 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 LEU cc_start: 0.9193 (pp) cc_final: 0.8981 (pp) REVERT: D 30 ARG cc_start: 0.9182 (mmm160) cc_final: 0.8693 (tpt-90) REVERT: D 45 TRP cc_start: 0.8042 (m-90) cc_final: 0.7527 (m-90) REVERT: E 170 GLU cc_start: 0.8610 (tp30) cc_final: 0.8134 (tp30) REVERT: F 135 ASP cc_start: 0.8811 (p0) cc_final: 0.8540 (p0) REVERT: G 368 ASP cc_start: 0.9130 (t0) cc_final: 0.8539 (t0) REVERT: I 170 GLU cc_start: 0.8601 (tp30) cc_final: 0.8165 (tp30) REVERT: J 135 ASP cc_start: 0.8767 (p0) cc_final: 0.8546 (p0) REVERT: J 338 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.7054 (m-80) REVERT: L 108 ASP cc_start: 0.9297 (t0) cc_final: 0.9059 (t0) REVERT: L 363 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8883 (p) REVERT: A 10 TRP cc_start: 0.7150 (p-90) cc_final: 0.6859 (p-90) outliers start: 113 outliers final: 85 residues processed: 466 average time/residue: 0.3061 time to fit residues: 222.6627 Evaluate side-chains 461 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 374 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 16 TRP Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 338 TYR Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 16 TRP Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 137 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 335 ILE Chi-restraints excluded: chain I residue 353 CYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 338 TYR Chi-restraints excluded: chain J residue 352 CYS Chi-restraints excluded: chain J residue 353 CYS Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain K residue 338 TYR Chi-restraints excluded: chain K residue 360 SER Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 10 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 5 optimal weight: 0.0770 chunk 32 optimal weight: 0.9980 chunk 238 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 250 optimal weight: 0.2980 chunk 221 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 218 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS F 169 ASN I 169 ASN I 173 HIS J 169 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.148668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.092794 restraints weight = 35738.966| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.34 r_work: 0.2903 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21862 Z= 0.126 Angle : 0.525 10.325 29660 Z= 0.264 Chirality : 0.040 0.176 3406 Planarity : 0.004 0.059 3720 Dihedral : 3.731 32.855 2953 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.76 % Allowed : 25.00 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.17), residues: 2590 helix: 1.96 (0.13), residues: 1578 sheet: 1.13 (0.30), residues: 336 loop : -1.10 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 16 HIS 0.004 0.001 HIS L 101 PHE 0.015 0.001 PHE A 90 TYR 0.024 0.001 TYR F 356 ARG 0.006 0.000 ARG G 47 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1348) hydrogen bonds : angle 4.13615 ( 3924) SS BOND : bond 0.00651 ( 4) SS BOND : angle 2.07309 ( 8) covalent geometry : bond 0.00286 (21858) covalent geometry : angle 0.52387 (29652) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 392 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 LEU cc_start: 0.9185 (pp) cc_final: 0.8980 (pp) REVERT: D 30 ARG cc_start: 0.9207 (mmm160) cc_final: 0.8660 (tpt-90) REVERT: E 170 GLU cc_start: 0.8625 (tp30) cc_final: 0.8134 (tp30) REVERT: F 20 TYR cc_start: 0.8115 (m-80) cc_final: 0.7565 (m-80) REVERT: F 135 ASP cc_start: 0.8738 (p0) cc_final: 0.8486 (p0) REVERT: G 320 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7588 (tttm) REVERT: G 368 ASP cc_start: 0.9106 (t0) cc_final: 0.8500 (t0) REVERT: H 12 LYS cc_start: 0.7694 (tttt) cc_final: 0.7238 (ttmt) REVERT: H 108 ASP cc_start: 0.9252 (t0) cc_final: 0.8995 (t0) REVERT: I 170 GLU cc_start: 0.8625 (tp30) cc_final: 0.8143 (tp30) REVERT: J 338 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6963 (m-80) REVERT: L 12 LYS cc_start: 0.7361 (ttmt) cc_final: 0.7060 (tttm) REVERT: L 47 ARG cc_start: 0.7954 (tpp80) cc_final: 0.7678 (tpp-160) REVERT: L 108 ASP cc_start: 0.9245 (t0) cc_final: 0.8978 (t0) REVERT: L 363 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8856 (p) REVERT: A 10 TRP cc_start: 0.7139 (p-90) cc_final: 0.6819 (p-90) outliers start: 87 outliers final: 64 residues processed: 445 average time/residue: 0.3465 time to fit residues: 242.4257 Evaluate side-chains 451 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 385 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 137 ILE Chi-restraints excluded: chain I residue 138 CYS Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 335 ILE Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 338 TYR Chi-restraints excluded: chain J residue 352 CYS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 360 SER Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 97 LYS Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 10 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 240 optimal weight: 20.0000 chunk 159 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 210 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 134 optimal weight: 0.0000 chunk 172 optimal weight: 8.9990 chunk 221 optimal weight: 0.0970 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 173 HIS F 15 GLN F 169 ASN H 173 HIS I 173 HIS J 169 ASN A 87 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.150244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.094463 restraints weight = 35760.372| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.37 r_work: 0.2929 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21862 Z= 0.103 Angle : 0.509 11.148 29660 Z= 0.254 Chirality : 0.039 0.149 3406 Planarity : 0.003 0.052 3720 Dihedral : 3.621 32.265 2953 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.84 % Allowed : 25.35 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.17), residues: 2590 helix: 2.04 (0.13), residues: 1582 sheet: 1.19 (0.30), residues: 336 loop : -1.00 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 45 HIS 0.004 0.001 HIS L 101 PHE 0.008 0.001 PHE E 167 TYR 0.021 0.001 TYR J 356 ARG 0.006 0.000 ARG G 47 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 1348) hydrogen bonds : angle 4.03458 ( 3924) SS BOND : bond 0.00269 ( 4) SS BOND : angle 1.42633 ( 8) covalent geometry : bond 0.00221 (21858) covalent geometry : angle 0.50862 (29652) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 409 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 MET cc_start: 0.8755 (mmt) cc_final: 0.8402 (mmt) REVERT: D 29 LEU cc_start: 0.9172 (pp) cc_final: 0.8955 (pp) REVERT: D 30 ARG cc_start: 0.9204 (mmm160) cc_final: 0.8651 (tpt-90) REVERT: E 170 GLU cc_start: 0.8653 (tp30) cc_final: 0.8209 (tp30) REVERT: F 135 ASP cc_start: 0.8662 (p0) cc_final: 0.8451 (p0) REVERT: G 320 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7518 (tttm) REVERT: G 368 ASP cc_start: 0.9098 (t0) cc_final: 0.8473 (t0) REVERT: H 12 LYS cc_start: 0.7660 (tttt) cc_final: 0.7200 (ttmt) REVERT: H 108 ASP cc_start: 0.9252 (t0) cc_final: 0.8917 (t0) REVERT: I 170 GLU cc_start: 0.8647 (tp30) cc_final: 0.8233 (tp30) REVERT: J 338 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: J 356 TYR cc_start: 0.8590 (t80) cc_final: 0.8300 (t80) REVERT: K 360 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.9051 (p) REVERT: L 12 LYS cc_start: 0.7313 (ttmt) cc_final: 0.7021 (tttm) REVERT: L 20 TYR cc_start: 0.8538 (m-80) cc_final: 0.8324 (m-80) REVERT: L 47 ARG cc_start: 0.8013 (tpp80) cc_final: 0.7718 (tpp-160) REVERT: L 108 ASP cc_start: 0.9211 (t0) cc_final: 0.8932 (t0) REVERT: L 138 CYS cc_start: 0.8238 (m) cc_final: 0.7961 (m) REVERT: L 363 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8848 (p) REVERT: A 10 TRP cc_start: 0.7149 (p-90) cc_final: 0.6781 (p-90) outliers start: 89 outliers final: 62 residues processed: 464 average time/residue: 0.3046 time to fit residues: 221.2585 Evaluate side-chains 451 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 386 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 137 ILE Chi-restraints excluded: chain I residue 138 CYS Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 353 CYS Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 338 TYR Chi-restraints excluded: chain J residue 352 CYS Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 360 SER Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 97 LYS Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 10 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 125 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 chunk 256 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 61 optimal weight: 3.9990 chunk 239 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 169 ASN I 173 HIS J 169 ASN L 173 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.149745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.093852 restraints weight = 35567.798| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.38 r_work: 0.2920 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21862 Z= 0.114 Angle : 0.519 11.551 29660 Z= 0.258 Chirality : 0.039 0.155 3406 Planarity : 0.003 0.048 3720 Dihedral : 3.598 32.315 2953 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.40 % Allowed : 25.35 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.17), residues: 2590 helix: 2.08 (0.13), residues: 1580 sheet: 1.20 (0.30), residues: 336 loop : -0.99 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 45 HIS 0.004 0.001 HIS H 101 PHE 0.017 0.001 PHE A 90 TYR 0.014 0.001 TYR J 356 ARG 0.006 0.000 ARG K 47 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 1348) hydrogen bonds : angle 4.01029 ( 3924) SS BOND : bond 0.00215 ( 4) SS BOND : angle 1.25213 ( 8) covalent geometry : bond 0.00257 (21858) covalent geometry : angle 0.51848 (29652) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 405 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 LEU cc_start: 0.9165 (pp) cc_final: 0.8948 (pp) REVERT: D 30 ARG cc_start: 0.9192 (mmm160) cc_final: 0.8679 (tpt-90) REVERT: D 45 TRP cc_start: 0.8016 (m-90) cc_final: 0.7595 (m-90) REVERT: E 170 GLU cc_start: 0.8650 (tp30) cc_final: 0.8199 (tp30) REVERT: F 20 TYR cc_start: 0.7993 (m-80) cc_final: 0.7701 (m-80) REVERT: F 135 ASP cc_start: 0.8688 (p0) cc_final: 0.8482 (p0) REVERT: G 320 LYS cc_start: 0.7788 (ttmt) cc_final: 0.7457 (tttm) REVERT: G 368 ASP cc_start: 0.9104 (t0) cc_final: 0.8483 (t0) REVERT: H 12 LYS cc_start: 0.7672 (tttt) cc_final: 0.7212 (ttmt) REVERT: H 108 ASP cc_start: 0.9032 (t0) cc_final: 0.8673 (t0) REVERT: I 170 GLU cc_start: 0.8648 (tp30) cc_final: 0.8216 (tp30) REVERT: J 134 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8231 (ttt) REVERT: J 338 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6875 (m-80) REVERT: L 12 LYS cc_start: 0.7284 (ttmt) cc_final: 0.6997 (tttm) REVERT: L 47 ARG cc_start: 0.8009 (tpp80) cc_final: 0.7682 (tpp80) REVERT: L 108 ASP cc_start: 0.9272 (t0) cc_final: 0.9007 (t0) REVERT: L 138 CYS cc_start: 0.8284 (m) cc_final: 0.8048 (m) REVERT: L 363 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8851 (p) REVERT: A 10 TRP cc_start: 0.7053 (p-90) cc_final: 0.6679 (p-90) outliers start: 102 outliers final: 77 residues processed: 467 average time/residue: 0.3074 time to fit residues: 221.6087 Evaluate side-chains 466 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 386 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 137 ILE Chi-restraints excluded: chain I residue 138 CYS Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 335 ILE Chi-restraints excluded: chain I residue 353 CYS Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 338 TYR Chi-restraints excluded: chain J residue 352 CYS Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 360 SER Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 97 LYS Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 10 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 167 optimal weight: 3.9990 chunk 91 optimal weight: 0.0870 chunk 82 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 234 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 119 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS F 169 ASN G 90 GLN I 173 HIS J 169 ASN L 173 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.149846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094122 restraints weight = 35271.772| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.36 r_work: 0.2922 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21862 Z= 0.115 Angle : 0.539 11.792 29660 Z= 0.265 Chirality : 0.039 0.149 3406 Planarity : 0.003 0.044 3720 Dihedral : 3.593 32.623 2953 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.36 % Allowed : 25.60 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.17), residues: 2590 helix: 2.08 (0.13), residues: 1580 sheet: 1.24 (0.31), residues: 322 loop : -0.93 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 45 HIS 0.003 0.000 HIS L 101 PHE 0.006 0.001 PHE E 167 TYR 0.030 0.001 TYR J 356 ARG 0.007 0.000 ARG H 47 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 1348) hydrogen bonds : angle 3.99552 ( 3924) SS BOND : bond 0.00235 ( 4) SS BOND : angle 1.57765 ( 8) covalent geometry : bond 0.00261 (21858) covalent geometry : angle 0.53834 (29652) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 396 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8830 (tp) REVERT: D 29 LEU cc_start: 0.9159 (pp) cc_final: 0.8936 (pp) REVERT: D 30 ARG cc_start: 0.9213 (mmm160) cc_final: 0.8728 (tpt-90) REVERT: D 45 TRP cc_start: 0.8072 (m-90) cc_final: 0.7634 (m-90) REVERT: E 170 GLU cc_start: 0.8675 (tp30) cc_final: 0.8138 (tp30) REVERT: F 20 TYR cc_start: 0.8088 (m-80) cc_final: 0.7624 (m-80) REVERT: G 320 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7442 (tttm) REVERT: G 368 ASP cc_start: 0.9139 (t0) cc_final: 0.8544 (t0) REVERT: H 12 LYS cc_start: 0.7708 (tttt) cc_final: 0.7276 (ttmt) REVERT: H 108 ASP cc_start: 0.9061 (t0) cc_final: 0.8698 (t0) REVERT: I 170 GLU cc_start: 0.8661 (tp30) cc_final: 0.8223 (tp30) REVERT: J 16 TRP cc_start: 0.7896 (t-100) cc_final: 0.7580 (t-100) REVERT: J 134 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8079 (ttt) REVERT: J 338 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.6861 (m-80) REVERT: L 12 LYS cc_start: 0.7279 (ttmt) cc_final: 0.6996 (tttm) REVERT: L 47 ARG cc_start: 0.8002 (tpp80) cc_final: 0.7697 (tpp80) REVERT: L 108 ASP cc_start: 0.9252 (t0) cc_final: 0.8960 (t0) REVERT: L 134 MET cc_start: 0.8784 (tpt) cc_final: 0.8359 (tpp) REVERT: L 138 CYS cc_start: 0.8306 (m) cc_final: 0.8080 (m) REVERT: L 363 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8874 (p) REVERT: A 10 TRP cc_start: 0.6983 (p-90) cc_final: 0.6589 (p-90) REVERT: B 123 MET cc_start: 0.4024 (mmm) cc_final: 0.3443 (mmt) outliers start: 101 outliers final: 77 residues processed: 464 average time/residue: 0.3072 time to fit residues: 222.7294 Evaluate side-chains 460 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 379 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 137 ILE Chi-restraints excluded: chain I residue 138 CYS Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 335 ILE Chi-restraints excluded: chain I residue 353 CYS Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 338 TYR Chi-restraints excluded: chain J residue 352 CYS Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 360 SER Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 97 LYS Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 138 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 32 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 224 optimal weight: 0.8980 chunk 254 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 169 ASN I 173 HIS J 15 GLN J 169 ASN L 173 HIS A 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.148872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.092772 restraints weight = 35679.073| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.37 r_work: 0.2901 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21862 Z= 0.144 Angle : 0.565 11.986 29660 Z= 0.279 Chirality : 0.040 0.172 3406 Planarity : 0.004 0.043 3720 Dihedral : 3.679 34.300 2953 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.10 % Allowed : 25.73 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.17), residues: 2590 helix: 2.04 (0.13), residues: 1582 sheet: 1.19 (0.31), residues: 322 loop : -0.98 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 45 HIS 0.004 0.001 HIS H 101 PHE 0.020 0.001 PHE A 90 TYR 0.033 0.001 TYR J 356 ARG 0.008 0.000 ARG G 73 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 1348) hydrogen bonds : angle 4.03905 ( 3924) SS BOND : bond 0.00178 ( 4) SS BOND : angle 1.57764 ( 8) covalent geometry : bond 0.00339 (21858) covalent geometry : angle 0.56425 (29652) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 376 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 29 LEU cc_start: 0.9159 (pp) cc_final: 0.8937 (pp) REVERT: D 30 ARG cc_start: 0.9200 (mmm160) cc_final: 0.8715 (tpt-90) REVERT: D 45 TRP cc_start: 0.8125 (m-90) cc_final: 0.7673 (m-90) REVERT: D 57 MET cc_start: 0.8634 (mmt) cc_final: 0.8333 (mmt) REVERT: E 170 GLU cc_start: 0.8626 (tp30) cc_final: 0.8102 (tp30) REVERT: F 20 TYR cc_start: 0.8112 (m-80) cc_final: 0.7610 (m-80) REVERT: G 320 LYS cc_start: 0.7794 (ttmt) cc_final: 0.7461 (tttm) REVERT: G 368 ASP cc_start: 0.9136 (t0) cc_final: 0.8551 (t0) REVERT: H 12 LYS cc_start: 0.7782 (tttt) cc_final: 0.7248 (ttmt) REVERT: H 108 ASP cc_start: 0.9063 (t0) cc_final: 0.8747 (t0) REVERT: I 170 GLU cc_start: 0.8602 (tp30) cc_final: 0.8112 (tp30) REVERT: J 76 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8961 (m) REVERT: J 338 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6987 (m-80) REVERT: L 12 LYS cc_start: 0.7346 (ttmt) cc_final: 0.7049 (tttm) REVERT: L 23 MET cc_start: 0.8805 (mmm) cc_final: 0.8504 (mmm) REVERT: L 47 ARG cc_start: 0.8094 (tpp80) cc_final: 0.7779 (tpp80) REVERT: L 108 ASP cc_start: 0.9261 (t0) cc_final: 0.8984 (t0) REVERT: L 134 MET cc_start: 0.8844 (tpt) cc_final: 0.8453 (tpp) REVERT: L 138 CYS cc_start: 0.8310 (m) cc_final: 0.8086 (m) REVERT: L 363 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8858 (p) REVERT: A 10 TRP cc_start: 0.7017 (p-90) cc_final: 0.6628 (p-90) outliers start: 95 outliers final: 80 residues processed: 441 average time/residue: 0.3133 time to fit residues: 216.3876 Evaluate side-chains 452 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 369 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 338 TYR Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 137 ILE Chi-restraints excluded: chain I residue 138 CYS Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 335 ILE Chi-restraints excluded: chain I residue 353 CYS Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 338 TYR Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 360 SER Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 97 LYS Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 10 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 90 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 224 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 169 ASN J 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.149339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.093542 restraints weight = 35495.882| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.38 r_work: 0.2915 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21862 Z= 0.122 Angle : 0.561 12.741 29660 Z= 0.275 Chirality : 0.040 0.162 3406 Planarity : 0.004 0.069 3720 Dihedral : 3.686 34.413 2953 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.06 % Allowed : 25.91 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.17), residues: 2590 helix: 2.02 (0.13), residues: 1580 sheet: 1.20 (0.31), residues: 322 loop : -0.98 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 16 HIS 0.004 0.000 HIS L 101 PHE 0.007 0.001 PHE E 167 TYR 0.032 0.001 TYR J 356 ARG 0.009 0.000 ARG L 314 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 1348) hydrogen bonds : angle 4.01800 ( 3924) SS BOND : bond 0.00216 ( 4) SS BOND : angle 1.69181 ( 8) covalent geometry : bond 0.00282 (21858) covalent geometry : angle 0.56012 (29652) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 383 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 LEU cc_start: 0.9149 (pp) cc_final: 0.8928 (pp) REVERT: D 30 ARG cc_start: 0.9189 (mmm160) cc_final: 0.8719 (tpt-90) REVERT: D 45 TRP cc_start: 0.8104 (m-90) cc_final: 0.7656 (m-90) REVERT: D 57 MET cc_start: 0.8684 (mmt) cc_final: 0.8379 (mmt) REVERT: E 78 TYR cc_start: 0.8533 (m-10) cc_final: 0.8309 (m-10) REVERT: E 170 GLU cc_start: 0.8616 (tp30) cc_final: 0.8050 (tp30) REVERT: G 320 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7521 (tttm) REVERT: G 368 ASP cc_start: 0.9146 (t0) cc_final: 0.8572 (t0) REVERT: H 12 LYS cc_start: 0.7754 (tttt) cc_final: 0.7229 (ttmt) REVERT: H 108 ASP cc_start: 0.9063 (t0) cc_final: 0.8713 (t0) REVERT: I 170 GLU cc_start: 0.8605 (tp30) cc_final: 0.8112 (tp30) REVERT: J 338 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: L 12 LYS cc_start: 0.7293 (ttmt) cc_final: 0.7008 (tttm) REVERT: L 47 ARG cc_start: 0.8089 (tpp80) cc_final: 0.7781 (tpp80) REVERT: L 108 ASP cc_start: 0.9260 (t0) cc_final: 0.8968 (t0) REVERT: L 134 MET cc_start: 0.8832 (tpt) cc_final: 0.8434 (tpp) REVERT: L 138 CYS cc_start: 0.8298 (m) cc_final: 0.8077 (m) REVERT: L 348 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8759 (tp) REVERT: L 363 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8854 (p) REVERT: A 10 TRP cc_start: 0.6997 (p-90) cc_final: 0.6638 (p-90) REVERT: B 123 MET cc_start: 0.4149 (mmm) cc_final: 0.3673 (mmt) outliers start: 94 outliers final: 87 residues processed: 450 average time/residue: 0.3199 time to fit residues: 223.2208 Evaluate side-chains 462 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 372 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 338 TYR Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 137 ILE Chi-restraints excluded: chain I residue 138 CYS Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 335 ILE Chi-restraints excluded: chain I residue 353 CYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 338 TYR Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 360 SER Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 97 LYS Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 83 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 chunk 236 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 169 ASN J 15 GLN J 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.148835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.094725 restraints weight = 35449.555| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.52 r_work: 0.2894 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21862 Z= 0.135 Angle : 0.569 12.352 29660 Z= 0.281 Chirality : 0.040 0.170 3406 Planarity : 0.004 0.063 3720 Dihedral : 3.729 35.573 2953 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.97 % Allowed : 25.86 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.17), residues: 2590 helix: 1.99 (0.13), residues: 1576 sheet: 1.18 (0.31), residues: 322 loop : -0.99 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 16 HIS 0.004 0.001 HIS L 101 PHE 0.023 0.001 PHE A 90 TYR 0.037 0.001 TYR J 356 ARG 0.009 0.000 ARG L 314 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 1348) hydrogen bonds : angle 4.04323 ( 3924) SS BOND : bond 0.00193 ( 4) SS BOND : angle 1.76911 ( 8) covalent geometry : bond 0.00316 (21858) covalent geometry : angle 0.56829 (29652) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 380 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 29 LEU cc_start: 0.9152 (pp) cc_final: 0.8933 (pp) REVERT: D 30 ARG cc_start: 0.9185 (mmm160) cc_final: 0.8729 (tpt-90) REVERT: D 45 TRP cc_start: 0.8103 (m-90) cc_final: 0.7627 (m-90) REVERT: D 57 MET cc_start: 0.8685 (mmt) cc_final: 0.8372 (mmt) REVERT: E 170 GLU cc_start: 0.8621 (tp30) cc_final: 0.8079 (tp30) REVERT: F 20 TYR cc_start: 0.7965 (m-80) cc_final: 0.7687 (m-80) REVERT: G 320 LYS cc_start: 0.7860 (ttmt) cc_final: 0.7519 (tttm) REVERT: G 368 ASP cc_start: 0.9154 (t0) cc_final: 0.8582 (t0) REVERT: H 23 MET cc_start: 0.8458 (mmm) cc_final: 0.8241 (mmm) REVERT: H 47 ARG cc_start: 0.7465 (tpp80) cc_final: 0.7263 (ttm-80) REVERT: H 108 ASP cc_start: 0.9053 (t0) cc_final: 0.8697 (t0) REVERT: I 170 GLU cc_start: 0.8618 (tp30) cc_final: 0.8118 (tp30) REVERT: J 47 ARG cc_start: 0.7524 (tpp-160) cc_final: 0.6550 (mmt90) REVERT: J 338 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.6956 (m-80) REVERT: L 12 LYS cc_start: 0.7331 (ttmt) cc_final: 0.7034 (tttm) REVERT: L 23 MET cc_start: 0.8784 (mmm) cc_final: 0.8514 (mmm) REVERT: L 47 ARG cc_start: 0.8095 (tpp80) cc_final: 0.7769 (tpp80) REVERT: L 108 ASP cc_start: 0.9282 (t0) cc_final: 0.9011 (t0) REVERT: L 134 MET cc_start: 0.8857 (tpt) cc_final: 0.8474 (tpp) REVERT: L 138 CYS cc_start: 0.8316 (m) cc_final: 0.8092 (m) REVERT: L 348 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8773 (tp) REVERT: L 363 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8845 (p) REVERT: A 10 TRP cc_start: 0.6983 (p-90) cc_final: 0.6645 (p-90) REVERT: B 48 MET cc_start: 0.8352 (ttp) cc_final: 0.8139 (ttp) REVERT: B 123 MET cc_start: 0.4158 (mmm) cc_final: 0.3679 (mmt) outliers start: 92 outliers final: 86 residues processed: 444 average time/residue: 0.3335 time to fit residues: 231.9727 Evaluate side-chains 462 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 373 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 137 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 335 ILE Chi-restraints excluded: chain I residue 353 CYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 338 TYR Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 360 SER Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 97 LYS Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 10 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 143 optimal weight: 0.0870 chunk 51 optimal weight: 0.0010 chunk 114 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 212 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 169 ASN J 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.150457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.094957 restraints weight = 35551.821| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.38 r_work: 0.2939 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21862 Z= 0.109 Angle : 0.558 12.410 29660 Z= 0.272 Chirality : 0.039 0.144 3406 Planarity : 0.004 0.073 3720 Dihedral : 3.684 35.871 2953 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.11 % Allowed : 26.90 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.17), residues: 2590 helix: 2.03 (0.13), residues: 1578 sheet: 1.21 (0.31), residues: 322 loop : -0.96 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 16 HIS 0.003 0.000 HIS L 101 PHE 0.009 0.001 PHE B 108 TYR 0.035 0.001 TYR J 356 ARG 0.008 0.000 ARG L 314 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 1348) hydrogen bonds : angle 3.97588 ( 3924) SS BOND : bond 0.00283 ( 4) SS BOND : angle 1.85964 ( 8) covalent geometry : bond 0.00243 (21858) covalent geometry : angle 0.55740 (29652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11452.17 seconds wall clock time: 198 minutes 23.96 seconds (11903.96 seconds total)