Starting phenix.real_space_refine on Wed Jun 18 13:36:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tsl_41595/06_2025/8tsl_41595.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tsl_41595/06_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_41595/06_2025/8tsl_41595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tsl_41595/06_2025/8tsl_41595.map" model { file = "/net/cci-nas-00/data/ceres_data/8tsl_41595/06_2025/8tsl_41595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tsl_41595/06_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-5710/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: 12.73, per 1000 atoms: 0.60 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: 4.72 Conformation dependent library (CDL) restraints added in 2.7 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: 1.97 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: 6.47 Time building geometry restraints manager: 5.62 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: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 45.120 Find NCS groups from input model: 0.980 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.800 ------------------------------------------------------------------------------- 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 : 2.711 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: 0.3562 time to fit residues: 224.8049 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 : 2.247 ------------------------------------------------------------------------------- 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 = 59)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.094306 restraints weight = 35496.899| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.36 r_work: 0.2925 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 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 : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.9037 (mmm160) cc_final: 0.8618 (tpt-90) REVERT: D 33 LYS cc_start: 0.9324 (tppt) cc_final: 0.9119 (tppt) REVERT: D 45 TRP cc_start: 0.7980 (m-90) cc_final: 0.7558 (m-90) REVERT: E 170 GLU cc_start: 0.8485 (tp30) cc_final: 0.8103 (tp30) REVERT: F 15 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7560 (mm110) REVERT: F 137 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8972 (pt) REVERT: I 170 GLU cc_start: 0.8498 (tp30) cc_final: 0.8134 (tp30) REVERT: J 135 ASP cc_start: 0.8712 (p0) cc_final: 0.8476 (p0) REVERT: J 338 TYR cc_start: 0.7005 (OUTLIER) cc_final: 0.6774 (m-80) REVERT: L 138 CYS cc_start: 0.8364 (m) cc_final: 0.8116 (m) REVERT: L 363 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8837 (p) REVERT: A 10 TRP cc_start: 0.7254 (p-90) cc_final: 0.6985 (p-90) outliers start: 65 outliers final: 38 residues processed: 440 average time/residue: 0.3917 time to fit residues: 263.9183 Evaluate side-chains 418 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 376 time to evaluate : 2.866 ------------------------------------------------------------------------------- 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 137 ILE 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: 0.7980 chunk 196 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 258 optimal weight: 7.9990 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: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 15 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.146824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.090549 restraints weight = 35312.295| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.36 r_work: 0.2858 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 21862 Z= 0.233 Angle : 0.594 9.817 29660 Z= 0.302 Chirality : 0.043 0.222 3406 Planarity : 0.004 0.067 3720 Dihedral : 3.881 33.890 2953 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.14 % Allowed : 23.53 % Favored : 71.33 % 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: 1.41 (0.17), residues: 2590 helix: 1.78 (0.13), residues: 1586 sheet: 1.04 (0.30), residues: 338 loop : -1.23 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 45 HIS 0.004 0.001 HIS D 221 PHE 0.010 0.001 PHE E 122 TYR 0.017 0.002 TYR F 356 ARG 0.007 0.000 ARG K 47 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 1348) hydrogen bonds : angle 4.31682 ( 3924) SS BOND : bond 0.00137 ( 4) SS BOND : angle 1.95039 ( 8) covalent geometry : bond 0.00556 (21858) covalent geometry : angle 0.59291 (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 503 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 384 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.9276 (mmm160) cc_final: 0.8830 (tpt-90) REVERT: D 45 TRP cc_start: 0.8172 (m-90) cc_final: 0.7605 (m-90) REVERT: E 170 GLU cc_start: 0.8790 (tp30) cc_final: 0.8312 (tp30) REVERT: F 135 ASP cc_start: 0.8909 (p0) cc_final: 0.8654 (p0) REVERT: G 368 ASP cc_start: 0.9247 (t0) cc_final: 0.8700 (t0) REVERT: H 108 ASP cc_start: 0.9377 (t0) cc_final: 0.9155 (t0) REVERT: I 170 GLU cc_start: 0.8778 (tp30) cc_final: 0.8316 (tp30) REVERT: L 108 ASP cc_start: 0.9386 (t0) cc_final: 0.9151 (t0) REVERT: L 363 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8941 (p) REVERT: A 10 TRP cc_start: 0.7173 (p-90) cc_final: 0.6926 (p-90) outliers start: 119 outliers final: 91 residues processed: 469 average time/residue: 0.3039 time to fit residues: 223.0697 Evaluate side-chains 459 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 367 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ILE 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 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 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 331 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 28 VAL 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 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 338 TYR Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain G residue 363 VAL 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 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 28 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 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 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 K residue 362 VAL 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: 0.4980 chunk 32 optimal weight: 0.0270 chunk 238 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 250 optimal weight: 0.3980 chunk 221 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.149515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.093441 restraints weight = 35738.126| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.38 r_work: 0.2911 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1243 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= 0.111 Angle : 0.523 11.428 29660 Z= 0.261 Chirality : 0.039 0.163 3406 Planarity : 0.004 0.058 3720 Dihedral : 3.726 32.898 2953 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.67 % Allowed : 25.43 % Favored : 70.90 % 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: 1.64 (0.17), residues: 2590 helix: 1.95 (0.13), residues: 1580 sheet: 1.15 (0.30), residues: 336 loop : -1.05 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 45 HIS 0.004 0.001 HIS G 101 PHE 0.014 0.001 PHE A 90 TYR 0.018 0.001 TYR H 343 ARG 0.006 0.000 ARG G 47 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 1348) hydrogen bonds : angle 4.10946 ( 3924) SS BOND : bond 0.00282 ( 4) SS BOND : angle 1.95008 ( 8) covalent geometry : bond 0.00241 (21858) covalent geometry : angle 0.52206 (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 484 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 399 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.9193 (mmm160) cc_final: 0.8702 (tpt-90) REVERT: E 170 GLU cc_start: 0.8635 (tp30) cc_final: 0.8180 (tp30) REVERT: F 135 ASP cc_start: 0.8702 (p0) cc_final: 0.8484 (p0) REVERT: G 320 LYS cc_start: 0.7833 (ttmt) cc_final: 0.7517 (tttm) REVERT: G 368 ASP cc_start: 0.9103 (t0) cc_final: 0.8504 (t0) REVERT: H 12 LYS cc_start: 0.7697 (tttt) cc_final: 0.7243 (ttmt) REVERT: H 108 ASP cc_start: 0.9246 (t0) cc_final: 0.8974 (t0) REVERT: H 348 LEU cc_start: 0.8938 (tp) cc_final: 0.8634 (tp) REVERT: I 170 GLU cc_start: 0.8619 (tp30) cc_final: 0.8151 (tp30) REVERT: J 338 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6856 (m-80) REVERT: K 360 SER cc_start: 0.9282 (OUTLIER) cc_final: 0.9011 (p) REVERT: L 12 LYS cc_start: 0.7349 (ttmt) cc_final: 0.7052 (tttm) REVERT: L 47 ARG cc_start: 0.7978 (tpp80) cc_final: 0.7707 (tpp-160) REVERT: L 108 ASP cc_start: 0.9222 (t0) cc_final: 0.8932 (t0) REVERT: L 363 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8841 (p) REVERT: A 10 TRP cc_start: 0.7148 (p-90) cc_final: 0.6835 (p-90) outliers start: 85 outliers final: 56 residues processed: 450 average time/residue: 0.3279 time to fit residues: 230.6165 Evaluate side-chains 444 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 385 time to evaluate : 2.528 ------------------------------------------------------------------------------- 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 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 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 E residue 335 ILE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 136 ASP 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 45 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 352 CYS Chi-restraints excluded: chain K residue 21 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 354 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 240 optimal weight: 20.0000 chunk 159 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 210 optimal weight: 8.9990 chunk 252 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 A 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.147579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.091280 restraints weight = 35746.009| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.37 r_work: 0.2875 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21862 Z= 0.175 Angle : 0.557 11.244 29660 Z= 0.279 Chirality : 0.041 0.190 3406 Planarity : 0.004 0.052 3720 Dihedral : 3.751 33.582 2953 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.62 % Allowed : 24.78 % Favored : 70.60 % 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: 1.61 (0.17), residues: 2590 helix: 1.94 (0.13), residues: 1582 sheet: 1.09 (0.30), residues: 336 loop : -1.07 (0.24), residues: 672 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 0.009 0.001 PHE H 122 TYR 0.023 0.001 TYR J 356 ARG 0.009 0.000 ARG L 314 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 1348) hydrogen bonds : angle 4.14599 ( 3924) SS BOND : bond 0.00140 ( 4) SS BOND : angle 1.75169 ( 8) covalent geometry : bond 0.00414 (21858) covalent geometry : angle 0.55593 (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 495 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 388 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 96 MET cc_start: 0.8799 (ptm) cc_final: 0.8550 (ptm) REVERT: D 30 ARG cc_start: 0.9238 (mmm160) cc_final: 0.8696 (tpt-90) REVERT: E 170 GLU cc_start: 0.8664 (tp30) cc_final: 0.8203 (tp30) REVERT: G 368 ASP cc_start: 0.9137 (t0) cc_final: 0.8529 (t0) REVERT: H 108 ASP cc_start: 0.9301 (t0) cc_final: 0.9052 (t0) REVERT: I 170 GLU cc_start: 0.8637 (tp30) cc_final: 0.8176 (tp30) REVERT: L 12 LYS cc_start: 0.7382 (ttmt) cc_final: 0.7058 (tttm) REVERT: L 47 ARG cc_start: 0.8019 (tpp80) cc_final: 0.7684 (tpp80) REVERT: L 108 ASP cc_start: 0.9284 (t0) cc_final: 0.9048 (t0) REVERT: A 10 TRP cc_start: 0.7182 (p-90) cc_final: 0.6875 (p-90) outliers start: 107 outliers final: 88 residues processed: 455 average time/residue: 0.3064 time to fit residues: 218.5068 Evaluate side-chains 467 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 379 time to evaluate : 2.432 ------------------------------------------------------------------------------- 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 122 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 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 205 THR 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 167 SER Chi-restraints excluded: chain D residue 175 VAL 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 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 335 ILE 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 324 LEU 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 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 136 ASP Chi-restraints excluded: chain G residue 325 VAL 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 32 VAL 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 162 GLU 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 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 133 LEU 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 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 321 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 125 optimal weight: 0.7980 chunk 172 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 256 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 239 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.148353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.092198 restraints weight = 35517.434| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.37 r_work: 0.2888 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21862 Z= 0.134 Angle : 0.547 11.834 29660 Z= 0.272 Chirality : 0.040 0.176 3406 Planarity : 0.004 0.051 3720 Dihedral : 3.726 33.700 2953 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.71 % Allowed : 25.39 % Favored : 69.91 % 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: 1.94 (0.13), residues: 1582 sheet: 1.09 (0.30), residues: 336 loop : -1.06 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 45 HIS 0.004 0.001 HIS L 101 PHE 0.017 0.001 PHE A 90 TYR 0.025 0.001 TYR J 356 ARG 0.014 0.000 ARG L 314 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 1348) hydrogen bonds : angle 4.09862 ( 3924) SS BOND : bond 0.00187 ( 4) SS BOND : angle 1.40738 ( 8) covalent geometry : bond 0.00311 (21858) covalent geometry : angle 0.54611 (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 498 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 389 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.9212 (mmm160) cc_final: 0.8701 (tpt-90) REVERT: E 170 GLU cc_start: 0.8606 (tp30) cc_final: 0.8106 (tp30) REVERT: G 368 ASP cc_start: 0.9137 (t0) cc_final: 0.8530 (t0) REVERT: H 108 ASP cc_start: 0.9286 (t0) cc_final: 0.9021 (t0) REVERT: I 170 GLU cc_start: 0.8633 (tp30) cc_final: 0.8193 (tp30) REVERT: J 338 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.7005 (m-80) REVERT: J 356 TYR cc_start: 0.8625 (t80) cc_final: 0.8263 (t80) REVERT: L 12 LYS cc_start: 0.7379 (ttmt) cc_final: 0.7057 (tttm) REVERT: L 47 ARG cc_start: 0.8040 (tpp80) cc_final: 0.7698 (tpp80) REVERT: L 108 ASP cc_start: 0.9273 (t0) cc_final: 0.9021 (t0) REVERT: L 135 ASP cc_start: 0.7929 (t0) cc_final: 0.7666 (t0) REVERT: L 138 CYS cc_start: 0.8456 (m) cc_final: 0.8185 (m) REVERT: A 10 TRP cc_start: 0.7081 (p-90) cc_final: 0.6769 (p-90) outliers start: 109 outliers final: 87 residues processed: 462 average time/residue: 0.3108 time to fit residues: 225.4714 Evaluate side-chains 465 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 377 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 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 205 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 45 TRP 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 133 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 175 VAL 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 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 40 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 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 162 GLU Chi-restraints excluded: chain H residue 318 THR 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 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 130 VAL Chi-restraints excluded: chain J residue 133 LEU 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 353 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 118 SER Chi-restraints excluded: chain K residue 325 VAL 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 354 LEU 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: 0.6980 chunk 91 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 110 optimal weight: 0.7980 chunk 234 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 134 optimal weight: 0.0470 chunk 119 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 160 optimal weight: 0.0970 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 ASN E 173 HIS F 169 ASN J 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.150204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.094319 restraints weight = 35271.318| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.37 r_work: 0.2924 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21862 Z= 0.104 Angle : 0.531 12.366 29660 Z= 0.262 Chirality : 0.039 0.161 3406 Planarity : 0.004 0.062 3720 Dihedral : 3.647 33.284 2953 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.58 % Allowed : 26.81 % Favored : 69.60 % 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: 2.00 (0.13), residues: 1580 sheet: 1.18 (0.30), residues: 336 loop : -0.97 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 16 HIS 0.004 0.001 HIS L 101 PHE 0.008 0.001 PHE E 167 TYR 0.015 0.001 TYR F 356 ARG 0.016 0.000 ARG L 314 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 1348) hydrogen bonds : angle 4.01241 ( 3924) SS BOND : bond 0.00260 ( 4) SS BOND : angle 1.59825 ( 8) covalent geometry : bond 0.00226 (21858) covalent geometry : angle 0.53053 (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 494 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 411 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 MET cc_start: 0.8745 (mmt) cc_final: 0.8415 (mmt) REVERT: D 30 ARG cc_start: 0.9140 (mmm160) cc_final: 0.8675 (tpt-90) REVERT: E 170 GLU cc_start: 0.8606 (tp30) cc_final: 0.8078 (tp30) REVERT: G 320 LYS cc_start: 0.7759 (ttmt) cc_final: 0.7426 (tttm) REVERT: G 368 ASP cc_start: 0.9138 (t0) cc_final: 0.8551 (t0) REVERT: H 108 ASP cc_start: 0.9254 (t0) cc_final: 0.8928 (t0) REVERT: I 170 GLU cc_start: 0.8584 (tp30) cc_final: 0.8130 (tp30) REVERT: K 360 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.9055 (p) REVERT: L 12 LYS cc_start: 0.7345 (ttmt) cc_final: 0.7044 (tttm) REVERT: L 47 ARG cc_start: 0.8020 (tpp80) cc_final: 0.7697 (tpp80) REVERT: L 108 ASP cc_start: 0.9224 (t0) cc_final: 0.8943 (t0) REVERT: L 135 ASP cc_start: 0.7794 (t0) cc_final: 0.7571 (t0) REVERT: L 138 CYS cc_start: 0.8284 (m) cc_final: 0.7989 (m) REVERT: A 10 TRP cc_start: 0.6989 (p-90) cc_final: 0.6604 (p-90) REVERT: B 123 MET cc_start: 0.4012 (mmm) cc_final: 0.3448 (mmt) outliers start: 83 outliers final: 63 residues processed: 460 average time/residue: 0.3243 time to fit residues: 231.8054 Evaluate side-chains 446 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 382 time to evaluate : 2.471 ------------------------------------------------------------------------------- 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 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 45 TRP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 69 MET 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 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 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 24 LEU 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 24 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 367 ARG 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 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 352 CYS 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 354 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 32 optimal weight: 2.9990 chunk 112 optimal weight: 0.0470 chunk 131 optimal weight: 2.9990 chunk 134 optimal weight: 0.0040 chunk 179 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 254 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 overall best weight: 0.9892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 169 ASN G 90 GLN I 173 HIS 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 = 0.3902 r_free = 0.3902 target = 0.148694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.092728 restraints weight = 35633.881| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.38 r_work: 0.2898 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21862 Z= 0.138 Angle : 0.566 12.506 29660 Z= 0.280 Chirality : 0.040 0.168 3406 Planarity : 0.004 0.054 3720 Dihedral : 3.711 34.246 2953 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.10 % Allowed : 26.47 % Favored : 69.43 % 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: 1.97 (0.13), residues: 1580 sheet: 1.17 (0.31), residues: 336 loop : -0.99 (0.24), residues: 674 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 0.019 0.001 PHE A 90 TYR 0.023 0.001 TYR F 356 ARG 0.007 0.000 ARG K 47 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 1348) hydrogen bonds : angle 4.03915 ( 3924) SS BOND : bond 0.00241 ( 4) SS BOND : angle 1.89985 ( 8) covalent geometry : bond 0.00324 (21858) covalent geometry : angle 0.56548 (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 476 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 381 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.9190 (mmm160) cc_final: 0.8715 (tpt-90) REVERT: E 170 GLU cc_start: 0.8612 (tp30) cc_final: 0.8093 (tp30) REVERT: G 368 ASP cc_start: 0.9148 (t0) cc_final: 0.8589 (t0) REVERT: H 108 ASP cc_start: 0.9065 (t0) cc_final: 0.8696 (t0) REVERT: I 170 GLU cc_start: 0.8595 (tp30) cc_final: 0.8099 (tp30) REVERT: J 338 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: L 12 LYS cc_start: 0.7380 (ttmt) cc_final: 0.7080 (tttm) REVERT: L 47 ARG cc_start: 0.8062 (tpp80) cc_final: 0.7718 (tpp80) REVERT: L 108 ASP cc_start: 0.9276 (t0) cc_final: 0.9017 (t0) REVERT: L 135 ASP cc_start: 0.7834 (t0) cc_final: 0.7409 (t0) REVERT: L 348 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8661 (tp) REVERT: A 10 TRP cc_start: 0.7002 (p-90) cc_final: 0.6689 (p-90) outliers start: 95 outliers final: 86 residues processed: 445 average time/residue: 0.3150 time to fit residues: 218.1415 Evaluate side-chains 456 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 368 time to evaluate : 2.257 ------------------------------------------------------------------------------- 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 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 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 54 ILE 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 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 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 130 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 331 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 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 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 162 GLU Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 367 ARG 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 142 THR Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 338 TYR 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 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 348 LEU Chi-restraints excluded: chain L residue 354 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 90 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 224 optimal weight: 8.9990 chunk 180 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** F 169 ASN I 173 HIS J 15 GLN J 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.148871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.092795 restraints weight = 35571.925| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.39 r_work: 0.2895 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21862 Z= 0.133 Angle : 0.570 12.300 29660 Z= 0.281 Chirality : 0.040 0.171 3406 Planarity : 0.004 0.053 3720 Dihedral : 3.768 34.983 2953 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.19 % Allowed : 26.17 % Favored : 69.65 % 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: 1.64 (0.17), residues: 2590 helix: 1.95 (0.13), residues: 1580 sheet: 1.13 (0.30), residues: 336 loop : -1.03 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 16 HIS 0.004 0.001 HIS L 101 PHE 0.009 0.001 PHE B 168 TYR 0.031 0.001 TYR B 190 ARG 0.007 0.000 ARG L 314 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 1348) hydrogen bonds : angle 4.04163 ( 3924) SS BOND : bond 0.00221 ( 4) SS BOND : angle 1.82181 ( 8) covalent geometry : bond 0.00311 (21858) covalent geometry : angle 0.56945 (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 475 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 378 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.9184 (mmm160) cc_final: 0.8724 (tpt-90) REVERT: E 170 GLU cc_start: 0.8612 (tp30) cc_final: 0.8084 (tp30) REVERT: F 135 ASP cc_start: 0.8637 (p0) cc_final: 0.8392 (p0) REVERT: G 368 ASP cc_start: 0.9166 (t0) cc_final: 0.8619 (t0) REVERT: H 47 ARG cc_start: 0.7277 (tpp80) cc_final: 0.6787 (ttm170) REVERT: H 108 ASP cc_start: 0.9060 (t0) cc_final: 0.8689 (t0) REVERT: I 134 MET cc_start: 0.9042 (tpt) cc_final: 0.8799 (tpt) REVERT: I 170 GLU cc_start: 0.8607 (tp30) cc_final: 0.8103 (tp30) REVERT: J 15 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7414 (mm110) REVERT: J 338 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: L 12 LYS cc_start: 0.7377 (ttmt) cc_final: 0.7069 (tttm) REVERT: L 23 MET cc_start: 0.8800 (mmm) cc_final: 0.8488 (mmm) REVERT: L 47 ARG cc_start: 0.8091 (tpp80) cc_final: 0.7746 (tpp80) REVERT: L 108 ASP cc_start: 0.9270 (t0) cc_final: 0.9017 (t0) REVERT: L 348 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8751 (tp) REVERT: A 10 TRP cc_start: 0.7006 (p-90) cc_final: 0.6714 (p-90) outliers start: 97 outliers final: 90 residues processed: 445 average time/residue: 0.3560 time to fit residues: 248.9224 Evaluate side-chains 463 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 370 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 SER 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 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 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 54 ILE 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 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 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 130 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 331 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 24 LEU 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 162 GLU Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 367 ARG 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 15 GLN 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 133 LEU 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 354 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 83 optimal weight: 0.6980 chunk 138 optimal weight: 0.5980 chunk 236 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 ASN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.148879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.092832 restraints weight = 35528.218| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.39 r_work: 0.2901 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 0.151 21862 Z= 0.154 Angle : 0.726 59.199 29660 Z= 0.388 Chirality : 0.040 0.169 3406 Planarity : 0.004 0.056 3720 Dihedral : 3.768 34.951 2953 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.19 % Allowed : 26.12 % Favored : 69.69 % Cbeta Deviations : 0.04 % 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: 1.65 (0.17), residues: 2590 helix: 1.96 (0.13), residues: 1580 sheet: 1.12 (0.30), residues: 336 loop : -1.03 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 16 HIS 0.004 0.001 HIS L 101 PHE 0.012 0.001 PHE A 90 TYR 0.046 0.002 TYR J 356 ARG 0.006 0.000 ARG G 47 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 1348) hydrogen bonds : angle 4.04551 ( 3924) SS BOND : bond 0.00234 ( 4) SS BOND : angle 1.77888 ( 8) covalent geometry : bond 0.00348 (21858) covalent geometry : angle 0.72556 (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 468 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 371 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.9171 (mmm160) cc_final: 0.8710 (tpt-90) REVERT: E 170 GLU cc_start: 0.8603 (tp30) cc_final: 0.8076 (tp30) REVERT: F 135 ASP cc_start: 0.8634 (p0) cc_final: 0.8391 (p0) REVERT: G 368 ASP cc_start: 0.9165 (t0) cc_final: 0.8616 (t0) REVERT: H 47 ARG cc_start: 0.7301 (tpp80) cc_final: 0.6808 (ttm170) REVERT: H 108 ASP cc_start: 0.9068 (t0) cc_final: 0.8713 (t0) REVERT: I 134 MET cc_start: 0.9044 (tpt) cc_final: 0.8815 (tpt) REVERT: I 170 GLU cc_start: 0.8593 (tp30) cc_final: 0.8088 (tp30) REVERT: J 338 TYR cc_start: 0.7203 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: L 12 LYS cc_start: 0.7367 (ttmt) cc_final: 0.7061 (tttm) REVERT: L 23 MET cc_start: 0.8791 (mmm) cc_final: 0.8469 (mmm) REVERT: L 47 ARG cc_start: 0.8105 (tpp80) cc_final: 0.7764 (tpp80) REVERT: L 108 ASP cc_start: 0.9273 (t0) cc_final: 0.9021 (t0) REVERT: L 348 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8744 (tp) REVERT: A 10 TRP cc_start: 0.7013 (p-90) cc_final: 0.6715 (p-90) outliers start: 97 outliers final: 93 residues processed: 439 average time/residue: 0.3351 time to fit residues: 233.7365 Evaluate side-chains 460 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 365 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 SER 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 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 203 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 54 ILE 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 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 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 48 GLN 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 338 TYR 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 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 162 GLU Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 367 ARG 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 130 VAL Chi-restraints excluded: chain J residue 133 LEU 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 354 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 143 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 78 optimal weight: 0.1980 chunk 104 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.148838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.093030 restraints weight = 35578.379| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.37 r_work: 0.2899 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 21862 Z= 0.154 Angle : 0.726 59.199 29660 Z= 0.388 Chirality : 0.040 0.169 3406 Planarity : 0.004 0.056 3720 Dihedral : 3.768 34.951 2953 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.10 % Allowed : 26.12 % Favored : 69.78 % Cbeta Deviations : 0.04 % 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: 1.65 (0.17), residues: 2590 helix: 1.96 (0.13), residues: 1580 sheet: 1.12 (0.30), residues: 336 loop : -1.03 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 16 HIS 0.004 0.001 HIS L 101 PHE 0.012 0.001 PHE A 90 TYR 0.046 0.002 TYR J 356 ARG 0.006 0.000 ARG G 47 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 1348) hydrogen bonds : angle 4.04551 ( 3924) SS BOND : bond 0.00234 ( 4) SS BOND : angle 1.77888 ( 8) covalent geometry : bond 0.00348 (21858) covalent geometry : angle 0.72557 (29652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12639.89 seconds wall clock time: 220 minutes 59.88 seconds (13259.88 seconds total)