Starting phenix.real_space_refine on Tue Jul 23 05:30:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsl_41595/07_2024/8tsl_41595.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsl_41595/07_2024/8tsl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsl_41595/07_2024/8tsl_41595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsl_41595/07_2024/8tsl_41595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsl_41595/07_2024/8tsl_41595.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsl_41595/07_2024/8tsl_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 Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "G TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 162": "OE1" <-> "OE2" Residue "I GLU 170": "OE1" <-> "OE2" Residue "J GLU 165": "OE1" <-> "OE2" Residue "J GLU 328": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 11.44, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 8.69 Conformation dependent library (CDL) restraints added in 4.2 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: 2.21 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: 6.61 Time building geometry restraints manager: 9.55 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: 98.01 - 105.24: 388 105.24 - 112.46: 11230 112.46 - 119.68: 7434 119.68 - 126.90: 10329 126.90 - 134.13: 271 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 2.520 nonbonded pdb=" NH2 ARG J 47 " pdb=" OH TYR K 78 " model vdw 2.234 2.520 nonbonded pdb=" OH TYR H 29 " pdb=" OD1 ASP H 108 " model vdw 2.236 2.440 nonbonded pdb=" O ILE D 54 " pdb=" OG1 THR D 58 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR L 29 " pdb=" OD1 ASP L 108 " model vdw 2.250 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 9 through 48 or resid 72 through 176 or resid 321 through \ 369)) selection = (chain 'F' and resid 9 through 369) selection = (chain 'G' and (resid 9 through 48 or resid 72 through 176 or resid 321 through \ 369)) selection = (chain 'H' and (resid 9 through 48 or resid 72 through 176 or resid 321 through \ 369)) selection = (chain 'I' and (resid 9 through 48 or resid 72 through 176 or resid 321 through \ 369)) selection = (chain 'J' and resid 9 through 369) selection = (chain 'K' and (resid 9 through 48 or resid 72 through 176 or resid 321 through \ 369)) selection = (chain 'L' and (resid 9 through 48 or resid 72 through 176 or resid 321 through \ 369)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 56.920 Find NCS groups from input model: 1.270 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: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.610 ------------------------------------------------------------------------------- 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 21858 Z= 0.238 Angle : 0.671 8.877 29652 Z= 0.363 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 *********************** 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 fitting. rotamer outliers: 11 poor density : 409 time to evaluate : 2.708 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: 0.3401 time to fit residues: 214.4689 Evaluate side-chains 392 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 388 time to evaluate : 2.383 ------------------------------------------------------------------------------- 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: 0.8980 chunk 132 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 203 optimal weight: 0.0470 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 236 optimal weight: 20.0000 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 173 HIS F 15 GLN F 169 ASN H 95 GLN H 169 ASN I 173 HIS J 169 ASN L 48 GLN L 169 ASN A 118 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21858 Z= 0.171 Angle : 0.515 7.338 29652 Z= 0.259 Chirality : 0.039 0.149 3406 Planarity : 0.004 0.076 3720 Dihedral : 3.865 38.875 2957 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.89 % Allowed : 25.30 % Favored : 71.80 % 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: 1.53 (0.17), residues: 2590 helix: 1.87 (0.13), residues: 1580 sheet: 1.19 (0.30), residues: 336 loop : -1.17 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 45 HIS 0.003 0.001 HIS L 101 PHE 0.012 0.001 PHE A 90 TYR 0.013 0.001 TYR F 356 ARG 0.009 0.000 ARG B 104 *********************** 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 468 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 401 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.8721 (mmm160) cc_final: 0.8338 (tpt-90) REVERT: D 45 TRP cc_start: 0.7718 (m-90) cc_final: 0.7335 (m-90) REVERT: E 170 GLU cc_start: 0.8153 (tp30) cc_final: 0.7878 (tp30) REVERT: F 15 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7326 (mm110) REVERT: F 137 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.9012 (pt) REVERT: I 170 GLU cc_start: 0.8173 (tp30) cc_final: 0.7918 (tp30) REVERT: J 135 ASP cc_start: 0.8856 (p0) cc_final: 0.8637 (p0) REVERT: J 338 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.7049 (m-80) REVERT: L 138 CYS cc_start: 0.8362 (m) cc_final: 0.8134 (m) REVERT: L 363 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8923 (p) REVERT: A 10 TRP cc_start: 0.7229 (p-90) cc_final: 0.6953 (p-90) outliers start: 67 outliers final: 38 residues processed: 437 average time/residue: 0.3206 time to fit residues: 215.7820 Evaluate side-chains 425 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 383 time to evaluate : 2.357 ------------------------------------------------------------------------------- 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 76 VAL 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 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 I residue 16 TRP Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 137 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 K residue 136 ASP 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 131 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 196 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 65 optimal weight: 0.0050 chunk 236 optimal weight: 50.0000 chunk 255 optimal weight: 40.0000 chunk 210 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- 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 H 48 GLN I 169 ASN I 173 HIS J 15 GLN J 169 ASN A 6 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21858 Z= 0.331 Angle : 0.570 9.850 29652 Z= 0.289 Chirality : 0.042 0.185 3406 Planarity : 0.004 0.067 3720 Dihedral : 3.831 35.815 2953 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.27 % Allowed : 24.48 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.17), residues: 2590 helix: 1.85 (0.13), residues: 1584 sheet: 1.16 (0.30), residues: 338 loop : -1.16 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 16 HIS 0.004 0.001 HIS D 221 PHE 0.010 0.001 PHE L 122 TYR 0.015 0.002 TYR F 356 ARG 0.006 0.000 ARG K 47 *********************** 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 506 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 384 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.8823 (mmm160) cc_final: 0.8351 (tpt-90) REVERT: D 45 TRP cc_start: 0.7835 (m-90) cc_final: 0.7371 (m-90) REVERT: E 170 GLU cc_start: 0.8188 (tp30) cc_final: 0.7817 (tp30) REVERT: F 137 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9194 (pt) REVERT: G 368 ASP cc_start: 0.8978 (t0) cc_final: 0.8381 (t0) REVERT: I 170 GLU cc_start: 0.8189 (tp30) cc_final: 0.7819 (tp30) REVERT: J 135 ASP cc_start: 0.8954 (p0) cc_final: 0.8729 (p0) REVERT: L 363 VAL cc_start: 0.9176 (OUTLIER) cc_final: 0.8963 (p) REVERT: A 10 TRP cc_start: 0.7092 (p-90) cc_final: 0.6817 (p-90) REVERT: B 105 LYS cc_start: 0.7222 (tppt) cc_final: 0.6894 (tppt) outliers start: 122 outliers final: 88 residues processed: 470 average time/residue: 0.3072 time to fit residues: 224.3128 Evaluate side-chains 461 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 371 time to evaluate : 2.576 ------------------------------------------------------------------------------- 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 76 VAL 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 C residue 257 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 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 16 TRP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 137 ILE 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 136 ASP Chi-restraints excluded: chain G residue 338 TYR Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 16 TRP Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 137 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 335 ILE Chi-restraints excluded: chain I residue 353 CYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 136 ASP 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 136 ASP 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 45 THR 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 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 233 optimal weight: 30.0000 chunk 177 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 237 optimal weight: 8.9990 chunk 251 optimal weight: 20.0000 chunk 124 optimal weight: 0.6980 chunk 224 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 I 169 ASN I 173 HIS J 15 GLN L 169 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21858 Z= 0.171 Angle : 0.514 11.821 29652 Z= 0.256 Chirality : 0.039 0.149 3406 Planarity : 0.003 0.059 3720 Dihedral : 3.726 35.825 2953 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.80 % Allowed : 26.21 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.17), residues: 2590 helix: 2.04 (0.13), residues: 1574 sheet: 1.21 (0.30), residues: 336 loop : -1.08 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 16 HIS 0.004 0.001 HIS K 101 PHE 0.015 0.001 PHE A 90 TYR 0.017 0.001 TYR F 356 ARG 0.006 0.000 ARG K 47 *********************** 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 486 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 398 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.8775 (mmm160) cc_final: 0.8302 (tpt-90) REVERT: E 170 GLU cc_start: 0.8313 (tp30) cc_final: 0.7879 (tp30) REVERT: F 135 ASP cc_start: 0.8783 (p0) cc_final: 0.8545 (p0) REVERT: G 368 ASP cc_start: 0.8979 (t0) cc_final: 0.8329 (t0) REVERT: H 12 LYS cc_start: 0.7644 (tttt) cc_final: 0.7271 (ttmt) REVERT: H 47 ARG cc_start: 0.7415 (tpp80) cc_final: 0.7034 (tpp80) REVERT: H 348 LEU cc_start: 0.9005 (tp) cc_final: 0.8697 (tp) REVERT: I 170 GLU cc_start: 0.8248 (tp30) cc_final: 0.7843 (tp30) REVERT: L 363 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8945 (p) REVERT: A 10 TRP cc_start: 0.7135 (p-90) cc_final: 0.6806 (p-90) REVERT: B 105 LYS cc_start: 0.7031 (tppt) cc_final: 0.6814 (tppt) outliers start: 88 outliers final: 59 residues processed: 448 average time/residue: 0.3179 time to fit residues: 220.5244 Evaluate side-chains 440 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 380 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 69 MET 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 69 MET Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 199 VAL 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 45 THR Chi-restraints excluded: chain F residue 130 VAL 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 118 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 16 TRP Chi-restraints excluded: chain I residue 136 ASP 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 130 VAL Chi-restraints excluded: chain J residue 136 ASP 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 21 LEU Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 136 ASP 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 L residue 363 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 138 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 H 169 ASN I 173 HIS J 15 GLN J 169 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21858 Z= 0.299 Angle : 0.569 10.748 29652 Z= 0.285 Chirality : 0.042 0.186 3406 Planarity : 0.004 0.053 3720 Dihedral : 3.811 38.160 2953 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.14 % Allowed : 25.35 % Favored : 69.52 % 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: 1.67 (0.17), residues: 2590 helix: 2.00 (0.13), residues: 1576 sheet: 1.19 (0.30), residues: 334 loop : -1.08 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 45 HIS 0.004 0.001 HIS H 101 PHE 0.009 0.001 PHE D 248 TYR 0.020 0.002 TYR F 356 ARG 0.006 0.000 ARG G 47 *********************** 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 501 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 382 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 96 MET cc_start: 0.8682 (ptm) cc_final: 0.8439 (ptm) REVERT: D 30 ARG cc_start: 0.8815 (mmm160) cc_final: 0.8346 (tpt-90) REVERT: E 170 GLU cc_start: 0.8273 (tp30) cc_final: 0.7805 (tp30) REVERT: G 368 ASP cc_start: 0.9016 (t0) cc_final: 0.8365 (t0) REVERT: H 12 LYS cc_start: 0.7864 (tttt) cc_final: 0.7323 (ttmt) REVERT: H 348 LEU cc_start: 0.9005 (tp) cc_final: 0.8661 (tp) REVERT: I 170 GLU cc_start: 0.8253 (tp30) cc_final: 0.7819 (tp30) REVERT: L 12 LYS cc_start: 0.7442 (ttmt) cc_final: 0.7126 (tttm) REVERT: L 138 CYS cc_start: 0.8415 (m) cc_final: 0.8179 (m) REVERT: L 363 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8947 (p) REVERT: A 10 TRP cc_start: 0.7090 (p-90) cc_final: 0.6782 (p-90) REVERT: B 105 LYS cc_start: 0.7140 (tppt) cc_final: 0.6828 (tppt) outliers start: 119 outliers final: 93 residues processed: 466 average time/residue: 0.3104 time to fit residues: 224.4316 Evaluate side-chains 465 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 371 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LYS 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 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 241 ASN 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 241 ASN 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 E residue 350 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 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 39 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 137 ILE 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 G residue 362 VAL Chi-restraints excluded: chain H residue 24 LEU 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 321 LEU Chi-restraints excluded: chain I residue 16 TRP Chi-restraints excluded: chain I residue 36 ASP 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 130 VAL Chi-restraints excluded: chain J residue 136 ASP 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 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 42 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 136 ASP 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 32 VAL Chi-restraints excluded: chain L residue 45 THR 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 L residue 363 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 10 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 2.9990 chunk 226 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 147 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 251 optimal weight: 20.0000 chunk 208 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 I 173 HIS J 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21858 Z= 0.167 Angle : 0.530 12.116 29652 Z= 0.262 Chirality : 0.040 0.153 3406 Planarity : 0.003 0.053 3720 Dihedral : 3.717 38.843 2953 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.45 % Allowed : 26.73 % Favored : 68.83 % 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: 1.81 (0.17), residues: 2590 helix: 2.10 (0.13), residues: 1574 sheet: 1.25 (0.30), residues: 336 loop : -1.03 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 45 HIS 0.004 0.001 HIS G 101 PHE 0.017 0.001 PHE A 90 TYR 0.023 0.001 TYR J 356 ARG 0.007 0.000 ARG K 47 *********************** 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 500 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 397 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.8725 (mmm160) cc_final: 0.8304 (tpt-90) REVERT: E 170 GLU cc_start: 0.8294 (tp30) cc_final: 0.7815 (tp30) REVERT: G 368 ASP cc_start: 0.8995 (t0) cc_final: 0.8338 (t0) REVERT: H 12 LYS cc_start: 0.7778 (tttt) cc_final: 0.7273 (ttmt) REVERT: H 47 ARG cc_start: 0.7634 (tpp80) cc_final: 0.7228 (tpp-160) REVERT: I 170 GLU cc_start: 0.8264 (tp30) cc_final: 0.7807 (tp30) REVERT: I 175 MET cc_start: 0.8235 (tpp) cc_final: 0.8028 (tpp) REVERT: J 76 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.9008 (m) REVERT: J 134 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8746 (ttt) REVERT: J 135 ASP cc_start: 0.8801 (p0) cc_final: 0.8581 (p0) REVERT: L 47 ARG cc_start: 0.7882 (tpp80) cc_final: 0.7474 (tpp-160) REVERT: L 135 ASP cc_start: 0.7956 (t0) cc_final: 0.7711 (t0) REVERT: L 138 CYS cc_start: 0.8400 (m) cc_final: 0.8114 (m) REVERT: L 363 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8932 (p) REVERT: A 10 TRP cc_start: 0.7040 (p-90) cc_final: 0.6673 (p-90) REVERT: B 105 LYS cc_start: 0.7047 (tppt) cc_final: 0.6637 (tppt) outliers start: 103 outliers final: 81 residues processed: 466 average time/residue: 0.3110 time to fit residues: 224.2643 Evaluate side-chains 467 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 383 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 122 MET 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 C residue 267 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 127 LEU Chi-restraints excluded: chain D residue 149 VAL 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 205 THR Chi-restraints excluded: chain E residue 16 TRP Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 36 ASP 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 E residue 353 CYS 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 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 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 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 H residue 367 ARG Chi-restraints excluded: chain I residue 16 TRP Chi-restraints excluded: chain I residue 36 ASP 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 6 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain J residue 136 ASP 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 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 118 SER Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain K residue 360 SER Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 97 LYS Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 10 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 250 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 G 94 GLN I 173 HIS J 15 GLN J 169 ASN K 94 GLN L 169 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21858 Z= 0.244 Angle : 0.561 11.955 29652 Z= 0.279 Chirality : 0.041 0.174 3406 Planarity : 0.004 0.045 3720 Dihedral : 3.760 40.757 2953 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.57 % Allowed : 26.04 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.17), residues: 2590 helix: 2.04 (0.13), residues: 1588 sheet: 1.26 (0.30), residues: 336 loop : -1.13 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 45 HIS 0.004 0.001 HIS L 101 PHE 0.007 0.001 PHE K 152 TYR 0.024 0.001 TYR F 356 ARG 0.007 0.000 ARG K 47 *********************** 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 516 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 387 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.8756 (mmm160) cc_final: 0.8352 (tpt-90) REVERT: E 170 GLU cc_start: 0.8279 (tp30) cc_final: 0.7791 (tp30) REVERT: E 175 MET cc_start: 0.8295 (tpp) cc_final: 0.8072 (tpp) REVERT: G 368 ASP cc_start: 0.9001 (t0) cc_final: 0.8334 (t0) REVERT: H 12 LYS cc_start: 0.7889 (tttt) cc_final: 0.7299 (ttmt) REVERT: I 170 GLU cc_start: 0.8255 (tp30) cc_final: 0.7807 (tp30) REVERT: J 15 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7647 (mm-40) REVERT: J 76 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9022 (m) REVERT: J 137 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9112 (pt) REVERT: L 47 ARG cc_start: 0.7809 (tpp80) cc_final: 0.7470 (tpp-160) REVERT: L 135 ASP cc_start: 0.7910 (t0) cc_final: 0.7701 (t0) REVERT: L 363 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8954 (p) REVERT: A 10 TRP cc_start: 0.7030 (p-90) cc_final: 0.6670 (p-90) REVERT: B 102 MET cc_start: 0.8238 (ppp) cc_final: 0.7992 (ppp) REVERT: B 105 LYS cc_start: 0.7095 (tppt) cc_final: 0.6738 (tppt) outliers start: 129 outliers final: 100 residues processed: 473 average time/residue: 0.3153 time to fit residues: 232.5391 Evaluate side-chains 478 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 374 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LYS 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 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 197 SER 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 C residue 267 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 127 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 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 D residue 213 LEU Chi-restraints excluded: chain E residue 16 TRP Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 36 ASP 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 34 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 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 360 SER Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 24 LEU 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 321 LEU Chi-restraints excluded: chain H residue 367 ARG Chi-restraints excluded: chain I residue 16 TRP Chi-restraints excluded: chain I residue 36 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 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 15 GLN Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 136 ASP Chi-restraints excluded: chain J residue 137 ILE 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 49 THR Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain K residue 360 SER Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 97 LYS Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 10 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 I 173 HIS J 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21858 Z= 0.176 Angle : 0.548 12.342 29652 Z= 0.269 Chirality : 0.040 0.160 3406 Planarity : 0.003 0.067 3720 Dihedral : 3.740 41.926 2953 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.71 % Allowed : 26.60 % Favored : 68.70 % 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: 1.78 (0.17), residues: 2590 helix: 2.06 (0.13), residues: 1588 sheet: 1.31 (0.30), residues: 336 loop : -1.12 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 16 HIS 0.004 0.001 HIS L 101 PHE 0.020 0.001 PHE A 90 TYR 0.016 0.001 TYR J 356 ARG 0.007 0.000 ARG G 47 *********************** 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 502 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 393 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.8729 (mmm160) cc_final: 0.8353 (tpt-90) REVERT: E 170 GLU cc_start: 0.8277 (tp30) cc_final: 0.7777 (tp30) REVERT: G 368 ASP cc_start: 0.8983 (t0) cc_final: 0.8323 (t0) REVERT: H 12 LYS cc_start: 0.7844 (tttt) cc_final: 0.7274 (ttmt) REVERT: H 47 ARG cc_start: 0.7752 (tpp80) cc_final: 0.7339 (tpp-160) REVERT: I 170 GLU cc_start: 0.8259 (tp30) cc_final: 0.7814 (tp30) REVERT: I 175 MET cc_start: 0.8201 (tpp) cc_final: 0.7977 (tpp) REVERT: J 137 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9076 (pt) REVERT: L 47 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7463 (tpp-160) REVERT: L 363 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8942 (p) REVERT: A 10 TRP cc_start: 0.7012 (p-90) cc_final: 0.6656 (p-90) REVERT: B 105 LYS cc_start: 0.6979 (tppt) cc_final: 0.6626 (tppt) outliers start: 109 outliers final: 93 residues processed: 469 average time/residue: 0.3152 time to fit residues: 227.1393 Evaluate side-chains 477 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 382 time to evaluate : 2.391 ------------------------------------------------------------------------------- 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 197 SER 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 267 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 138 THR Chi-restraints excluded: chain D residue 149 VAL 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 16 TRP Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 36 ASP 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 331 VAL 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 324 LEU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 16 TRP Chi-restraints excluded: chain I residue 36 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 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 130 VAL Chi-restraints excluded: chain J residue 136 ASP Chi-restraints excluded: chain J residue 137 ILE 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 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 136 ASP 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 L residue 354 LEU Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 10 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 6.9990 chunk 240 optimal weight: 0.9990 chunk 219 optimal weight: 20.0000 chunk 233 optimal weight: 6.9990 chunk 140 optimal weight: 0.1980 chunk 101 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 GLN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS I 173 HIS J 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 21858 Z= 0.366 Angle : 0.630 12.249 29652 Z= 0.314 Chirality : 0.043 0.222 3406 Planarity : 0.004 0.059 3720 Dihedral : 3.953 45.715 2953 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.88 % Allowed : 26.68 % Favored : 68.44 % 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: 1.56 (0.17), residues: 2590 helix: 1.90 (0.13), residues: 1588 sheet: 1.24 (0.30), residues: 334 loop : -1.23 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 16 HIS 0.004 0.001 HIS L 101 PHE 0.010 0.001 PHE D 248 TYR 0.026 0.002 TYR J 356 ARG 0.009 0.000 ARG L 314 *********************** 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 483 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 370 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.8772 (mmm160) cc_final: 0.8378 (tpt-90) REVERT: E 170 GLU cc_start: 0.8237 (tp30) cc_final: 0.7741 (tp30) REVERT: G 368 ASP cc_start: 0.9084 (t0) cc_final: 0.8500 (t0) REVERT: H 12 LYS cc_start: 0.7936 (tttt) cc_final: 0.7332 (ttmt) REVERT: I 170 GLU cc_start: 0.8296 (tp30) cc_final: 0.7831 (tp30) REVERT: L 138 CYS cc_start: 0.8464 (m) cc_final: 0.8221 (m) REVERT: L 363 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8935 (p) REVERT: A 10 TRP cc_start: 0.7010 (p-90) cc_final: 0.6667 (p-90) REVERT: B 102 MET cc_start: 0.8280 (ppp) cc_final: 0.8058 (ppp) REVERT: B 105 LYS cc_start: 0.7162 (tppt) cc_final: 0.6794 (tppt) outliers start: 113 outliers final: 103 residues processed: 451 average time/residue: 0.3161 time to fit residues: 223.2447 Evaluate side-chains 467 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 363 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 33 LYS 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 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 197 SER 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 C residue 267 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 127 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 36 ASP 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 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 324 LEU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 110 LEU 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 G residue 362 VAL Chi-restraints excluded: chain H residue 24 LEU 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 321 LEU Chi-restraints excluded: chain H residue 367 ARG Chi-restraints excluded: chain I residue 36 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 331 VAL Chi-restraints excluded: chain I residue 335 ILE Chi-restraints excluded: chain I residue 350 VAL 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 130 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 136 ASP 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 39 VAL Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 136 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 7.9990 chunk 246 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 259 optimal weight: 7.9990 chunk 238 optimal weight: 7.9990 chunk 206 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 I 173 HIS L 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21858 Z= 0.176 Angle : 0.566 12.841 29652 Z= 0.277 Chirality : 0.040 0.163 3406 Planarity : 0.004 0.055 3720 Dihedral : 3.826 46.278 2953 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.02 % Allowed : 27.03 % Favored : 68.96 % 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: 1.98 (0.13), residues: 1588 sheet: 1.26 (0.30), residues: 336 loop : -1.14 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 16 HIS 0.004 0.001 HIS K 101 PHE 0.010 0.001 PHE D 86 TYR 0.027 0.001 TYR J 356 ARG 0.008 0.000 ARG L 314 ********************** 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 477 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 384 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.8681 (mmm160) cc_final: 0.8333 (tpt-90) REVERT: E 170 GLU cc_start: 0.8260 (tp30) cc_final: 0.7747 (tp30) REVERT: G 368 ASP cc_start: 0.9013 (t0) cc_final: 0.8451 (t0) REVERT: H 12 LYS cc_start: 0.7879 (tttt) cc_final: 0.7313 (ttmt) REVERT: I 170 GLU cc_start: 0.8270 (tp30) cc_final: 0.7813 (tp30) REVERT: J 47 ARG cc_start: 0.7636 (tpp80) cc_final: 0.6789 (mmt90) REVERT: L 47 ARG cc_start: 0.7604 (tpp80) cc_final: 0.7289 (tpp-160) REVERT: L 138 CYS cc_start: 0.8422 (m) cc_final: 0.8171 (m) REVERT: L 363 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8924 (p) REVERT: A 10 TRP cc_start: 0.6983 (p-90) cc_final: 0.6595 (p-90) REVERT: B 102 MET cc_start: 0.8293 (ppp) cc_final: 0.8072 (ppp) REVERT: B 105 LYS cc_start: 0.7266 (tppt) cc_final: 0.6902 (tppt) outliers start: 93 outliers final: 85 residues processed: 451 average time/residue: 0.3128 time to fit residues: 218.6921 Evaluate side-chains 466 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 380 time to evaluate : 2.541 ------------------------------------------------------------------------------- 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 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 197 SER 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 C residue 267 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 138 THR Chi-restraints excluded: chain D residue 149 VAL 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 E residue 23 MET Chi-restraints excluded: chain E residue 36 ASP 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 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 24 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 49 THR 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 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 H residue 367 ARG Chi-restraints excluded: chain I residue 16 TRP Chi-restraints excluded: chain I residue 36 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 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 34 SER Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 136 ASP 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 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 49 THR Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 136 ASP 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 L residue 363 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 10 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.8980 chunk 219 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 57 optimal weight: 0.0020 chunk 206 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 ASN J 15 GLN J 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.148388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.093131 restraints weight = 35555.265| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.34 r_work: 0.2913 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21858 Z= 0.174 Angle : 0.561 12.726 29652 Z= 0.273 Chirality : 0.040 0.162 3406 Planarity : 0.004 0.052 3720 Dihedral : 3.774 47.508 2953 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.02 % Allowed : 27.59 % Favored : 68.39 % 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: 2.01 (0.13), residues: 1590 sheet: 1.31 (0.30), residues: 336 loop : -1.13 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 16 HIS 0.004 0.001 HIS L 101 PHE 0.012 0.001 PHE A 90 TYR 0.019 0.001 TYR J 356 ARG 0.008 0.000 ARG L 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4974.67 seconds wall clock time: 89 minutes 5.23 seconds (5345.23 seconds total)