Starting phenix.real_space_refine on Mon Mar 11 12:05:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iac_4435/03_2024/6iac_4435.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iac_4435/03_2024/6iac_4435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iac_4435/03_2024/6iac_4435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iac_4435/03_2024/6iac_4435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iac_4435/03_2024/6iac_4435.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iac_4435/03_2024/6iac_4435.pdb" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.010 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 23 5.16 5 C 5208 2.51 5 N 1384 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 26": "NH1" <-> "NH2" Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 61": "NH1" <-> "NH2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8210 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2353 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1763 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1164 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 135} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1259 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain: "F" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1019 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "I" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "J" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "K" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 112 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "L" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 4.70, per 1000 atoms: 0.57 Number of scatterers: 8210 At special positions: 0 Unit cell: (126.497, 184.962, 255.12, 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 23 16.00 O 1595 8.00 N 1384 7.00 C 5208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.91 Conformation dependent library (CDL) restraints added in 1.5 seconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 61.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 15 through 39 removed outlier: 4.322A pdb=" N VAL A 21 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 152 through 177 removed outlier: 3.960A pdb=" N ILE A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 200 Processing helix chain 'A' and resid 227 through 247 removed outlier: 4.174A pdb=" N THR A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.522A pdb=" N GLY A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.567A pdb=" N THR A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.653A pdb=" N PHE A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.721A pdb=" N ASP A 324 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 removed outlier: 3.583A pdb=" N LYS B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 46 removed outlier: 3.585A pdb=" N LYS B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 58 Processing helix chain 'B' and resid 68 through 79 removed outlier: 3.651A pdb=" N LEU B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.562A pdb=" N ILE B 99 " --> pdb=" O GLY B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.567A pdb=" N LYS B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 246 removed outlier: 4.109A pdb=" N GLU B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 removed outlier: 3.626A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP D 19 " --> pdb=" O ARG D 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 14 through 19' Processing helix chain 'D' and resid 20 through 23 removed outlier: 3.840A pdb=" N LYS D 23 " --> pdb=" O GLU D 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 42 through 53 removed outlier: 3.550A pdb=" N ARG D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 84 removed outlier: 4.089A pdb=" N ALA D 60 " --> pdb=" O ILE D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 98 removed outlier: 4.946A pdb=" N ASP D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 141 removed outlier: 3.939A pdb=" N ILE D 104 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP D 140 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.335A pdb=" N ILE D 145 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP D 146 " --> pdb=" O LYS D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing helix chain 'E' and resid 14 through 17 Processing helix chain 'E' and resid 18 through 27 removed outlier: 3.772A pdb=" N TYR E 22 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU E 26 " --> pdb=" O TYR E 22 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG E 27 " --> pdb=" O LYS E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 65 removed outlier: 3.722A pdb=" N LYS E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU E 55 " --> pdb=" O ARG E 51 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG E 62 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 74 removed outlier: 4.097A pdb=" N GLU E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 104 removed outlier: 4.129A pdb=" N ASP E 78 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Proline residue: E 85 - end of helix removed outlier: 3.719A pdb=" N TRP E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E 96 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP E 98 " --> pdb=" O GLY E 94 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE E 101 " --> pdb=" O ASN E 97 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP E 102 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 146 removed outlier: 3.670A pdb=" N LYS E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA E 119 " --> pdb=" O GLY E 115 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'F' and resid 44 through 83 removed outlier: 3.960A pdb=" N LYS F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP F 79 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 80 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.713A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 110 through 135 removed outlier: 3.517A pdb=" N ALA F 114 " --> pdb=" O LYS F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 removed outlier: 3.923A pdb=" N LYS F 139 " --> pdb=" O SER F 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'G' and resid 78 through 94 Processing helix chain 'H' and resid 78 through 94 Processing helix chain 'I' and resid 78 through 98 Processing helix chain 'J' and resid 78 through 97 removed outlier: 3.599A pdb=" N GLN J 97 " --> pdb=" O PHE J 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 94 Processing helix chain 'L' and resid 78 through 95 removed outlier: 3.508A pdb=" N PHE L 93 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 3.984A pdb=" N VAL A 68 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 removed outlier: 4.017A pdb=" N SER A 181 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 127 removed outlier: 3.779A pdb=" N GLN B 125 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 132 removed outlier: 3.500A pdb=" N ARG B 206 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 135 through 139 Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 150 435 hydrogen bonds defined for protein. 1278 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: 1.85 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2182 1.33 - 1.45: 1673 1.45 - 1.57: 4450 1.57 - 1.69: 0 1.69 - 1.81: 43 Bond restraints: 8348 Sorted by residual: bond pdb=" C ARG D 15 " pdb=" N PRO D 16 " ideal model delta sigma weight residual 1.334 1.368 -0.035 8.40e-03 1.42e+04 1.71e+01 bond pdb=" C GLU A 286 " pdb=" N PRO A 287 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.08e-02 8.57e+03 1.58e+01 bond pdb=" CA ASP A 153 " pdb=" C ASP A 153 " ideal model delta sigma weight residual 1.523 1.570 -0.046 1.80e-02 3.09e+03 6.65e+00 bond pdb=" CB MET B 6 " pdb=" CG MET B 6 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.09e+00 bond pdb=" CB TYR A 45 " pdb=" CG TYR A 45 " ideal model delta sigma weight residual 1.512 1.461 0.051 2.20e-02 2.07e+03 5.44e+00 ... (remaining 8343 not shown) Histogram of bond angle deviations from ideal: 97.08 - 104.54: 77 104.54 - 112.00: 3713 112.00 - 119.46: 3238 119.46 - 126.91: 4171 126.91 - 134.37: 72 Bond angle restraints: 11271 Sorted by residual: angle pdb=" C THR A 308 " pdb=" N SER A 309 " pdb=" CA SER A 309 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C LYS D 89 " pdb=" N ASP D 90 " pdb=" CA ASP D 90 " ideal model delta sigma weight residual 121.54 132.27 -10.73 1.91e+00 2.74e-01 3.15e+01 angle pdb=" CA TYR A 45 " pdb=" CB TYR A 45 " pdb=" CG TYR A 45 " ideal model delta sigma weight residual 113.90 123.83 -9.93 1.80e+00 3.09e-01 3.04e+01 angle pdb=" C ASP A 153 " pdb=" CA ASP A 153 " pdb=" CB ASP A 153 " ideal model delta sigma weight residual 110.36 100.37 9.99 1.85e+00 2.92e-01 2.92e+01 angle pdb=" C ASP A 264 " pdb=" N GLU A 265 " pdb=" CA GLU A 265 " ideal model delta sigma weight residual 121.54 131.79 -10.25 1.91e+00 2.74e-01 2.88e+01 ... (remaining 11266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 4589 16.07 - 32.14: 371 32.14 - 48.21: 78 48.21 - 64.28: 1 64.28 - 80.34: 6 Dihedral angle restraints: 5045 sinusoidal: 1896 harmonic: 3149 Sorted by residual: dihedral pdb=" CA GLU A 187 " pdb=" C GLU A 187 " pdb=" N ILE A 188 " pdb=" CA ILE A 188 " ideal model delta harmonic sigma weight residual -180.00 -139.12 -40.88 0 5.00e+00 4.00e-02 6.68e+01 dihedral pdb=" CA SER B 114 " pdb=" C SER B 114 " pdb=" N SER B 115 " pdb=" CA SER B 115 " ideal model delta harmonic sigma weight residual -180.00 -141.37 -38.63 0 5.00e+00 4.00e-02 5.97e+01 dihedral pdb=" CA TYR B 113 " pdb=" C TYR B 113 " pdb=" N SER B 114 " pdb=" CA SER B 114 " ideal model delta harmonic sigma weight residual 180.00 143.38 36.62 0 5.00e+00 4.00e-02 5.36e+01 ... (remaining 5042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 997 0.079 - 0.158: 210 0.158 - 0.237: 40 0.237 - 0.316: 6 0.316 - 0.395: 2 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CA TYR A 45 " pdb=" N TYR A 45 " pdb=" C TYR A 45 " pdb=" CB TYR A 45 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CG LEU A 8 " pdb=" CB LEU A 8 " pdb=" CD1 LEU A 8 " pdb=" CD2 LEU A 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB THR A 46 " pdb=" CA THR A 46 " pdb=" OG1 THR A 46 " pdb=" CG2 THR A 46 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1252 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 90 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C ASP D 90 " -0.070 2.00e-02 2.50e+03 pdb=" O ASP D 90 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU D 91 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 46 " -0.034 2.00e-02 2.50e+03 2.77e-02 1.53e+01 pdb=" CG TYR F 46 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR F 46 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR F 46 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 46 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR F 46 " -0.024 2.00e-02 2.50e+03 pdb=" CZ TYR F 46 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 46 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 45 " -0.035 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR A 45 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR A 45 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 45 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 45 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 45 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 45 " 0.003 2.00e-02 2.50e+03 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2080 2.78 - 3.31: 7828 3.31 - 3.84: 12670 3.84 - 4.37: 13537 4.37 - 4.90: 22438 Nonbonded interactions: 58553 Sorted by model distance: nonbonded pdb=" O ILE A 157 " pdb=" OG1 THR A 161 " model vdw 2.250 2.440 nonbonded pdb=" OG SER A 292 " pdb=" O LEU A 297 " model vdw 2.261 2.440 nonbonded pdb=" O PHE A 273 " pdb=" OG SER A 276 " model vdw 2.296 2.440 nonbonded pdb=" OH TYR D 66 " pdb=" OD1 ASP F 67 " model vdw 2.314 2.440 nonbonded pdb=" O THR A 108 " pdb=" OH TYR A 132 " model vdw 2.318 2.440 ... (remaining 58548 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 'D' and (resid 24 through 25 or (resid 26 through 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or nam \ e CA or name C or name O or name CB )) or resid 30 through 34 or (resid 35 throu \ gh 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ gh 144)) selection = (chain 'E' and (resid 24 through 25 or (resid 26 through 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or nam \ e CA or name C or name O or name CB )) or resid 30 through 34 or (resid 35 throu \ gh 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ gh 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or r \ esid 52 through 105 or (resid 106 through 107 and (name N or name CA or name C o \ r name O or name CB )) or resid 108 through 110 or (resid 111 and (name N or nam \ e CA or name C or name O or name CB )) or resid 112 through 144)) selection = (chain 'F' and (resid 24 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 50 or (resid 51 and (name N or nam \ e CA or name C or name O or name CB )) or resid 52 through 105 or (resid 106 thr \ ough 107 and (name N or name CA or name C or name O or name CB )) or resid 108 t \ hrough 110 or (resid 111 and (name N or name CA or name C or name O or name CB ) \ ) or resid 112 through 144)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 77 through 98) selection = (chain 'J' and resid 77 through 98) selection = (chain 'K' and (name N or name CA or name C or name O or name CB )) selection = (chain 'L' and resid 77 through 98) } 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 group one per residue 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: 4.460 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: 0.000 Extract box with map and model: 14.300 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.760 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.009 0.082 8348 Z= 0.607 Angle : 1.315 17.897 11271 Z= 0.721 Chirality : 0.069 0.395 1255 Planarity : 0.007 0.073 1460 Dihedral : 12.355 80.344 2989 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.95 % Favored : 87.85 % Rotamer: Outliers : 1.10 % Allowed : 6.11 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.78 % 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: -4.54 (0.20), residues: 1029 helix: -2.28 (0.16), residues: 582 sheet: -3.46 (0.43), residues: 84 loop : -3.95 (0.27), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP F 95 HIS 0.021 0.006 HIS E 106 PHE 0.064 0.005 PHE D 31 TYR 0.066 0.005 TYR A 45 ARG 0.014 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 417 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8464 (tm-30) REVERT: A 77 GLN cc_start: 0.9381 (mp10) cc_final: 0.9033 (mp10) REVERT: A 185 LYS cc_start: 0.8027 (ttmt) cc_final: 0.7669 (ttmt) REVERT: A 201 TYR cc_start: 0.9084 (t80) cc_final: 0.8456 (t80) REVERT: A 241 LYS cc_start: 0.8972 (ttmm) cc_final: 0.8346 (tppt) REVERT: A 244 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 248 TYR cc_start: 0.8663 (t80) cc_final: 0.8438 (t80) REVERT: A 259 GLU cc_start: 0.7944 (mp0) cc_final: 0.7744 (mp0) REVERT: A 303 TYR cc_start: 0.8185 (t80) cc_final: 0.7853 (t80) REVERT: A 306 GLU cc_start: 0.6681 (pt0) cc_final: 0.6439 (pt0) REVERT: B 18 LYS cc_start: 0.9060 (tmmm) cc_final: 0.8796 (ttpt) REVERT: B 47 ASP cc_start: 0.8620 (p0) cc_final: 0.8159 (p0) REVERT: B 51 LEU cc_start: 0.9506 (tp) cc_final: 0.9250 (tp) REVERT: B 125 GLN cc_start: 0.8587 (tm-30) cc_final: 0.7909 (tm-30) REVERT: B 145 ASN cc_start: 0.8448 (t0) cc_final: 0.8204 (t0) REVERT: B 188 ASP cc_start: 0.8873 (p0) cc_final: 0.8222 (m-30) REVERT: B 250 ILE cc_start: 0.8450 (tp) cc_final: 0.8177 (tt) REVERT: D 25 ARG cc_start: 0.8125 (ttt180) cc_final: 0.7589 (mpp-170) REVERT: D 47 ASP cc_start: 0.7655 (t0) cc_final: 0.7420 (t0) REVERT: D 75 LYS cc_start: 0.8163 (tmtt) cc_final: 0.7704 (mmpt) REVERT: D 87 GLN cc_start: 0.9137 (mt0) cc_final: 0.8898 (mt0) REVERT: D 89 LYS cc_start: 0.8266 (tmmt) cc_final: 0.7979 (tmtt) REVERT: D 90 ASP cc_start: 0.7751 (t0) cc_final: 0.7397 (p0) REVERT: D 133 ASP cc_start: 0.8682 (t0) cc_final: 0.8155 (t70) REVERT: E 14 ILE cc_start: 0.8274 (mm) cc_final: 0.7959 (pt) REVERT: E 17 PHE cc_start: 0.9141 (m-80) cc_final: 0.8862 (m-10) REVERT: E 22 TYR cc_start: 0.8511 (t80) cc_final: 0.7943 (t80) REVERT: E 23 LYS cc_start: 0.9392 (tptp) cc_final: 0.9189 (tptt) REVERT: E 51 ARG cc_start: 0.7862 (tpt-90) cc_final: 0.7402 (tmt170) REVERT: E 86 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8593 (tm-30) REVERT: E 90 ASP cc_start: 0.8850 (t0) cc_final: 0.8376 (m-30) REVERT: E 104 ILE cc_start: 0.8808 (mt) cc_final: 0.8007 (mm) REVERT: F 27 ARG cc_start: 0.8032 (ptp90) cc_final: 0.7752 (tpt-90) REVERT: F 43 LYS cc_start: 0.8892 (mtpm) cc_final: 0.8338 (mptt) REVERT: F 54 LYS cc_start: 0.6338 (tmmt) cc_final: 0.5470 (mttt) REVERT: F 57 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8379 (tm-30) REVERT: F 68 ASN cc_start: 0.8697 (t0) cc_final: 0.8439 (t0) REVERT: F 87 GLN cc_start: 0.8538 (tp-100) cc_final: 0.8150 (tp-100) REVERT: F 91 LEU cc_start: 0.7608 (pp) cc_final: 0.6593 (pp) REVERT: F 123 PHE cc_start: 0.7056 (t80) cc_final: 0.6732 (t80) REVERT: F 125 VAL cc_start: 0.9406 (t) cc_final: 0.9038 (p) REVERT: F 131 MET cc_start: 0.7930 (mmt) cc_final: 0.7729 (mmm) REVERT: F 143 LYS cc_start: 0.5689 (mppt) cc_final: 0.4091 (mmtt) outliers start: 9 outliers final: 2 residues processed: 420 average time/residue: 0.2232 time to fit residues: 121.3437 Evaluate side-chains 310 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 308 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 30.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS E 6 ASN E 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8348 Z= 0.260 Angle : 0.782 12.139 11271 Z= 0.416 Chirality : 0.048 0.232 1255 Planarity : 0.005 0.045 1460 Dihedral : 6.832 36.321 1138 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 5.50 % Allowed : 17.73 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.56 (0.25), residues: 1029 helix: -0.32 (0.20), residues: 598 sheet: -3.02 (0.46), residues: 87 loop : -3.82 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 95 HIS 0.005 0.001 HIS E 106 PHE 0.028 0.002 PHE F 84 TYR 0.028 0.002 TYR A 45 ARG 0.006 0.001 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 345 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8903 (p90) cc_final: 0.7524 (p90) REVERT: A 55 PHE cc_start: 0.8729 (m-80) cc_final: 0.8507 (m-80) REVERT: A 57 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8231 (tm-30) REVERT: A 76 LYS cc_start: 0.8627 (pttt) cc_final: 0.8025 (ptmt) REVERT: A 77 GLN cc_start: 0.9215 (mp10) cc_final: 0.8701 (mp10) REVERT: A 160 TYR cc_start: 0.8705 (m-80) cc_final: 0.8103 (m-80) REVERT: A 185 LYS cc_start: 0.7415 (ttmt) cc_final: 0.6707 (tmtt) REVERT: A 248 TYR cc_start: 0.8568 (t80) cc_final: 0.8321 (t80) REVERT: A 251 ILE cc_start: 0.9332 (pp) cc_final: 0.8905 (pp) REVERT: A 303 TYR cc_start: 0.7919 (t80) cc_final: 0.7514 (t80) REVERT: B 125 GLN cc_start: 0.8470 (tm-30) cc_final: 0.7895 (tm-30) REVERT: B 229 ASP cc_start: 0.7861 (t0) cc_final: 0.7629 (t0) REVERT: B 250 ILE cc_start: 0.8395 (tp) cc_final: 0.8184 (tt) REVERT: D 25 ARG cc_start: 0.8059 (ttt180) cc_final: 0.7492 (mpp-170) REVERT: D 122 LEU cc_start: 0.8999 (pp) cc_final: 0.8713 (mp) REVERT: D 141 LEU cc_start: 0.9138 (mt) cc_final: 0.8861 (pp) REVERT: E 17 PHE cc_start: 0.9040 (m-80) cc_final: 0.8834 (m-10) REVERT: E 22 TYR cc_start: 0.8483 (t80) cc_final: 0.7944 (t80) REVERT: E 46 TYR cc_start: 0.9180 (t80) cc_final: 0.8577 (t80) REVERT: E 51 ARG cc_start: 0.8032 (tpt-90) cc_final: 0.7560 (tmt170) REVERT: E 69 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8606 (tm-30) REVERT: E 86 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8649 (tm-30) REVERT: E 90 ASP cc_start: 0.8808 (t0) cc_final: 0.8463 (m-30) REVERT: F 27 ARG cc_start: 0.8190 (ptp90) cc_final: 0.7628 (tpt-90) REVERT: F 43 LYS cc_start: 0.8804 (mtpm) cc_final: 0.8365 (mptt) REVERT: F 54 LYS cc_start: 0.6184 (tmmt) cc_final: 0.5589 (mttt) REVERT: F 57 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8347 (tm-30) REVERT: F 61 ARG cc_start: 0.8807 (tpp-160) cc_final: 0.8560 (tpp80) REVERT: F 78 ASP cc_start: 0.8271 (m-30) cc_final: 0.7846 (m-30) REVERT: F 87 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8009 (tp-100) REVERT: F 91 LEU cc_start: 0.7555 (pp) cc_final: 0.6616 (pp) REVERT: F 143 LYS cc_start: 0.5482 (mppt) cc_final: 0.3700 (mmtt) outliers start: 45 outliers final: 28 residues processed: 363 average time/residue: 0.2129 time to fit residues: 102.2315 Evaluate side-chains 337 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 309 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8348 Z= 0.273 Angle : 0.760 9.240 11271 Z= 0.401 Chirality : 0.048 0.201 1255 Planarity : 0.004 0.040 1460 Dihedral : 6.302 36.215 1136 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.30 % Favored : 89.60 % Rotamer: Outliers : 7.33 % Allowed : 19.07 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.26), residues: 1029 helix: 0.50 (0.22), residues: 597 sheet: -2.96 (0.47), residues: 87 loop : -3.73 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 95 HIS 0.017 0.003 HIS B 130 PHE 0.025 0.003 PHE F 31 TYR 0.022 0.002 TYR A 160 ARG 0.007 0.001 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 320 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6403 (tt0) cc_final: 0.5833 (tt0) REVERT: A 45 TYR cc_start: 0.8862 (p90) cc_final: 0.8553 (p90) REVERT: A 57 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8161 (tm-30) REVERT: A 76 LYS cc_start: 0.8538 (pttt) cc_final: 0.7748 (ptmt) REVERT: A 77 GLN cc_start: 0.9243 (mp10) cc_final: 0.8693 (mp10) REVERT: A 155 GLU cc_start: 0.7824 (tp30) cc_final: 0.7565 (tp30) REVERT: B 30 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8406 (mm) REVERT: B 38 GLN cc_start: 0.8294 (pm20) cc_final: 0.7522 (pt0) REVERT: B 47 ASP cc_start: 0.8699 (p0) cc_final: 0.8377 (p0) REVERT: B 250 ILE cc_start: 0.8361 (tp) cc_final: 0.8145 (tt) REVERT: D 25 ARG cc_start: 0.8096 (ttt180) cc_final: 0.7447 (mpp-170) REVERT: D 75 LYS cc_start: 0.8147 (tmtt) cc_final: 0.7640 (mmpt) REVERT: D 122 LEU cc_start: 0.8998 (pp) cc_final: 0.8704 (mp) REVERT: E 22 TYR cc_start: 0.8392 (t80) cc_final: 0.7817 (t80) REVERT: E 51 ARG cc_start: 0.8238 (tpt-90) cc_final: 0.7805 (tmt170) REVERT: E 69 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8597 (tm-30) REVERT: E 86 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8587 (tm-30) REVERT: E 90 ASP cc_start: 0.8857 (t0) cc_final: 0.8537 (m-30) REVERT: F 27 ARG cc_start: 0.8153 (ptp90) cc_final: 0.7516 (tpt-90) REVERT: F 43 LYS cc_start: 0.8780 (mtpm) cc_final: 0.8315 (mptt) REVERT: F 54 LYS cc_start: 0.6454 (tmmt) cc_final: 0.5767 (mttm) REVERT: F 57 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8386 (tm-30) REVERT: F 78 ASP cc_start: 0.8221 (m-30) cc_final: 0.7760 (m-30) REVERT: F 87 GLN cc_start: 0.8484 (tp-100) cc_final: 0.8036 (tp-100) REVERT: F 91 LEU cc_start: 0.7602 (pp) cc_final: 0.6735 (pp) REVERT: F 105 ILE cc_start: 0.8003 (tt) cc_final: 0.7692 (tp) outliers start: 60 outliers final: 43 residues processed: 343 average time/residue: 0.1924 time to fit residues: 89.3416 Evaluate side-chains 346 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 302 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS B 189 ASN F 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8348 Z= 0.227 Angle : 0.738 9.686 11271 Z= 0.384 Chirality : 0.047 0.216 1255 Planarity : 0.004 0.036 1460 Dihedral : 5.928 35.513 1136 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 7.95 % Allowed : 22.00 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.25 (0.27), residues: 1029 helix: 0.87 (0.22), residues: 602 sheet: -2.61 (0.49), residues: 87 loop : -3.57 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 95 HIS 0.002 0.001 HIS B 105 PHE 0.039 0.002 PHE D 109 TYR 0.020 0.002 TYR A 160 ARG 0.006 0.001 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 319 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6160 (tt0) cc_final: 0.5597 (tt0) REVERT: A 45 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.8133 (p90) REVERT: A 77 GLN cc_start: 0.9222 (mp10) cc_final: 0.8675 (mp10) REVERT: A 241 LYS cc_start: 0.8918 (tppp) cc_final: 0.8709 (tppp) REVERT: A 248 TYR cc_start: 0.8559 (t80) cc_final: 0.8321 (t80) REVERT: B 30 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8388 (mm) REVERT: B 38 GLN cc_start: 0.8023 (pm20) cc_final: 0.7614 (pt0) REVERT: B 47 ASP cc_start: 0.8637 (p0) cc_final: 0.8435 (p0) REVERT: B 76 SER cc_start: 0.9436 (OUTLIER) cc_final: 0.8996 (m) REVERT: B 222 GLN cc_start: 0.8648 (tp40) cc_final: 0.8389 (tp40) REVERT: B 250 ILE cc_start: 0.8275 (tp) cc_final: 0.8073 (tt) REVERT: D 25 ARG cc_start: 0.8043 (ttt180) cc_final: 0.7443 (mpp-170) REVERT: D 75 LYS cc_start: 0.8141 (tmtt) cc_final: 0.7635 (mmpt) REVERT: D 122 LEU cc_start: 0.8974 (pp) cc_final: 0.8664 (mp) REVERT: E 22 TYR cc_start: 0.8414 (t80) cc_final: 0.7995 (t80) REVERT: E 51 ARG cc_start: 0.8092 (tpt-90) cc_final: 0.7680 (tmt170) REVERT: E 52 LEU cc_start: 0.9117 (tp) cc_final: 0.8726 (tt) REVERT: E 69 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8530 (tm-30) REVERT: E 86 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8517 (tm-30) REVERT: E 90 ASP cc_start: 0.8791 (t0) cc_final: 0.8471 (m-30) REVERT: E 120 PHE cc_start: 0.7219 (m-10) cc_final: 0.6728 (m-10) REVERT: F 27 ARG cc_start: 0.8307 (ptp90) cc_final: 0.7524 (tpt-90) REVERT: F 43 LYS cc_start: 0.8805 (mtpm) cc_final: 0.8334 (mptt) REVERT: F 54 LYS cc_start: 0.6354 (tmmt) cc_final: 0.5736 (mttm) REVERT: F 57 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8413 (tm-30) REVERT: F 78 ASP cc_start: 0.8228 (m-30) cc_final: 0.7709 (m-30) REVERT: F 87 GLN cc_start: 0.8432 (tp-100) cc_final: 0.7974 (tp-100) REVERT: F 91 LEU cc_start: 0.7644 (pp) cc_final: 0.6729 (pp) REVERT: F 131 MET cc_start: 0.8179 (mmp) cc_final: 0.7481 (mmm) outliers start: 65 outliers final: 52 residues processed: 344 average time/residue: 0.2107 time to fit residues: 97.7151 Evaluate side-chains 359 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 304 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.0010 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS F 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8348 Z= 0.185 Angle : 0.723 9.272 11271 Z= 0.374 Chirality : 0.046 0.215 1255 Planarity : 0.004 0.046 1460 Dihedral : 5.574 34.002 1136 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 7.09 % Allowed : 24.57 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.96 (0.27), residues: 1029 helix: 1.15 (0.22), residues: 598 sheet: -2.58 (0.54), residues: 71 loop : -3.47 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 77 HIS 0.005 0.001 HIS B 130 PHE 0.046 0.002 PHE D 109 TYR 0.019 0.002 TYR F 112 ARG 0.008 0.001 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 317 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.5293 (tt0) cc_final: 0.4742 (tt0) REVERT: A 45 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.7944 (p90) REVERT: A 74 ARG cc_start: 0.7292 (mmp-170) cc_final: 0.6489 (tpt-90) REVERT: A 77 GLN cc_start: 0.9167 (mp10) cc_final: 0.8639 (mp10) REVERT: A 248 TYR cc_start: 0.8562 (t80) cc_final: 0.8327 (t80) REVERT: B 30 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8363 (mm) REVERT: B 40 MET cc_start: 0.8736 (tpp) cc_final: 0.7502 (mtp) REVERT: B 97 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8497 (tm-30) REVERT: B 243 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8665 (t0) REVERT: B 244 LYS cc_start: 0.7361 (mptt) cc_final: 0.7129 (mmtt) REVERT: D 25 ARG cc_start: 0.8044 (ttt180) cc_final: 0.7444 (mpp-170) REVERT: D 75 LYS cc_start: 0.8173 (tmtt) cc_final: 0.7622 (mmpt) REVERT: D 122 LEU cc_start: 0.8992 (pp) cc_final: 0.8702 (mp) REVERT: D 123 PHE cc_start: 0.9229 (t80) cc_final: 0.8887 (t80) REVERT: E 22 TYR cc_start: 0.8398 (t80) cc_final: 0.8062 (t80) REVERT: E 43 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8603 (mmtm) REVERT: E 51 ARG cc_start: 0.8049 (tpt-90) cc_final: 0.7588 (tmt170) REVERT: E 52 LEU cc_start: 0.9062 (tp) cc_final: 0.8761 (tt) REVERT: E 69 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8595 (tm-30) REVERT: E 86 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8523 (tm-30) REVERT: E 90 ASP cc_start: 0.8746 (t0) cc_final: 0.8437 (m-30) REVERT: F 27 ARG cc_start: 0.8326 (ptp90) cc_final: 0.7483 (tpt-90) REVERT: F 43 LYS cc_start: 0.8750 (mtpm) cc_final: 0.8336 (mptt) REVERT: F 54 LYS cc_start: 0.6400 (tmmt) cc_final: 0.5772 (mttm) REVERT: F 57 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8334 (tm-30) REVERT: F 61 ARG cc_start: 0.8786 (tpp-160) cc_final: 0.8538 (tpp80) REVERT: F 69 GLU cc_start: 0.8807 (pp20) cc_final: 0.8555 (pp20) REVERT: F 78 ASP cc_start: 0.7994 (m-30) cc_final: 0.7734 (m-30) REVERT: F 87 GLN cc_start: 0.8421 (tp-100) cc_final: 0.7931 (tp-100) REVERT: F 91 LEU cc_start: 0.7646 (pp) cc_final: 0.6687 (pp) outliers start: 58 outliers final: 47 residues processed: 340 average time/residue: 0.2004 time to fit residues: 90.9373 Evaluate side-chains 350 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 300 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.0060 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.0070 chunk 51 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN F 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8348 Z= 0.169 Angle : 0.728 9.060 11271 Z= 0.369 Chirality : 0.046 0.238 1255 Planarity : 0.004 0.049 1460 Dihedral : 5.265 32.581 1136 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 6.11 % Allowed : 26.89 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.76 (0.28), residues: 1029 helix: 1.30 (0.23), residues: 598 sheet: -2.15 (0.52), residues: 81 loop : -3.47 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 77 HIS 0.003 0.001 HIS A 159 PHE 0.023 0.002 PHE F 109 TYR 0.020 0.001 TYR F 112 ARG 0.007 0.001 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 308 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.5190 (tt0) cc_final: 0.4604 (tt0) REVERT: A 45 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.8103 (p90) REVERT: A 74 ARG cc_start: 0.7236 (mmp-170) cc_final: 0.6465 (tpt170) REVERT: A 77 GLN cc_start: 0.9068 (mp10) cc_final: 0.8568 (mp10) REVERT: A 79 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6787 (mtp) REVERT: A 248 TYR cc_start: 0.8515 (t80) cc_final: 0.8245 (t80) REVERT: B 30 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8165 (mm) REVERT: B 40 MET cc_start: 0.8560 (tpp) cc_final: 0.7452 (mtt) REVERT: B 56 GLU cc_start: 0.7766 (mp0) cc_final: 0.7445 (mp0) REVERT: B 88 ARG cc_start: 0.6240 (mmt180) cc_final: 0.5695 (mmm160) REVERT: B 97 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8475 (tm-30) REVERT: B 244 LYS cc_start: 0.7413 (mptt) cc_final: 0.7153 (mmtt) REVERT: D 25 ARG cc_start: 0.8050 (ttt180) cc_final: 0.7449 (mpp-170) REVERT: D 75 LYS cc_start: 0.8084 (tmtt) cc_final: 0.7759 (tppt) REVERT: D 93 ARG cc_start: 0.8686 (mmm-85) cc_final: 0.8285 (mtp-110) REVERT: D 122 LEU cc_start: 0.8951 (pp) cc_final: 0.8603 (mp) REVERT: D 123 PHE cc_start: 0.9212 (t80) cc_final: 0.8901 (t80) REVERT: E 20 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7264 (tm-30) REVERT: E 22 TYR cc_start: 0.8363 (t80) cc_final: 0.7962 (t80) REVERT: E 43 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8478 (mmtm) REVERT: E 51 ARG cc_start: 0.8083 (tpt-90) cc_final: 0.7873 (tmt170) REVERT: E 69 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8435 (tm-30) REVERT: E 86 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8503 (tm-30) REVERT: E 90 ASP cc_start: 0.8712 (t0) cc_final: 0.8403 (m-30) REVERT: E 145 ILE cc_start: 0.7429 (pt) cc_final: 0.7141 (mm) REVERT: F 27 ARG cc_start: 0.8391 (ptp90) cc_final: 0.7475 (tpt-90) REVERT: F 43 LYS cc_start: 0.8745 (mtpm) cc_final: 0.8343 (mptt) REVERT: F 54 LYS cc_start: 0.6396 (tmmt) cc_final: 0.5824 (mttm) REVERT: F 57 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8346 (tm-30) REVERT: F 69 GLU cc_start: 0.8818 (pp20) cc_final: 0.8594 (pp20) REVERT: F 87 GLN cc_start: 0.8452 (tp-100) cc_final: 0.7964 (tp-100) outliers start: 50 outliers final: 40 residues processed: 327 average time/residue: 0.1992 time to fit residues: 87.6107 Evaluate side-chains 333 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 290 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 9.9990 chunk 55 optimal weight: 0.0570 chunk 71 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8348 Z= 0.180 Angle : 0.747 11.494 11271 Z= 0.379 Chirality : 0.046 0.213 1255 Planarity : 0.004 0.056 1460 Dihedral : 5.122 32.411 1136 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 6.85 % Allowed : 28.12 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.63 (0.28), residues: 1029 helix: 1.36 (0.22), residues: 599 sheet: -1.89 (0.54), residues: 81 loop : -3.39 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 77 HIS 0.003 0.001 HIS A 159 PHE 0.042 0.002 PHE D 109 TYR 0.028 0.001 TYR E 112 ARG 0.010 0.001 ARG D 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 302 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.2046 (ptt-90) cc_final: 0.1564 (ptt-90) REVERT: A 12 LEU cc_start: 0.7797 (tp) cc_final: 0.7472 (mt) REVERT: A 37 GLU cc_start: 0.5087 (tt0) cc_final: 0.4279 (tt0) REVERT: A 45 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8128 (p90) REVERT: A 77 GLN cc_start: 0.9089 (mp10) cc_final: 0.8576 (mp10) REVERT: A 248 TYR cc_start: 0.8631 (t80) cc_final: 0.8345 (t80) REVERT: B 30 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8216 (mm) REVERT: B 40 MET cc_start: 0.8597 (tpp) cc_final: 0.7429 (mtt) REVERT: B 88 ARG cc_start: 0.6321 (mmt180) cc_final: 0.5764 (mmm160) REVERT: B 97 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8581 (tm-30) REVERT: B 244 LYS cc_start: 0.7420 (mptt) cc_final: 0.7134 (mmtt) REVERT: D 25 ARG cc_start: 0.8066 (ttt180) cc_final: 0.7441 (mpp-170) REVERT: D 53 SER cc_start: 0.8974 (m) cc_final: 0.8622 (t) REVERT: D 93 ARG cc_start: 0.8671 (mmm-85) cc_final: 0.8281 (mtp-110) REVERT: D 109 PHE cc_start: 0.6828 (m-80) cc_final: 0.6623 (m-80) REVERT: D 122 LEU cc_start: 0.8923 (pp) cc_final: 0.8608 (mp) REVERT: D 123 PHE cc_start: 0.9212 (t80) cc_final: 0.9006 (t80) REVERT: E 51 ARG cc_start: 0.8052 (tpt-90) cc_final: 0.7851 (tmt170) REVERT: E 86 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8471 (tm-30) REVERT: E 90 ASP cc_start: 0.8715 (t0) cc_final: 0.8396 (m-30) REVERT: E 123 PHE cc_start: 0.8427 (m-80) cc_final: 0.8018 (m-80) REVERT: E 145 ILE cc_start: 0.7436 (pt) cc_final: 0.7193 (mm) REVERT: F 27 ARG cc_start: 0.8394 (ptp90) cc_final: 0.7448 (tpt-90) REVERT: F 43 LYS cc_start: 0.8801 (mtpm) cc_final: 0.8365 (mptt) REVERT: F 54 LYS cc_start: 0.6422 (tmmt) cc_final: 0.5783 (mttm) REVERT: F 57 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8350 (tm-30) REVERT: F 87 GLN cc_start: 0.8438 (tp-100) cc_final: 0.7855 (tp-100) REVERT: F 131 MET cc_start: 0.7910 (mmp) cc_final: 0.7483 (mmm) outliers start: 56 outliers final: 45 residues processed: 326 average time/residue: 0.1902 time to fit residues: 84.2509 Evaluate side-chains 343 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 296 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 66 optimal weight: 0.0270 chunk 48 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 overall best weight: 0.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8348 Z= 0.176 Angle : 0.749 10.322 11271 Z= 0.377 Chirality : 0.045 0.174 1255 Planarity : 0.004 0.052 1460 Dihedral : 5.005 31.838 1136 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 6.85 % Allowed : 28.97 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.50 (0.28), residues: 1029 helix: 1.46 (0.22), residues: 597 sheet: -1.66 (0.54), residues: 81 loop : -3.35 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 77 HIS 0.003 0.001 HIS A 159 PHE 0.036 0.002 PHE D 109 TYR 0.048 0.002 TYR E 112 ARG 0.009 0.001 ARG D 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 305 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.2175 (ptt-90) cc_final: 0.1205 (ptt90) REVERT: A 12 LEU cc_start: 0.7835 (tp) cc_final: 0.7579 (mt) REVERT: A 37 GLU cc_start: 0.4839 (tt0) cc_final: 0.3719 (tt0) REVERT: A 45 TYR cc_start: 0.9010 (OUTLIER) cc_final: 0.8115 (p90) REVERT: A 77 GLN cc_start: 0.9082 (mp10) cc_final: 0.8683 (mp10) REVERT: A 79 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6841 (mtp) REVERT: A 155 GLU cc_start: 0.7630 (tp30) cc_final: 0.7397 (tp30) REVERT: A 248 TYR cc_start: 0.8612 (t80) cc_final: 0.8308 (t80) REVERT: A 252 ASN cc_start: 0.8686 (p0) cc_final: 0.8415 (p0) REVERT: B 30 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8175 (mm) REVERT: B 40 MET cc_start: 0.8534 (tpp) cc_final: 0.7284 (mtt) REVERT: B 76 SER cc_start: 0.9352 (OUTLIER) cc_final: 0.9060 (m) REVERT: B 243 ASP cc_start: 0.8475 (t0) cc_final: 0.8239 (t70) REVERT: B 244 LYS cc_start: 0.7405 (mptt) cc_final: 0.7092 (mmtt) REVERT: D 25 ARG cc_start: 0.8060 (ttt180) cc_final: 0.7437 (mpp-170) REVERT: D 53 SER cc_start: 0.8942 (m) cc_final: 0.8648 (t) REVERT: D 93 ARG cc_start: 0.8694 (mmm-85) cc_final: 0.8331 (mtp-110) REVERT: D 122 LEU cc_start: 0.8928 (pp) cc_final: 0.8607 (mp) REVERT: D 123 PHE cc_start: 0.9219 (t80) cc_final: 0.9002 (t80) REVERT: E 20 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7252 (tm-30) REVERT: E 69 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8499 (tm-30) REVERT: E 73 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.5731 (ttt-90) REVERT: E 86 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8450 (tm-30) REVERT: E 90 ASP cc_start: 0.8694 (t0) cc_final: 0.8412 (m-30) REVERT: E 123 PHE cc_start: 0.8382 (m-80) cc_final: 0.7933 (m-80) REVERT: E 147 ARG cc_start: 0.7296 (mmm160) cc_final: 0.6888 (mmp80) REVERT: F 27 ARG cc_start: 0.8381 (ptp90) cc_final: 0.7449 (tpt-90) REVERT: F 43 LYS cc_start: 0.8801 (mtpm) cc_final: 0.8387 (mptt) REVERT: F 54 LYS cc_start: 0.6398 (tmmt) cc_final: 0.5770 (mttm) REVERT: F 57 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8354 (tm-30) REVERT: F 87 GLN cc_start: 0.8415 (tp-100) cc_final: 0.7812 (tp-100) outliers start: 56 outliers final: 47 residues processed: 328 average time/residue: 0.1924 time to fit residues: 86.3241 Evaluate side-chains 346 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 294 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 97 ASN Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 0.0670 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8348 Z= 0.181 Angle : 0.771 10.511 11271 Z= 0.379 Chirality : 0.045 0.200 1255 Planarity : 0.004 0.053 1460 Dihedral : 4.919 31.236 1136 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 5.99 % Allowed : 29.34 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.44 (0.28), residues: 1029 helix: 1.46 (0.22), residues: 599 sheet: -1.50 (0.54), residues: 81 loop : -3.30 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 77 HIS 0.003 0.000 HIS A 159 PHE 0.024 0.002 PHE F 109 TYR 0.044 0.002 TYR E 112 ARG 0.007 0.001 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 299 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.2144 (ptt-90) cc_final: 0.1212 (ptt90) REVERT: A 12 LEU cc_start: 0.7870 (tp) cc_final: 0.7475 (mt) REVERT: A 37 GLU cc_start: 0.4894 (tt0) cc_final: 0.3672 (tt0) REVERT: A 45 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.7941 (p90) REVERT: A 77 GLN cc_start: 0.9125 (mp10) cc_final: 0.8696 (mp10) REVERT: A 79 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6766 (mtp) REVERT: A 248 TYR cc_start: 0.8601 (t80) cc_final: 0.8371 (t80) REVERT: B 30 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8178 (mm) REVERT: B 76 SER cc_start: 0.9340 (OUTLIER) cc_final: 0.9071 (m) REVERT: B 123 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7241 (tm-30) REVERT: B 199 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: B 244 LYS cc_start: 0.7384 (mptt) cc_final: 0.7083 (mmtt) REVERT: D 25 ARG cc_start: 0.8076 (ttt180) cc_final: 0.7483 (mpp-170) REVERT: D 93 ARG cc_start: 0.8701 (mmm-85) cc_final: 0.8363 (mtp-110) REVERT: D 122 LEU cc_start: 0.8916 (pp) cc_final: 0.8610 (mp) REVERT: D 123 PHE cc_start: 0.9211 (t80) cc_final: 0.9011 (t80) REVERT: E 20 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7282 (tm-30) REVERT: E 69 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8431 (tm-30) REVERT: E 73 ARG cc_start: 0.6454 (OUTLIER) cc_final: 0.5294 (ttt-90) REVERT: E 86 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8454 (tm-30) REVERT: E 90 ASP cc_start: 0.8698 (t0) cc_final: 0.8394 (m-30) REVERT: E 123 PHE cc_start: 0.8278 (m-80) cc_final: 0.7959 (m-80) REVERT: E 145 ILE cc_start: 0.7520 (pt) cc_final: 0.7206 (mm) REVERT: F 27 ARG cc_start: 0.8398 (ptp90) cc_final: 0.7435 (tpt-90) REVERT: F 43 LYS cc_start: 0.8749 (mtpm) cc_final: 0.8324 (mptt) REVERT: F 54 LYS cc_start: 0.6256 (tmmt) cc_final: 0.5663 (mttm) REVERT: F 57 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8261 (tm-30) REVERT: F 61 ARG cc_start: 0.8893 (tpp-160) cc_final: 0.8641 (tpp80) REVERT: F 87 GLN cc_start: 0.8416 (tp-100) cc_final: 0.7810 (tp-100) outliers start: 49 outliers final: 38 residues processed: 320 average time/residue: 0.1904 time to fit residues: 82.6762 Evaluate side-chains 333 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 289 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 97 ASN Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 61 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8348 Z= 0.188 Angle : 0.806 12.319 11271 Z= 0.397 Chirality : 0.046 0.243 1255 Planarity : 0.004 0.053 1460 Dihedral : 4.922 30.643 1136 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 5.50 % Allowed : 30.44 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.36 (0.28), residues: 1029 helix: 1.51 (0.22), residues: 599 sheet: -1.29 (0.55), residues: 81 loop : -3.26 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 77 HIS 0.003 0.001 HIS A 159 PHE 0.027 0.002 PHE D 109 TYR 0.041 0.001 TYR E 112 ARG 0.007 0.001 ARG A 285 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 298 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.2160 (ptt-90) cc_final: 0.1234 (ptt90) REVERT: A 12 LEU cc_start: 0.7896 (tp) cc_final: 0.7633 (mt) REVERT: A 37 GLU cc_start: 0.4761 (tt0) cc_final: 0.3538 (tt0) REVERT: A 45 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8153 (p90) REVERT: A 77 GLN cc_start: 0.9017 (mp10) cc_final: 0.8626 (mp10) REVERT: A 241 LYS cc_start: 0.8619 (tppt) cc_final: 0.8191 (tppt) REVERT: B 18 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8895 (ttpt) REVERT: B 30 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8189 (mm) REVERT: B 40 MET cc_start: 0.8479 (tpp) cc_final: 0.7132 (mtt) REVERT: B 56 GLU cc_start: 0.7895 (mp0) cc_final: 0.7582 (mp0) REVERT: B 76 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.9096 (m) REVERT: B 123 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7300 (tm-30) REVERT: B 199 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: B 244 LYS cc_start: 0.7419 (mptt) cc_final: 0.7114 (mmtt) REVERT: D 25 ARG cc_start: 0.8090 (ttt180) cc_final: 0.7491 (mpp-170) REVERT: D 93 ARG cc_start: 0.8693 (mmm-85) cc_final: 0.8359 (mtp-110) REVERT: D 122 LEU cc_start: 0.8944 (pp) cc_final: 0.8658 (mp) REVERT: E 20 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7257 (tm-30) REVERT: E 34 ASP cc_start: 0.7299 (p0) cc_final: 0.7046 (t0) REVERT: E 69 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8470 (tm-30) REVERT: E 73 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.5341 (ttt-90) REVERT: E 86 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8472 (tm-30) REVERT: E 90 ASP cc_start: 0.8699 (t0) cc_final: 0.8401 (m-30) REVERT: E 145 ILE cc_start: 0.7540 (pt) cc_final: 0.7208 (mm) REVERT: F 27 ARG cc_start: 0.8404 (ptp90) cc_final: 0.7421 (tpt-90) REVERT: F 43 LYS cc_start: 0.8800 (mtpm) cc_final: 0.8320 (mptt) REVERT: F 54 LYS cc_start: 0.6287 (tmmt) cc_final: 0.5683 (mttp) REVERT: F 57 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8244 (tm-30) REVERT: F 61 ARG cc_start: 0.8892 (tpp-160) cc_final: 0.8648 (tpp80) REVERT: F 87 GLN cc_start: 0.8434 (tp-100) cc_final: 0.7804 (tp-100) REVERT: F 131 MET cc_start: 0.7999 (mmp) cc_final: 0.7500 (mmm) REVERT: F 134 PHE cc_start: 0.7021 (p90) cc_final: 0.6735 (p90) outliers start: 45 outliers final: 35 residues processed: 320 average time/residue: 0.1971 time to fit residues: 84.9265 Evaluate side-chains 337 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 296 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 97 ASN Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 0.0980 chunk 70 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 57 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: B 143 ASN B 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.156959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134680 restraints weight = 19054.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136964 restraints weight = 9471.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.138266 restraints weight = 5642.195| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8348 Z= 0.189 Angle : 0.799 11.305 11271 Z= 0.394 Chirality : 0.046 0.231 1255 Planarity : 0.004 0.054 1460 Dihedral : 4.856 30.511 1136 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.62 % Allowed : 30.56 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.28 (0.28), residues: 1029 helix: 1.56 (0.22), residues: 600 sheet: -1.18 (0.56), residues: 81 loop : -3.24 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 77 HIS 0.003 0.000 HIS A 159 PHE 0.025 0.002 PHE F 109 TYR 0.040 0.002 TYR E 112 ARG 0.010 0.001 ARG F 73 =============================================================================== Job complete usr+sys time: 2466.29 seconds wall clock time: 44 minutes 55.98 seconds (2695.98 seconds total)