Starting phenix.real_space_refine on Tue Nov 14 08:30:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iac_4435/11_2023/6iac_4435.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iac_4435/11_2023/6iac_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_4435/11_2023/6iac_4435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iac_4435/11_2023/6iac_4435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iac_4435/11_2023/6iac_4435.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iac_4435/11_2023/6iac_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-1.21rc1-5144/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: 4.87, per 1000 atoms: 0.59 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: 3.05 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: 0.77 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: 1.91 Time building geometry restraints manager: 3.30 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: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.230 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.320 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 420 average time/residue: 0.2232 time to fit residues: 121.7738 Evaluate side-chains 299 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 297 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0712 time to fit residues: 1.5185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 30.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.7472 moved from start: 0.3786 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= 0.190 Angle : 0.767 11.948 11271 Z= 0.404 Chirality : 0.047 0.217 1255 Planarity : 0.005 0.053 1460 Dihedral : 6.489 36.993 1135 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 5.75 % Allowed : 17.48 % 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: -2.54 (0.24), residues: 1029 helix: -0.34 (0.20), residues: 595 sheet: -2.83 (0.46), residues: 87 loop : -3.76 (0.28), residues: 347 *********************** 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 398 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 351 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 24 residues processed: 366 average time/residue: 0.2174 time to fit residues: 106.4873 Evaluate side-chains 313 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 289 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.0725 time to fit residues: 4.4518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.0370 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 GLN F 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8348 Z= 0.241 Angle : 0.761 11.337 11271 Z= 0.396 Chirality : 0.047 0.255 1255 Planarity : 0.004 0.039 1460 Dihedral : 6.038 35.162 1135 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 5.01 % Allowed : 22.00 % Favored : 72.98 % 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: -1.61 (0.26), residues: 1029 helix: 0.54 (0.22), residues: 595 sheet: -2.71 (0.47), residues: 87 loop : -3.57 (0.29), residues: 347 *********************** 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 352 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 311 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 23 residues processed: 330 average time/residue: 0.2107 time to fit residues: 93.5962 Evaluate side-chains 313 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 290 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1145 time to fit residues: 7.4864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN F 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8348 Z= 0.365 Angle : 0.855 13.213 11271 Z= 0.448 Chirality : 0.051 0.251 1255 Planarity : 0.004 0.040 1460 Dihedral : 6.298 38.205 1135 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 4.40 % Allowed : 25.31 % Favored : 70.29 % 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: -1.48 (0.27), residues: 1029 helix: 0.65 (0.22), residues: 603 sheet: -2.66 (0.48), residues: 87 loop : -3.61 (0.31), residues: 339 *********************** 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 344 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 308 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 29 residues processed: 319 average time/residue: 0.1980 time to fit residues: 85.9631 Evaluate side-chains 315 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 286 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.0754 time to fit residues: 5.3512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 87 optimal weight: 0.0870 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 145 ASN F 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8348 Z= 0.175 Angle : 0.741 10.057 11271 Z= 0.380 Chirality : 0.046 0.257 1255 Planarity : 0.003 0.034 1460 Dihedral : 5.543 33.590 1135 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 3.55 % Allowed : 25.18 % Favored : 71.27 % 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: -1.11 (0.27), residues: 1029 helix: 0.95 (0.22), residues: 598 sheet: -2.54 (0.52), residues: 71 loop : -3.40 (0.29), residues: 360 *********************** 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 353 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 324 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 334 average time/residue: 0.1925 time to fit residues: 86.4584 Evaluate side-chains 317 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 300 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0764 time to fit residues: 3.6996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 F 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 8348 Z= 0.324 Angle : 0.850 12.347 11271 Z= 0.436 Chirality : 0.050 0.258 1255 Planarity : 0.004 0.047 1460 Dihedral : 5.887 37.696 1135 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 4.03 % Allowed : 28.12 % Favored : 67.85 % 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: -1.16 (0.27), residues: 1029 helix: 0.88 (0.22), residues: 605 sheet: -2.18 (0.48), residues: 99 loop : -3.58 (0.31), residues: 325 *********************** 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 342 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 309 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 25 residues processed: 318 average time/residue: 0.1965 time to fit residues: 84.2331 Evaluate side-chains 306 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 281 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0737 time to fit residues: 4.5626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN F 76 ASN F 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8348 Z= 0.216 Angle : 0.794 10.916 11271 Z= 0.407 Chirality : 0.049 0.273 1255 Planarity : 0.004 0.056 1460 Dihedral : 5.592 35.702 1135 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.44 % Allowed : 29.58 % Favored : 67.97 % 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: -1.04 (0.27), residues: 1029 helix: 1.00 (0.22), residues: 600 sheet: -2.04 (0.48), residues: 101 loop : -3.58 (0.31), residues: 328 *********************** 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 313 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 293 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 298 average time/residue: 0.1962 time to fit residues: 79.0979 Evaluate side-chains 306 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 292 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0790 time to fit residues: 3.3239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8348 Z= 0.213 Angle : 0.830 11.766 11271 Z= 0.416 Chirality : 0.049 0.250 1255 Planarity : 0.004 0.059 1460 Dihedral : 5.408 35.033 1135 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 1.71 % Allowed : 31.78 % Favored : 66.50 % 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: -0.92 (0.28), residues: 1029 helix: 1.13 (0.23), residues: 598 sheet: -2.11 (0.53), residues: 83 loop : -3.49 (0.30), residues: 348 *********************** 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 322 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 308 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 312 average time/residue: 0.1871 time to fit residues: 79.6782 Evaluate side-chains 293 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 284 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0832 time to fit residues: 2.5909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8348 Z= 0.208 Angle : 0.827 10.570 11271 Z= 0.415 Chirality : 0.048 0.229 1255 Planarity : 0.004 0.062 1460 Dihedral : 5.261 34.616 1135 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.32 % Allowed : 32.27 % Favored : 65.40 % 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: -0.78 (0.28), residues: 1029 helix: 1.19 (0.22), residues: 598 sheet: -1.74 (0.54), residues: 83 loop : -3.42 (0.30), residues: 348 *********************** 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 318 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 299 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 303 average time/residue: 0.1833 time to fit residues: 76.3917 Evaluate side-chains 296 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 281 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0811 time to fit residues: 3.4014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 100 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 61 optimal weight: 0.0870 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.6360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8348 Z= 0.220 Angle : 0.856 11.400 11271 Z= 0.429 Chirality : 0.049 0.245 1255 Planarity : 0.004 0.063 1460 Dihedral : 5.233 34.469 1135 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.61 % Allowed : 34.11 % Favored : 65.28 % 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: -0.80 (0.28), residues: 1029 helix: 1.13 (0.22), residues: 598 sheet: -1.42 (0.57), residues: 83 loop : -3.41 (0.30), residues: 348 ********************** 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 300 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 295 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 295 average time/residue: 0.1868 time to fit residues: 75.7205 Evaluate side-chains 288 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 283 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0916 time to fit residues: 2.0929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 0.0470 chunk 57 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.156995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134451 restraints weight = 19257.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136612 restraints weight = 9674.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137861 restraints weight = 5873.677| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8348 Z= 0.215 Angle : 0.854 10.576 11271 Z= 0.427 Chirality : 0.048 0.209 1255 Planarity : 0.004 0.058 1460 Dihedral : 5.108 33.316 1135 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.86 % Allowed : 35.70 % Favored : 63.45 % 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: -0.67 (0.28), residues: 1029 helix: 1.20 (0.22), residues: 598 sheet: -1.11 (0.59), residues: 83 loop : -3.35 (0.30), residues: 348 =============================================================================== Job complete usr+sys time: 2380.52 seconds wall clock time: 43 minutes 35.23 seconds (2615.23 seconds total)