Starting phenix.real_space_refine (version: dev) on Wed Apr 6 05:35:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0p_22606/04_2022/7k0p_22606_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0p_22606/04_2022/7k0p_22606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0p_22606/04_2022/7k0p_22606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0p_22606/04_2022/7k0p_22606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0p_22606/04_2022/7k0p_22606_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0p_22606/04_2022/7k0p_22606_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.094 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 18572 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3582 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1230 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 144} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3582 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1236 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'POV': 2, 'PLP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'POV': 2, 'PLP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 11.03, per 1000 atoms: 0.59 Number of scatterers: 18572 At special positions: 0 Unit cell: (92.46, 120.6, 153.765, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 4 15.00 O 3352 8.00 N 3116 7.00 C 12000 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 2.6 seconds 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 9 sheets defined 47.8% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 Processing helix chain 'A' and resid 22 through 39 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 167 through 178 removed outlier: 4.122A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 322 through 331 removed outlier: 4.706A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 358 Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 405 through 422 Processing helix chain 'A' and resid 454 through 472 Processing helix chain 'B' and resid 68 through 93 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 117 through 125 removed outlier: 4.761A pdb=" N TYR B 122 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN B 125 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 removed outlier: 5.463A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.636A pdb=" N GLU B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.761A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 285 through 298 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 348 through 351 No H-bonds generated for 'chain 'B' and resid 348 through 351' Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 392 through 400 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 437 through 456 Processing helix chain 'B' and resid 476 through 488 removed outlier: 3.909A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 535 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 31 through 54 Processing helix chain 'C' and resid 59 through 68 Processing helix chain 'D' and resid 12 through 18 removed outlier: 4.694A pdb=" N MET D 17 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 39 Processing helix chain 'D' and resid 45 through 65 Processing helix chain 'D' and resid 85 through 92 removed outlier: 6.106A pdb=" N ASP D 90 " --> pdb=" O TRP D 86 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TYR D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 121 through 137 removed outlier: 3.781A pdb=" N LEU D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'E' and resid 11 through 18 Processing helix chain 'E' and resid 22 through 39 Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 115 through 128 Processing helix chain 'E' and resid 143 through 155 Processing helix chain 'E' and resid 167 through 178 removed outlier: 4.152A pdb=" N ILE E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) Proline residue: E 176 - end of helix Processing helix chain 'E' and resid 193 through 201 Processing helix chain 'E' and resid 214 through 230 Processing helix chain 'E' and resid 232 through 236 Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 289 through 293 Processing helix chain 'E' and resid 322 through 331 removed outlier: 4.772A pdb=" N HIS E 327 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' Processing helix chain 'E' and resid 343 through 358 Processing helix chain 'E' and resid 361 through 377 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 454 through 472 Processing helix chain 'F' and resid 68 through 93 Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 117 through 125 removed outlier: 4.610A pdb=" N TYR F 122 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN F 125 " --> pdb=" O TYR F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 133 removed outlier: 3.684A pdb=" N ARG F 131 " --> pdb=" O MET F 128 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP F 132 " --> pdb=" O ARG F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 199 Processing helix chain 'F' and resid 214 through 227 Processing helix chain 'F' and resid 238 through 249 Proline residue: F 247 - end of helix Processing helix chain 'F' and resid 264 through 272 Processing helix chain 'F' and resid 285 through 298 Processing helix chain 'F' and resid 327 through 337 Processing helix chain 'F' and resid 348 through 351 No H-bonds generated for 'chain 'F' and resid 348 through 351' Processing helix chain 'F' and resid 359 through 363 Processing helix chain 'F' and resid 392 through 400 Processing helix chain 'F' and resid 403 through 407 Processing helix chain 'F' and resid 413 through 427 Processing helix chain 'F' and resid 436 through 456 Processing helix chain 'F' and resid 476 through 488 removed outlier: 3.975A pdb=" N GLY F 480 " --> pdb=" O PRO F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 535 Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 31 through 54 Processing helix chain 'G' and resid 59 through 68 Processing helix chain 'H' and resid 12 through 18 removed outlier: 4.766A pdb=" N MET H 17 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 39 Processing helix chain 'H' and resid 45 through 64 Processing helix chain 'H' and resid 85 through 92 removed outlier: 6.087A pdb=" N ASP H 90 " --> pdb=" O TRP H 86 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY H 92 " --> pdb=" O GLN H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 116 Proline residue: H 106 - end of helix Processing helix chain 'H' and resid 121 through 138 removed outlier: 3.799A pdb=" N LEU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Proline residue: H 137 - end of helix Processing helix chain 'H' and resid 147 through 149 No H-bonds generated for 'chain 'H' and resid 147 through 149' Processing sheet with id= A, first strand: chain 'A' and resid 93 through 95 Processing sheet with id= B, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.614A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 184 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL A 243 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE A 186 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N GLU A 245 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N ASP A 188 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP A 205 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL A 187 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LYS A 207 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 383 through 386 Processing sheet with id= D, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.480A pdb=" N LEU B 255 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU B 313 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 257 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N GLU B 315 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR B 276 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N SER B 258 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG B 278 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.822A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 160 through 164 removed outlier: 3.756A pdb=" N LEU E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE E 184 " --> pdb=" O PHE E 241 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL E 243 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE E 186 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLU E 245 " --> pdb=" O PHE E 186 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASP E 188 " --> pdb=" O GLU E 245 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP E 205 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL E 187 " --> pdb=" O ASP E 205 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS E 207 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 383 through 386 Processing sheet with id= H, first strand: chain 'F' and resid 231 through 235 removed outlier: 6.553A pdb=" N LEU F 255 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU F 313 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU F 257 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N GLU F 315 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR F 276 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N SER F 258 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ARG F 278 " --> pdb=" O SER F 258 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 468 through 472 removed outlier: 3.505A pdb=" N ARG F 507 " --> pdb=" O VAL F 496 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL F 494 " --> pdb=" O ARG F 509 " (cutoff:3.500A) 812 hydrogen bonds defined for protein. 2334 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: 5.22 Time building geometry restraints manager: 7.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5891 1.34 - 1.46: 2690 1.46 - 1.57: 10207 1.57 - 1.69: 4 1.69 - 1.81: 168 Bond restraints: 18960 Sorted by residual: bond pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 1.333 1.520 -0.187 2.00e-02 2.50e+03 8.78e+01 bond pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 1.333 1.520 -0.187 2.00e-02 2.50e+03 8.73e+01 bond pdb=" O12 POV B 602 " pdb=" P POV B 602 " ideal model delta sigma weight residual 1.657 1.740 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" O12 POV F 602 " pdb=" P POV F 602 " ideal model delta sigma weight residual 1.657 1.740 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.16e-02 7.43e+03 6.85e+00 ... (remaining 18955 not shown) Histogram of bond angle deviations from ideal: 96.04 - 103.64: 270 103.64 - 111.25: 7959 111.25 - 118.85: 7186 118.85 - 126.45: 9957 126.45 - 134.05: 247 Bond angle restraints: 25619 Sorted by residual: angle pdb=" C28 POV D 901 " pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 127.79 109.91 17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C28 POV H 901 " pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 127.79 109.94 17.85 3.00e+00 1.11e-01 3.54e+01 angle pdb=" C29 POV D 901 " pdb="C210 POV D 901 " pdb="C211 POV D 901 " ideal model delta sigma weight residual 127.67 110.20 17.47 3.00e+00 1.11e-01 3.39e+01 angle pdb=" C29 POV H 901 " pdb="C210 POV H 901 " pdb="C211 POV H 901 " ideal model delta sigma weight residual 127.67 110.22 17.45 3.00e+00 1.11e-01 3.38e+01 angle pdb=" N GLU E 414 " pdb=" CA GLU E 414 " pdb=" CB GLU E 414 " ideal model delta sigma weight residual 110.28 116.82 -6.54 1.55e+00 4.16e-01 1.78e+01 ... (remaining 25614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.26: 10880 26.26 - 52.53: 424 52.53 - 78.79: 47 78.79 - 105.06: 9 105.06 - 131.32: 1 Dihedral angle restraints: 11361 sinusoidal: 4575 harmonic: 6786 Sorted by residual: dihedral pdb=" C5A PLP F 601 " pdb=" O4P PLP F 601 " pdb=" P PLP F 601 " pdb=" O1P PLP F 601 " ideal model delta sinusoidal sigma weight residual 76.43 -54.89 131.32 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" CA VAL D 93 " pdb=" C VAL D 93 " pdb=" N GLN D 94 " pdb=" CA GLN D 94 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA THR B 501 " pdb=" C THR B 501 " pdb=" N PRO B 502 " pdb=" CA PRO B 502 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 11358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2006 0.038 - 0.076: 591 0.076 - 0.113: 216 0.113 - 0.151: 38 0.151 - 0.189: 3 Chirality restraints: 2854 Sorted by residual: chirality pdb=" CA THR H 105 " pdb=" N THR H 105 " pdb=" C THR H 105 " pdb=" CB THR H 105 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA PHE F 498 " pdb=" N PHE F 498 " pdb=" C PHE F 498 " pdb=" CB PHE F 498 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CB THR D 74 " pdb=" CA THR D 74 " pdb=" OG1 THR D 74 " pdb=" CG2 THR D 74 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 2851 not shown) Planarity restraints: 3245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " 0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO B 413 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 901 " 0.026 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C29 POV D 901 " -0.026 2.00e-02 2.50e+03 pdb="C210 POV D 901 " -0.026 2.00e-02 2.50e+03 pdb="C211 POV D 901 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER F 412 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO F 413 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO F 413 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 413 " -0.027 5.00e-02 4.00e+02 ... (remaining 3242 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 948 2.73 - 3.27: 18131 3.27 - 3.81: 29434 3.81 - 4.36: 35912 4.36 - 4.90: 64036 Nonbonded interactions: 148461 Sorted by model distance: nonbonded pdb=" OH TYR E 178 " pdb=" O VAL E 324 " model vdw 2.183 2.440 nonbonded pdb=" OE2 GLU A 56 " pdb=" NH2 ARG F 302 " model vdw 2.213 2.520 nonbonded pdb=" OD2 ASP F 259 " pdb=" OH TYR F 318 " model vdw 2.218 2.440 nonbonded pdb=" OG1 THR B 355 " pdb=" OE2 GLU B 361 " model vdw 2.220 2.440 nonbonded pdb=" OE2 GLU H 9 " pdb=" OH TYR H 91 " model vdw 2.230 2.440 ... (remaining 148456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 53 through 544 or resid 601 or (resid 602 and (name C1 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O12 or na \ me O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) \ or resid 603)) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 8 through 69 or resid 101 through 102)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 1 through 147 or (resid 148 and (name N or name CA or name \ C or name O or name CB )) or resid 149 through 153 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 C 12000 2.51 5 N 3116 2.21 5 O 3352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.060 Check model and map are aligned: 0.260 Convert atoms to be neutral: 0.160 Process input model: 48.210 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 : 0.005 0.187 18960 Z= 0.331 Angle : 0.715 17.880 25619 Z= 0.386 Chirality : 0.043 0.189 2854 Planarity : 0.005 0.069 3245 Dihedral : 13.655 131.321 7017 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2326 helix: 1.83 (0.16), residues: 1109 sheet: -0.56 (0.39), residues: 182 loop : -0.49 (0.18), residues: 1035 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.443 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.3176 time to fit residues: 102.0457 Evaluate side-chains 171 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.097 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 110 optimal weight: 0.1980 chunk 135 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN B 440 GLN B 441 GLN E 77 HIS F 172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.0544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 18960 Z= 0.183 Angle : 0.494 9.888 25619 Z= 0.258 Chirality : 0.040 0.180 2854 Planarity : 0.004 0.064 3245 Dihedral : 6.359 110.574 2703 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.18), residues: 2326 helix: 2.10 (0.16), residues: 1106 sheet: -0.54 (0.35), residues: 227 loop : -0.41 (0.19), residues: 993 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 187 time to evaluate : 2.204 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 195 average time/residue: 0.2887 time to fit residues: 88.3998 Evaluate side-chains 178 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 2.198 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1631 time to fit residues: 5.4910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 228 optimal weight: 0.0770 chunk 187 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 169 optimal weight: 0.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 441 GLN E 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 18960 Z= 0.169 Angle : 0.475 11.395 25619 Z= 0.247 Chirality : 0.040 0.176 2854 Planarity : 0.004 0.058 3245 Dihedral : 5.934 94.084 2703 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.18), residues: 2326 helix: 2.24 (0.16), residues: 1108 sheet: -0.35 (0.34), residues: 248 loop : -0.39 (0.19), residues: 970 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 178 time to evaluate : 2.133 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 185 average time/residue: 0.2876 time to fit residues: 83.9917 Evaluate side-chains 171 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 2.197 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1668 time to fit residues: 4.0101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 100 optimal weight: 20.0000 chunk 141 optimal weight: 0.6980 chunk 211 optimal weight: 0.9980 chunk 224 optimal weight: 0.0570 chunk 110 optimal weight: 6.9990 chunk 200 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN B 172 ASN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN E 77 HIS E 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 18960 Z= 0.163 Angle : 0.456 7.610 25619 Z= 0.236 Chirality : 0.040 0.173 2854 Planarity : 0.004 0.054 3245 Dihedral : 5.532 74.072 2703 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2326 helix: 2.32 (0.16), residues: 1113 sheet: -0.31 (0.34), residues: 248 loop : -0.37 (0.19), residues: 965 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 189 time to evaluate : 2.274 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 197 average time/residue: 0.3008 time to fit residues: 93.0170 Evaluate side-chains 183 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 179 time to evaluate : 2.152 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1714 time to fit residues: 4.2036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 155 optimal weight: 0.0770 chunk 0 optimal weight: 60.0000 chunk 114 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 GLN E 77 HIS H 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.106 18960 Z= 0.210 Angle : 0.493 11.325 25619 Z= 0.255 Chirality : 0.040 0.173 2854 Planarity : 0.004 0.065 3245 Dihedral : 5.415 62.258 2703 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.18), residues: 2326 helix: 2.32 (0.16), residues: 1113 sheet: -0.27 (0.34), residues: 247 loop : -0.42 (0.19), residues: 966 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 2.412 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 194 average time/residue: 0.3065 time to fit residues: 92.7541 Evaluate side-chains 178 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 2.213 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1694 time to fit residues: 4.6914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 44 optimal weight: 0.0010 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 186 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 441 GLN E 77 HIS E 114 ASN E 428 GLN H 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 18960 Z= 0.189 Angle : 0.488 14.105 25619 Z= 0.252 Chirality : 0.040 0.171 2854 Planarity : 0.004 0.053 3245 Dihedral : 5.277 61.952 2703 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.18), residues: 2326 helix: 2.36 (0.16), residues: 1114 sheet: -0.26 (0.34), residues: 247 loop : -0.41 (0.20), residues: 965 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 183 time to evaluate : 2.167 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 194 average time/residue: 0.3176 time to fit residues: 95.6664 Evaluate side-chains 178 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 176 time to evaluate : 2.448 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1739 time to fit residues: 3.7064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.0070 chunk 25 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 136 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 441 GLN E 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.058 18960 Z= 0.148 Angle : 0.449 7.774 25619 Z= 0.235 Chirality : 0.039 0.168 2854 Planarity : 0.004 0.110 3245 Dihedral : 5.090 59.782 2703 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.18), residues: 2326 helix: 2.44 (0.16), residues: 1115 sheet: -0.39 (0.36), residues: 227 loop : -0.34 (0.19), residues: 984 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 2.284 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 196 average time/residue: 0.3284 time to fit residues: 100.4568 Evaluate side-chains 179 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 2.203 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1674 time to fit residues: 3.6490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 441 GLN E 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 18960 Z= 0.182 Angle : 0.467 6.871 25619 Z= 0.242 Chirality : 0.040 0.170 2854 Planarity : 0.004 0.079 3245 Dihedral : 5.101 60.986 2703 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2326 helix: 2.42 (0.16), residues: 1115 sheet: -0.19 (0.34), residues: 247 loop : -0.41 (0.20), residues: 964 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 2.211 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 192 average time/residue: 0.3040 time to fit residues: 91.9033 Evaluate side-chains 181 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 178 time to evaluate : 2.186 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1635 time to fit residues: 3.9739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 90 optimal weight: 0.0370 chunk 163 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN B 441 GLN E 77 HIS E 114 ASN ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 18960 Z= 0.160 Angle : 0.457 7.313 25619 Z= 0.237 Chirality : 0.040 0.167 2854 Planarity : 0.004 0.065 3245 Dihedral : 5.052 60.060 2703 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.18), residues: 2326 helix: 2.45 (0.16), residues: 1115 sheet: -0.37 (0.36), residues: 227 loop : -0.36 (0.19), residues: 984 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 178 time to evaluate : 2.304 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 184 average time/residue: 0.3062 time to fit residues: 88.8854 Evaluate side-chains 176 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 2.302 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1715 time to fit residues: 3.4891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 212 optimal weight: 0.3980 chunk 184 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN E 77 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 18960 Z= 0.313 Angle : 0.552 8.485 25619 Z= 0.284 Chirality : 0.043 0.177 2854 Planarity : 0.004 0.064 3245 Dihedral : 5.393 63.679 2703 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2326 helix: 2.17 (0.16), residues: 1126 sheet: -0.30 (0.34), residues: 247 loop : -0.58 (0.19), residues: 953 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 2.291 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 186 average time/residue: 0.3343 time to fit residues: 95.0741 Evaluate side-chains 178 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 176 time to evaluate : 2.350 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1767 time to fit residues: 3.9416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 51 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 441 GLN E 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.137090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110812 restraints weight = 24881.159| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.32 r_work: 0.3534 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work: 0.3501 rms_B_bonded: 2.13 restraints_weight: 0.1250 r_work: 0.3484 rms_B_bonded: 2.24 restraints_weight: 0.0625 r_work: 0.3465 rms_B_bonded: 2.39 restraints_weight: 0.0312 r_work: 0.3446 rms_B_bonded: 2.59 restraints_weight: 0.0156 r_work: 0.3424 rms_B_bonded: 2.84 restraints_weight: 0.0078 r_work: 0.3401 rms_B_bonded: 3.13 restraints_weight: 0.0039 r_work: 0.3376 rms_B_bonded: 3.48 restraints_weight: 0.0020 r_work: 0.3349 rms_B_bonded: 3.89 restraints_weight: 0.0010 r_work: 0.3319 rms_B_bonded: 4.37 restraints_weight: 0.0005 r_work: 0.3287 rms_B_bonded: 4.93 restraints_weight: 0.0002 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.966 18960 Z= 0.641 Angle : 0.604 39.022 25619 Z= 0.327 Chirality : 0.041 0.194 2854 Planarity : 0.004 0.058 3245 Dihedral : 5.282 60.525 2703 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 2326 helix: 2.26 (0.16), residues: 1126 sheet: -0.29 (0.34), residues: 247 loop : -0.55 (0.19), residues: 953 =============================================================================== Job complete usr+sys time: 3111.18 seconds wall clock time: 58 minutes 15.69 seconds (3495.69 seconds total)