Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 16:27:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0i_22598/04_2023/7k0i_22598_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0i_22598/04_2023/7k0i_22598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0i_22598/04_2023/7k0i_22598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0i_22598/04_2023/7k0i_22598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0i_22598/04_2023/7k0i_22598_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0i_22598/04_2023/7k0i_22598_updated.pdb" } resolution = 3.3 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= 0.000 sd= 0.079 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 88 5.16 5 C 9840 2.51 5 N 2610 2.21 5 O 2826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 63": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D ARG 270": "NH1" <-> "NH2" Residue "D GLU 358": "OE1" <-> "OE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D GLU 433": "OE1" <-> "OE2" Residue "D GLU 454": "OE1" <-> "OE2" Residue "D GLU 455": "OE1" <-> "OE2" Residue "D ARG 459": "NH1" <-> "NH2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "E ARG 145": "NH1" <-> "NH2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E ARG 183": "NH1" <-> "NH2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E ARG 225": "NH1" <-> "NH2" Residue "E ARG 271": "NH1" <-> "NH2" Residue "E ARG 278": "NH1" <-> "NH2" Residue "E ARG 304": "NH1" <-> "NH2" Residue "E ARG 305": "NH1" <-> "NH2" Residue "E ARG 326": "NH1" <-> "NH2" Residue "E GLU 393": "OE1" <-> "OE2" Residue "E GLU 437": "OE1" <-> "OE2" Residue "E ARG 450": "NH1" <-> "NH2" Residue "E ARG 451": "NH1" <-> "NH2" Residue "E ARG 452": "NH1" <-> "NH2" Residue "E ARG 484": "NH1" <-> "NH2" Residue "E ARG 507": "NH1" <-> "NH2" Residue "E GLU 527": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 15366 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3287 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3287 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" 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: "E" 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: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 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: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 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: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 8.35, per 1000 atoms: 0.54 Number of scatterers: 15366 At special positions: 0 Unit cell: (101.05, 155.077, 114.057, 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 88 16.00 P 2 15.00 O 2826 8.00 N 2610 7.00 C 9840 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: 6.20 Conformation dependent library (CDL) restraints added in 2.4 seconds 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3608 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 12 sheets defined 44.5% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 54 through 63 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: 4.530A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 175 " --> pdb=" O ILE A 171 " (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 237 removed outlier: 4.180A pdb=" N VAL A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.615A pdb=" N LYS A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 322 through 331 removed outlier: 4.681A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.433A 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 361 through 376 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 118 through 125 removed outlier: 4.973A pdb=" N TYR B 122 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN B 125 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 removed outlier: 3.767A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 133 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 238 through 249 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 359 through 363 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 426 Processing helix chain 'B' and resid 434 through 454 removed outlier: 4.080A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 489 removed outlier: 4.173A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 489 " --> pdb=" O GLU B 485 " (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 54 through 63 Processing helix chain 'D' and resid 115 through 128 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 167 through 178 removed outlier: 4.531A pdb=" N ILE D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE D 175 " --> pdb=" O ILE D 171 " (cutoff:3.500A) Proline residue: D 176 - end of helix Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 214 through 230 Processing helix chain 'D' and resid 232 through 237 removed outlier: 4.181A pdb=" N VAL D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.615A pdb=" N LYS D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 322 through 331 removed outlier: 4.681A pdb=" N HIS D 327 " --> pdb=" O PHE D 323 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN D 328 " --> pdb=" O VAL D 324 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG D 329 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU D 330 " --> pdb=" O ASP D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 343 through 358 Processing helix chain 'D' and resid 361 through 376 Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 454 through 472 Processing helix chain 'F' and resid 9 through 23 Processing helix chain 'F' and resid 31 through 54 Processing helix chain 'F' and resid 59 through 68 Processing helix chain 'E' and resid 68 through 93 Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 118 through 125 removed outlier: 4.973A pdb=" N TYR E 122 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN E 125 " --> pdb=" O TYR E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 133 removed outlier: 3.767A pdb=" N ARG E 131 " --> pdb=" O MET E 128 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASP E 132 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN E 133 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 198 Processing helix chain 'E' and resid 214 through 227 Processing helix chain 'E' and resid 238 through 249 Proline residue: E 247 - end of helix Processing helix chain 'E' and resid 264 through 272 Processing helix chain 'E' and resid 285 through 298 Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 367 through 369 No H-bonds generated for 'chain 'E' and resid 367 through 369' Processing helix chain 'E' and resid 392 through 401 Processing helix chain 'E' and resid 403 through 407 Processing helix chain 'E' and resid 413 through 426 Processing helix chain 'E' and resid 434 through 454 removed outlier: 4.080A pdb=" N VAL E 439 " --> pdb=" O GLY E 435 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 440 " --> pdb=" O LYS E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 489 removed outlier: 4.171A pdb=" N GLY E 480 " --> pdb=" O PRO E 476 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 483 " --> pdb=" O ILE E 479 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG E 489 " --> pdb=" O GLU E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 535 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: 3.784A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 184 through 188 removed outlier: 6.425A pdb=" N ASP A 205 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL A 187 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS A 207 " --> pdb=" O VAL A 187 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 383 through 386 Processing sheet with id= E, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.504A pdb=" N ASP B 259 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR B 276 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N SER B 258 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG B 278 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.754A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 93 through 95 Processing sheet with id= H, first strand: chain 'D' and resid 160 through 164 removed outlier: 3.785A pdb=" N LEU D 302 " --> pdb=" O ILE D 271 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 184 through 188 removed outlier: 6.427A pdb=" N ASP D 205 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL D 187 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS D 207 " --> pdb=" O VAL D 187 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 383 through 386 Processing sheet with id= K, first strand: chain 'E' and resid 231 through 235 removed outlier: 3.505A pdb=" N ASP E 259 " --> pdb=" O LEU E 313 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N GLU E 315 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR E 276 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N SER E 258 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG E 278 " --> pdb=" O SER E 258 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 468 through 472 removed outlier: 3.755A pdb=" N VAL E 494 " --> pdb=" O ARG E 509 " (cutoff:3.500A) 658 hydrogen bonds defined for protein. 1896 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: 4.49 Time building geometry restraints manager: 6.65 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: 4995 1.34 - 1.46: 2296 1.46 - 1.57: 8243 1.57 - 1.69: 2 1.69 - 1.81: 142 Bond restraints: 15678 Sorted by residual: bond pdb=" N GLU D 275 " pdb=" CA GLU D 275 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.31e+00 bond pdb=" N GLU A 275 " pdb=" CA GLU A 275 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.26e-02 6.30e+03 6.93e+00 bond pdb=" N SER A 276 " pdb=" CA SER A 276 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.62e+00 bond pdb=" N SER D 276 " pdb=" CA SER D 276 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.55e+00 bond pdb=" N GLU D 274 " pdb=" CA GLU D 274 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.27e-02 6.20e+03 5.93e+00 ... (remaining 15673 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.76: 340 105.76 - 112.82: 8212 112.82 - 119.89: 5319 119.89 - 126.95: 7159 126.95 - 134.01: 152 Bond angle restraints: 21182 Sorted by residual: angle pdb=" N GLU D 58 " pdb=" CA GLU D 58 " pdb=" CB GLU D 58 " ideal model delta sigma weight residual 110.12 113.68 -3.56 1.47e+00 4.63e-01 5.86e+00 angle pdb=" N GLU A 58 " pdb=" CA GLU A 58 " pdb=" CB GLU A 58 " ideal model delta sigma weight residual 110.12 113.67 -3.55 1.47e+00 4.63e-01 5.83e+00 angle pdb=" C GLU D 58 " pdb=" N GLU D 59 " pdb=" CA GLU D 59 " ideal model delta sigma weight residual 120.72 116.76 3.96 1.67e+00 3.59e-01 5.64e+00 angle pdb=" CA GLU D 274 " pdb=" C GLU D 274 " pdb=" O GLU D 274 " ideal model delta sigma weight residual 120.46 117.94 2.52 1.07e+00 8.73e-01 5.54e+00 angle pdb=" C GLU A 58 " pdb=" N GLU A 59 " pdb=" CA GLU A 59 " ideal model delta sigma weight residual 120.72 116.80 3.92 1.67e+00 3.59e-01 5.51e+00 ... (remaining 21177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 8870 21.47 - 42.94: 514 42.94 - 64.42: 38 64.42 - 85.89: 10 85.89 - 107.36: 2 Dihedral angle restraints: 9434 sinusoidal: 3788 harmonic: 5646 Sorted by residual: dihedral pdb=" C5A PLP E 601 " pdb=" O4P PLP E 601 " pdb=" P PLP E 601 " pdb=" O1P PLP E 601 " ideal model delta sinusoidal sigma weight residual 76.43 -176.21 -107.36 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" C5A PLP B 601 " pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " pdb=" O1P PLP B 601 " ideal model delta sinusoidal sigma weight residual 76.43 -176.22 -107.36 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" CA ILE A 101 " pdb=" C ILE A 101 " pdb=" N ASN A 102 " pdb=" CA ASN A 102 " ideal model delta harmonic sigma weight residual -180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 9431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1225 0.030 - 0.060: 710 0.060 - 0.090: 240 0.090 - 0.120: 145 0.120 - 0.151: 18 Chirality restraints: 2338 Sorted by residual: chirality pdb=" CA ILE D 242 " pdb=" N ILE D 242 " pdb=" C ILE D 242 " pdb=" CB ILE D 242 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE A 242 " pdb=" N ILE A 242 " pdb=" C ILE A 242 " pdb=" CB ILE A 242 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA VAL E 469 " pdb=" N VAL E 469 " pdb=" C VAL E 469 " pdb=" CB VAL E 469 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 2335 not shown) Planarity restraints: 2720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 412 " -0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO E 413 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 413 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 413 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " 0.048 5.00e-02 4.00e+02 7.26e-02 8.44e+00 pdb=" N PRO B 413 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO B 502 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " 0.028 5.00e-02 4.00e+02 ... (remaining 2717 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2514 2.76 - 3.29: 14379 3.29 - 3.83: 24242 3.83 - 4.36: 29591 4.36 - 4.90: 52672 Nonbonded interactions: 123398 Sorted by model distance: nonbonded pdb=" OG1 THR B 378 " pdb=" O1P PLP B 601 " model vdw 2.222 2.440 nonbonded pdb=" OG1 THR E 378 " pdb=" O1P PLP E 601 " model vdw 2.222 2.440 nonbonded pdb=" OH TYR A 178 " pdb=" O VAL A 324 " model vdw 2.301 2.440 nonbonded pdb=" OH TYR D 178 " pdb=" O VAL D 324 " model vdw 2.301 2.440 nonbonded pdb=" OE2 GLU A 436 " pdb=" OH TYR B 407 " model vdw 2.302 2.440 ... (remaining 123393 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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=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: 2.360 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: 13.120 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 40.370 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 0.046 15678 Z= 0.351 Angle : 0.643 6.753 21182 Z= 0.358 Chirality : 0.045 0.151 2338 Planarity : 0.005 0.073 2720 Dihedral : 12.839 107.361 5826 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 0.25 % 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: 0.10 (0.19), residues: 1942 helix: 1.44 (0.17), residues: 862 sheet: -1.10 (0.34), residues: 222 loop : -1.02 (0.20), residues: 858 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 2.214 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 162 average time/residue: 0.2876 time to fit residues: 70.4637 Evaluate side-chains 129 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.929 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1428 time to fit residues: 3.7991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 78 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 15678 Z= 0.208 Angle : 0.499 6.540 21182 Z= 0.263 Chirality : 0.041 0.140 2338 Planarity : 0.005 0.062 2720 Dihedral : 5.170 76.485 2184 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.81 % 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: 0.56 (0.19), residues: 1942 helix: 1.85 (0.18), residues: 860 sheet: -0.50 (0.34), residues: 244 loop : -0.92 (0.20), residues: 838 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.876 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 147 average time/residue: 0.3005 time to fit residues: 66.3156 Evaluate side-chains 131 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 2.010 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1343 time to fit residues: 4.7886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 0.0970 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 176 optimal weight: 0.0970 chunk 190 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 175 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 15678 Z= 0.155 Angle : 0.451 6.517 21182 Z= 0.238 Chirality : 0.040 0.136 2338 Planarity : 0.004 0.054 2720 Dihedral : 4.467 52.963 2184 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 1.12 % 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: 0.81 (0.19), residues: 1942 helix: 2.09 (0.18), residues: 860 sheet: -0.49 (0.33), residues: 248 loop : -0.80 (0.21), residues: 834 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.945 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 147 average time/residue: 0.3339 time to fit residues: 74.2152 Evaluate side-chains 130 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.958 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1851 time to fit residues: 5.2891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 92 optimal weight: 0.3980 chunk 167 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 15678 Z= 0.244 Angle : 0.502 6.639 21182 Z= 0.263 Chirality : 0.042 0.170 2338 Planarity : 0.004 0.057 2720 Dihedral : 4.413 42.335 2184 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.68 % 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: 0.72 (0.19), residues: 1942 helix: 2.06 (0.18), residues: 860 sheet: -0.52 (0.33), residues: 248 loop : -0.90 (0.21), residues: 834 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.889 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 135 average time/residue: 0.3038 time to fit residues: 60.7569 Evaluate side-chains 126 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 2.038 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1497 time to fit residues: 3.8210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 2 optimal weight: 0.0670 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 95 optimal weight: 0.0020 chunk 168 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.5326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 15678 Z= 0.169 Angle : 0.455 6.532 21182 Z= 0.241 Chirality : 0.040 0.138 2338 Planarity : 0.004 0.053 2720 Dihedral : 4.199 34.157 2184 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.81 % 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: 0.84 (0.19), residues: 1942 helix: 2.16 (0.18), residues: 862 sheet: -0.47 (0.34), residues: 248 loop : -0.83 (0.21), residues: 832 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.846 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 134 average time/residue: 0.2836 time to fit residues: 58.0943 Evaluate side-chains 124 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.971 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1410 time to fit residues: 3.8543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN D 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 15678 Z= 0.431 Angle : 0.605 6.879 21182 Z= 0.317 Chirality : 0.046 0.157 2338 Planarity : 0.005 0.067 2720 Dihedral : 4.647 31.533 2184 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.99 % 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: 0.20 (0.19), residues: 1942 helix: 1.57 (0.18), residues: 888 sheet: -0.93 (0.35), residues: 218 loop : -1.16 (0.20), residues: 836 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 1.971 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 137 average time/residue: 0.2831 time to fit residues: 58.9418 Evaluate side-chains 132 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.834 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1370 time to fit residues: 4.6216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 104 optimal weight: 0.1980 chunk 186 optimal weight: 0.5980 chunk 117 optimal weight: 0.0000 chunk 113 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 15678 Z= 0.171 Angle : 0.460 6.563 21182 Z= 0.245 Chirality : 0.040 0.135 2338 Planarity : 0.004 0.056 2720 Dihedral : 4.238 26.109 2184 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 0.75 % 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: 0.57 (0.19), residues: 1942 helix: 1.98 (0.18), residues: 864 sheet: -0.83 (0.35), residues: 218 loop : -0.98 (0.20), residues: 860 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.831 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 143 average time/residue: 0.2987 time to fit residues: 64.1584 Evaluate side-chains 128 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1386 time to fit residues: 3.6410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 118 optimal weight: 0.4980 chunk 127 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 179 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15678 Z= 0.169 Angle : 0.464 6.586 21182 Z= 0.246 Chirality : 0.040 0.138 2338 Planarity : 0.004 0.055 2720 Dihedral : 4.083 25.012 2184 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.31 % 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: 0.67 (0.19), residues: 1942 helix: 2.08 (0.18), residues: 864 sheet: -0.85 (0.35), residues: 222 loop : -0.93 (0.20), residues: 856 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 1.860 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 130 average time/residue: 0.3099 time to fit residues: 60.5872 Evaluate side-chains 127 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 1.724 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1424 time to fit residues: 3.3390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 104 optimal weight: 0.0970 chunk 75 optimal weight: 0.8980 chunk 136 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 164 optimal weight: 0.2980 chunk 173 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 15678 Z= 0.157 Angle : 0.459 6.556 21182 Z= 0.242 Chirality : 0.040 0.135 2338 Planarity : 0.004 0.051 2720 Dihedral : 3.989 23.456 2184 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.19 % 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: 0.76 (0.19), residues: 1942 helix: 2.18 (0.18), residues: 862 sheet: -0.77 (0.36), residues: 222 loop : -0.92 (0.20), residues: 858 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 1.748 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 132 average time/residue: 0.2801 time to fit residues: 55.9761 Evaluate side-chains 128 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.754 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1396 time to fit residues: 3.0129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN E 177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15678 Z= 0.224 Angle : 0.499 6.654 21182 Z= 0.264 Chirality : 0.042 0.173 2338 Planarity : 0.004 0.055 2720 Dihedral : 4.075 24.496 2184 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 0.19 % 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: 0.64 (0.19), residues: 1942 helix: 2.06 (0.18), residues: 866 sheet: -0.73 (0.36), residues: 218 loop : -0.99 (0.20), residues: 858 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.977 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 129 average time/residue: 0.2912 time to fit residues: 57.0995 Evaluate side-chains 122 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.944 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1562 time to fit residues: 3.0002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 141 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 0.0170 chunk 154 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 135 optimal weight: 0.0670 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN E 177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.176286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.160848 restraints weight = 17014.236| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.08 r_work: 0.3799 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 15678 Z= 0.147 Angle : 0.453 6.554 21182 Z= 0.243 Chirality : 0.040 0.214 2338 Planarity : 0.004 0.049 2720 Dihedral : 3.874 21.534 2184 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.37 % 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: 0.83 (0.19), residues: 1942 helix: 2.23 (0.18), residues: 862 sheet: -0.58 (0.36), residues: 218 loop : -0.91 (0.20), residues: 862 =============================================================================== Job complete usr+sys time: 2835.47 seconds wall clock time: 52 minutes 42.01 seconds (3162.01 seconds total)