Starting phenix.real_space_refine on Fri Feb 16 13:00:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0i_22598/02_2024/7k0i_22598_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0i_22598/02_2024/7k0i_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_22598/02_2024/7k0i_22598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0i_22598/02_2024/7k0i_22598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0i_22598/02_2024/7k0i_22598_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0i_22598/02_2024/7k0i_22598_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 72 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: 72 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: 8.05, per 1000 atoms: 0.52 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: 5.77 Conformation dependent library (CDL) restraints added in 2.8 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: 3.05 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: 4.84 Time building geometry restraints manager: 6.22 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: 3.380 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: 12.780 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 41.740 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.030 ------------------------------------------------------------------------------- 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 % Allowed : 0.37 % Favored : 99.38 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.005 0.001 HIS A 292 PHE 0.019 0.002 PHE D 209 TYR 0.022 0.002 TYR A 166 ARG 0.005 0.001 ARG E 95 *********************** 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 : 1.797 Fit side-chains REVERT: A 230 LYS cc_start: 0.7455 (tttm) cc_final: 0.6954 (mmtt) REVERT: A 455 GLU cc_start: 0.6401 (tm-30) cc_final: 0.6104 (tm-30) REVERT: B 244 MET cc_start: 0.7974 (mtt) cc_final: 0.7748 (mtt) REVERT: E 244 MET cc_start: 0.7945 (mtt) cc_final: 0.7709 (mtt) outliers start: 4 outliers final: 4 residues processed: 162 average time/residue: 0.2741 time to fit residues: 66.6659 Evaluate side-chains 130 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 355 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.5980 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: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0643 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= 0.209 Angle : 0.502 6.576 21182 Z= 0.265 Chirality : 0.042 0.140 2338 Planarity : 0.005 0.063 2720 Dihedral : 6.029 81.991 2190 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.06 % Allowed : 5.22 % Favored : 93.73 % 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: 0.55 (0.19), residues: 1942 helix: 1.82 (0.18), residues: 862 sheet: -0.50 (0.34), residues: 244 loop : -0.91 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.002 0.001 HIS A 292 PHE 0.015 0.001 PHE D 209 TYR 0.013 0.001 TYR A 166 ARG 0.004 0.000 ARG A 410 *********************** 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 156 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.796 Fit side-chains REVERT: A 214 MET cc_start: 0.7685 (mmt) cc_final: 0.7481 (mmt) REVERT: A 230 LYS cc_start: 0.7398 (tttm) cc_final: 0.6854 (mmtt) REVERT: A 455 GLU cc_start: 0.6240 (tm-30) cc_final: 0.5947 (tm-30) REVERT: E 244 MET cc_start: 0.7914 (mtt) cc_final: 0.7700 (mtt) outliers start: 17 outliers final: 15 residues processed: 152 average time/residue: 0.2805 time to fit residues: 63.3871 Evaluate side-chains 139 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 355 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 176 optimal weight: 0.0570 chunk 190 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN E 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.0911 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= 0.200 Angle : 0.479 6.585 21182 Z= 0.252 Chirality : 0.041 0.141 2338 Planarity : 0.004 0.057 2720 Dihedral : 5.302 56.605 2190 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.74 % Allowed : 7.45 % Favored : 90.81 % 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: 0.72 (0.19), residues: 1942 helix: 2.01 (0.18), residues: 860 sheet: -0.42 (0.34), residues: 244 loop : -0.88 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.002 0.001 HIS D 91 PHE 0.016 0.001 PHE A 168 TYR 0.009 0.001 TYR D 166 ARG 0.010 0.000 ARG E 136 *********************** 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 159 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.629 Fit side-chains REVERT: A 58 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: D 58 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: D 181 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7679 (ttm-80) REVERT: E 244 MET cc_start: 0.7986 (mtt) cc_final: 0.7752 (mtt) REVERT: E 290 LYS cc_start: 0.8222 (tttp) cc_final: 0.8014 (tttp) outliers start: 28 outliers final: 19 residues processed: 152 average time/residue: 0.2858 time to fit residues: 65.1186 Evaluate side-chains 140 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 487 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 3.9990 chunk 132 optimal weight: 0.0870 chunk 91 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 187 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 50 optimal weight: 0.0980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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: 0.7737 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15678 Z= 0.160 Angle : 0.452 6.532 21182 Z= 0.238 Chirality : 0.040 0.136 2338 Planarity : 0.004 0.055 2720 Dihedral : 4.993 56.328 2190 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.55 % Allowed : 8.82 % Favored : 89.63 % 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: 0.87 (0.19), residues: 1942 helix: 2.20 (0.18), residues: 858 sheet: -0.47 (0.34), residues: 248 loop : -0.82 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 32 HIS 0.002 0.001 HIS A 91 PHE 0.013 0.001 PHE B 118 TYR 0.009 0.001 TYR D 267 ARG 0.002 0.000 ARG B 95 *********************** 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 151 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 1.710 Fit side-chains REVERT: A 58 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: D 58 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: D 181 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7649 (ttm-80) outliers start: 25 outliers final: 19 residues processed: 146 average time/residue: 0.2861 time to fit residues: 61.9988 Evaluate side-chains 141 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 355 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 0.0170 chunk 106 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 47 optimal weight: 0.0980 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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: 0.7762 moved from start: 0.1148 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= 0.212 Angle : 0.472 6.618 21182 Z= 0.248 Chirality : 0.041 0.140 2338 Planarity : 0.004 0.055 2720 Dihedral : 4.888 55.682 2190 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.99 % Allowed : 9.38 % Favored : 88.63 % 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: 0.85 (0.19), residues: 1942 helix: 2.16 (0.18), residues: 860 sheet: -0.37 (0.34), residues: 244 loop : -0.85 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 32 HIS 0.002 0.001 HIS D 91 PHE 0.018 0.001 PHE D 168 TYR 0.010 0.001 TYR B 448 ARG 0.003 0.000 ARG E 95 *********************** 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 152 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 1.769 Fit side-chains REVERT: A 58 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: A 59 GLU cc_start: 0.7500 (pp20) cc_final: 0.6691 (pp20) REVERT: D 58 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: D 181 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7637 (ttm-80) outliers start: 32 outliers final: 18 residues processed: 148 average time/residue: 0.2654 time to fit residues: 60.2487 Evaluate side-chains 140 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 355 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN B 108 GLN D 102 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 15678 Z= 0.509 Angle : 0.653 7.065 21182 Z= 0.343 Chirality : 0.048 0.163 2338 Planarity : 0.006 0.072 2720 Dihedral : 5.425 53.509 2190 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.17 % Allowed : 10.43 % Favored : 87.39 % 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: 0.04 (0.19), residues: 1942 helix: 1.44 (0.17), residues: 886 sheet: -1.00 (0.35), residues: 218 loop : -1.24 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.006 0.002 HIS A 292 PHE 0.023 0.003 PHE A 209 TYR 0.021 0.002 TYR E 448 ARG 0.004 0.001 ARG B 151 *********************** 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 167 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.928 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: D 58 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7000 (mp0) outliers start: 35 outliers final: 21 residues processed: 162 average time/residue: 0.2827 time to fit residues: 69.2275 Evaluate side-chains 150 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 495 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 0.5980 chunk 21 optimal weight: 0.0170 chunk 106 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 186 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 115 optimal weight: 0.0270 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15678 Z= 0.153 Angle : 0.459 6.501 21182 Z= 0.243 Chirality : 0.040 0.136 2338 Planarity : 0.004 0.057 2720 Dihedral : 4.866 52.240 2190 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.68 % Allowed : 11.43 % Favored : 86.89 % 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: 0.54 (0.19), residues: 1942 helix: 1.96 (0.18), residues: 864 sheet: -0.90 (0.35), residues: 218 loop : -0.99 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.002 0.001 HIS B 516 PHE 0.013 0.001 PHE D 209 TYR 0.007 0.001 TYR B 397 ARG 0.002 0.000 ARG B 95 *********************** 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 152 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 1.785 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: D 58 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: D 181 ARG cc_start: 0.8100 (ttm110) cc_final: 0.7806 (ttm-80) REVERT: D 214 MET cc_start: 0.7679 (mmt) cc_final: 0.7478 (mmt) outliers start: 27 outliers final: 18 residues processed: 149 average time/residue: 0.2788 time to fit residues: 62.6088 Evaluate side-chains 141 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 495 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7781 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15678 Z= 0.220 Angle : 0.488 6.656 21182 Z= 0.256 Chirality : 0.041 0.145 2338 Planarity : 0.004 0.058 2720 Dihedral : 4.767 49.593 2190 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.55 % Allowed : 12.42 % Favored : 86.02 % 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: 0.55 (0.19), residues: 1942 helix: 1.97 (0.18), residues: 868 sheet: -0.91 (0.35), residues: 218 loop : -0.99 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.002 0.001 HIS D 91 PHE 0.014 0.001 PHE A 209 TYR 0.010 0.001 TYR E 448 ARG 0.003 0.000 ARG B 95 *********************** 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 150 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 2.587 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: D 58 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: D 181 ARG cc_start: 0.8121 (ttm110) cc_final: 0.7817 (ttm-80) outliers start: 25 outliers final: 20 residues processed: 147 average time/residue: 0.2853 time to fit residues: 63.8754 Evaluate side-chains 146 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.0020 chunk 174 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 157 optimal weight: 0.0870 chunk 164 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.5766 ------------------------------------------------------------------------------- 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: 0.7758 moved from start: 0.1417 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= 0.180 Angle : 0.465 6.581 21182 Z= 0.245 Chirality : 0.040 0.138 2338 Planarity : 0.004 0.055 2720 Dihedral : 4.564 46.371 2190 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.37 % Allowed : 12.55 % Favored : 86.09 % 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: 2.07 (0.18), residues: 866 sheet: -0.87 (0.35), residues: 218 loop : -0.96 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.002 0.001 HIS E 542 PHE 0.014 0.001 PHE D 168 TYR 0.007 0.001 TYR E 448 ARG 0.003 0.000 ARG B 95 *********************** 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 151 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: D 58 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: D 181 ARG cc_start: 0.8099 (ttm110) cc_final: 0.7802 (ttm-80) outliers start: 22 outliers final: 18 residues processed: 148 average time/residue: 0.2787 time to fit residues: 62.3810 Evaluate side-chains 143 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 193 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7771 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15678 Z= 0.209 Angle : 0.483 6.630 21182 Z= 0.253 Chirality : 0.041 0.157 2338 Planarity : 0.004 0.055 2720 Dihedral : 4.515 44.252 2190 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.37 % Allowed : 12.61 % Favored : 86.02 % 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: 0.59 (0.19), residues: 1942 helix: 2.04 (0.18), residues: 866 sheet: -0.89 (0.35), residues: 218 loop : -1.00 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.002 0.001 HIS D 91 PHE 0.014 0.001 PHE D 168 TYR 0.009 0.001 TYR E 448 ARG 0.003 0.000 ARG B 95 ********************** 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 145 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.734 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: D 58 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: D 181 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7812 (ttm-80) outliers start: 22 outliers final: 19 residues processed: 141 average time/residue: 0.2750 time to fit residues: 58.7482 Evaluate side-chains 141 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 495 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 154 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.156933 restraints weight = 17082.184| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.11 r_work: 0.3775 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15678 Z= 0.205 Angle : 0.481 6.629 21182 Z= 0.252 Chirality : 0.041 0.141 2338 Planarity : 0.004 0.055 2720 Dihedral : 4.433 43.369 2190 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.30 % Allowed : 12.73 % Favored : 85.96 % 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: 0.61 (0.19), residues: 1942 helix: 2.08 (0.18), residues: 862 sheet: -0.90 (0.34), residues: 218 loop : -1.00 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.002 0.001 HIS A 145 PHE 0.013 0.001 PHE D 209 TYR 0.009 0.001 TYR E 448 ARG 0.003 0.000 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2931.57 seconds wall clock time: 54 minutes 27.82 seconds (3267.82 seconds total)