Starting phenix.real_space_refine on Fri Feb 16 18:09:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qru_14124/02_2024/7qru_14124_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qru_14124/02_2024/7qru_14124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qru_14124/02_2024/7qru_14124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qru_14124/02_2024/7qru_14124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qru_14124/02_2024/7qru_14124_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qru_14124/02_2024/7qru_14124_updated.pdb" } resolution = 2.24 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= 0.002 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 3 5.49 5 S 92 5.16 5 C 10600 2.51 5 N 2388 2.21 5 O 3017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 403": "OE1" <-> "OE2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 488": "OE1" <-> "OE2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "E TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 100": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16100 Number of models: 1 Model: "" Number of chains: 18 Chain: "D" Number of atoms: 3906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 491, 3844 Classifications: {'peptide': 491} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 474} Conformer: "B" Number of residues, atoms: 491, 3844 Classifications: {'peptide': 491} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 474} bond proxies already assigned to first conformer: 3877 Chain: "A" Number of atoms: 6440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 805, 6306 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 776} Conformer: "B" Number of residues, atoms: 805, 6306 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 776} bond proxies already assigned to first conformer: 6327 Chain: "B" Number of atoms: 1089 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 140, 1078 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Conformer: "B" Number of residues, atoms: 140, 1078 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} bond proxies already assigned to first conformer: 1090 Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "E" Number of atoms: 1305 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 158, 1297 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Conformer: "B" Number of residues, atoms: 158, 1297 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} bond proxies already assigned to first conformer: 1317 Chain: "F" Number of atoms: 723 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 701 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 89} Conformer: "B" Number of residues, atoms: 91, 701 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 89} bond proxies already assigned to first conformer: 685 Chain: "G" Number of atoms: 888 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 113, 877 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Conformer: "B" Number of residues, atoms: 113, 877 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} bond proxies already assigned to first conformer: 883 Chain: "e" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 395 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 140 Classifications: {'water': 140} Link IDs: {None: 139} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "F" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 29 residue: pdb=" N AMET D 139 " occ=0.47 ... (14 atoms not shown) pdb=" CE BMET D 139 " occ=0.53 residue: pdb=" N ALEU D 172 " occ=0.43 ... (14 atoms not shown) pdb=" CD2BLEU D 172 " occ=0.57 residue: pdb=" N AMET D 218 " occ=0.45 ... (14 atoms not shown) pdb=" CE BMET D 218 " occ=0.55 residue: pdb=" N ALYS D 219 " occ=0.45 ... (16 atoms not shown) pdb=" NZ BLYS D 219 " occ=0.55 residue: pdb=" N AGLN D 307 " occ=0.69 ... (16 atoms not shown) pdb=" NE2BGLN D 307 " occ=0.31 residue: pdb=" N ATYR D 328 " occ=0.54 ... (22 atoms not shown) pdb=" OH BTYR D 328 " occ=0.46 residue: pdb=" N AMET D 423 " occ=0.54 ... (14 atoms not shown) pdb=" CE BMET D 423 " occ=0.46 residue: pdb=" N AMET A 118 " occ=0.45 ... (14 atoms not shown) pdb=" CE BMET A 118 " occ=0.55 residue: pdb=" N APHE A 119 " occ=0.45 ... (20 atoms not shown) pdb=" CZ BPHE A 119 " occ=0.55 residue: pdb=" N AMET A 167 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 167 " occ=0.50 residue: pdb=" N ATYR A 246 " occ=0.43 ... (22 atoms not shown) pdb=" OH BTYR A 246 " occ=0.57 residue: pdb=" N ALEU A 247 " occ=0.43 ... (14 atoms not shown) pdb=" CD2BLEU A 247 " occ=0.57 ... (remaining 17 not shown) Time building chain proxies: 16.18, per 1000 atoms: 1.00 Number of scatterers: 16100 At special positions: 0 Unit cell: (175.703, 92.137, 96.4224, 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 92 16.00 P 3 15.00 O 3017 8.00 N 2388 7.00 C 10600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.32 Conformation dependent library (CDL) restraints added in 5.7 seconds 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3678 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 85 helices and 4 sheets defined 75.1% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'D' and resid 3 through 20 Proline residue: D 8 - end of helix removed outlier: 4.643A pdb=" N ILE D 11 " --> pdb=" O PRO D 8 " (cutoff:3.500A) Proline residue: D 12 - end of helix removed outlier: 3.554A pdb=" N GLY D 16 " --> pdb=" O PHE D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 54 Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 76 through 98 removed outlier: 3.699A pdb=" N GLN D 98 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.873A pdb=" N TYR D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 125 Processing helix chain 'D' and resid 129 through 148 removed outlier: 3.687A pdb=" N VAL D 148 " --> pdb=" O TYR D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 184 Processing helix chain 'D' and resid 189 through 198 Processing helix chain 'D' and resid 203 through 220 Processing helix chain 'D' and resid 227 through 230 No H-bonds generated for 'chain 'D' and resid 227 through 230' Processing helix chain 'D' and resid 232 through 234 No H-bonds generated for 'chain 'D' and resid 232 through 234' Processing helix chain 'D' and resid 238 through 262 removed outlier: 5.540A pdb=" N THR D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS D 250 " --> pdb=" O GLY D 246 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 291 removed outlier: 4.250A pdb=" N MET D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 317 removed outlier: 3.954A pdb=" N ILE D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 311 " --> pdb=" O AGLN D 307 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 315 " --> pdb=" O MET D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 351 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 367 through 380 Processing helix chain 'D' and resid 387 through 401 Processing helix chain 'D' and resid 405 through 429 Processing helix chain 'D' and resid 438 through 442 Processing helix chain 'D' and resid 446 through 464 Proline residue: D 451 - end of helix Proline residue: D 454 - end of helix Processing helix chain 'D' and resid 466 through 480 Processing helix chain 'D' and resid 483 through 490 Processing helix chain 'A' and resid 3 through 23 Proline residue: A 11 - end of helix Proline residue: A 19 - end of helix Processing helix chain 'A' and resid 30 through 54 removed outlier: 3.962A pdb=" N ALA A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU A 37 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Proline residue: A 38 - end of helix removed outlier: 4.209A pdb=" N TYR A 48 " --> pdb=" O TYR A 44 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 78 through 101 removed outlier: 3.814A pdb=" N PHE A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 128 Processing helix chain 'A' and resid 132 through 150 Processing helix chain 'A' and resid 157 through 188 Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.581A pdb=" N THR A 204 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 229 through 238 removed outlier: 3.824A pdb=" N TRP A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Proline residue: A 234 - end of helix removed outlier: 3.686A pdb=" N MET A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 238 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.577A pdb=" N BHIS A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N BSER A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 267 removed outlier: 4.345A pdb=" N GLY A 256 " --> pdb=" O AMET A 252 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 271 through 293 Processing helix chain 'A' and resid 298 through 329 removed outlier: 4.220A pdb=" N ALA A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE A 324 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER A 329 " --> pdb=" O TYR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 367 removed outlier: 5.003A pdb=" N ALA A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 426 through 456 removed outlier: 5.985A pdb=" N ILE A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE A 432 " --> pdb=" O THR A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 474 through 492 removed outlier: 4.526A pdb=" N SER A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Proline residue: A 480 - end of helix removed outlier: 3.547A pdb=" N ILE A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 532 through 549 Processing helix chain 'A' and resid 551 through 556 removed outlier: 4.646A pdb=" N LYS A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 561 No H-bonds generated for 'chain 'A' and resid 558 through 561' Processing helix chain 'A' and resid 566 through 589 removed outlier: 3.639A pdb=" N TRP A 569 " --> pdb=" O PRO A 566 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 575 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 577 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 578 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 581 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 582 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'A' and resid 631 through 649 removed outlier: 3.743A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Proline residue: A 648 - end of helix Processing helix chain 'A' and resid 653 through 673 Processing helix chain 'A' and resid 677 through 699 removed outlier: 3.527A pdb=" N TYR A 699 " --> pdb=" O MET A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 742 Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.644A pdb=" N ASN A 754 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 770 Processing helix chain 'A' and resid 774 through 796 Processing helix chain 'B' and resid 9 through 32 removed outlier: 3.908A pdb=" N PHE B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 57 Processing helix chain 'B' and resid 60 through 66 Processing helix chain 'B' and resid 71 through 91 removed outlier: 3.551A pdb=" N GLY B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY B 88 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLY B 89 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 140 Processing helix chain 'C' and resid 2 through 21 Processing helix chain 'C' and resid 25 through 46 Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 67 through 98 Processing helix chain 'C' and resid 103 through 106 Processing helix chain 'E' and resid 2 through 18 removed outlier: 3.654A pdb=" N ASN E 17 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.756A pdb=" N LEU E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 79 Processing helix chain 'E' and resid 100 through 112 Processing helix chain 'E' and resid 136 through 147 removed outlier: 4.624A pdb=" N GLU E 139 " --> pdb=" O PRO E 136 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP E 147 " --> pdb=" O ASP E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 157 removed outlier: 3.724A pdb=" N VAL E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 26 removed outlier: 3.925A pdb=" N ARG F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 24 " --> pdb=" O CYS F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 54 removed outlier: 3.538A pdb=" N ILE F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY F 46 " --> pdb=" O ILE F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 84 removed outlier: 3.634A pdb=" N LEU F 65 " --> pdb=" O SER F 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 28 Processing helix chain 'G' and resid 32 through 62 removed outlier: 3.570A pdb=" N ALA G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR G 44 " --> pdb=" O THR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 94 Proline residue: G 81 - end of helix Processing helix chain 'G' and resid 106 through 112 removed outlier: 3.783A pdb=" N MET G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 19 removed outlier: 4.001A pdb=" N ASN e 17 " --> pdb=" O VAL e 13 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE e 18 " --> pdb=" O ILE e 14 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN e 19 " --> pdb=" O TRP e 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 24 through 40 Processing sheet with id= A, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= B, first strand: chain 'A' and resid 58 through 65 removed outlier: 7.188A pdb=" N ILE A 70 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 101 through 105 Processing sheet with id= D, first strand: chain 'E' and resid 89 through 94 removed outlier: 3.652A pdb=" N ASP E 120 " --> pdb=" O TYR E 129 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N HIS E 131 " --> pdb=" O SER E 118 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER E 118 " --> pdb=" O HIS E 131 " (cutoff:3.500A) 1095 hydrogen bonds defined for protein. 3129 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: 4.94 Time building geometry restraints manager: 7.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 2498 1.31 - 1.46: 5800 1.46 - 1.61: 7651 1.61 - 1.76: 20 1.76 - 1.91: 168 Bond restraints: 16137 Sorted by residual: bond pdb=" CE1 HIS D 266 " pdb=" NE2 HIS D 266 " ideal model delta sigma weight residual 1.321 1.451 -0.130 1.00e-02 1.00e+04 1.70e+02 bond pdb=" C29 3PE A 901 " pdb=" C2A 3PE A 901 " ideal model delta sigma weight residual 1.524 1.292 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" CE1 HIS D 303 " pdb=" NE2 HIS D 303 " ideal model delta sigma weight residual 1.321 1.428 -0.107 1.00e-02 1.00e+04 1.15e+02 bond pdb=" C29 3PE E 201 " pdb=" C2A 3PE E 201 " ideal model delta sigma weight residual 1.524 1.331 0.193 2.00e-02 2.50e+03 9.30e+01 bond pdb=" C29 3PE E 202 " pdb=" C2A 3PE E 202 " ideal model delta sigma weight residual 1.524 1.337 0.187 2.00e-02 2.50e+03 8.76e+01 ... (remaining 16132 not shown) Histogram of bond angle deviations from ideal: 90.17 - 99.13: 47 99.13 - 108.10: 1723 108.10 - 117.07: 9561 117.07 - 126.04: 10412 126.04 - 135.01: 196 Bond angle restraints: 21939 Sorted by residual: angle pdb=" O VAL D 453 " pdb=" C VAL D 453 " pdb=" N PRO D 454 " ideal model delta sigma weight residual 120.42 114.51 5.91 6.40e-01 2.44e+00 8.54e+01 angle pdb=" O PRO C 54 " pdb=" C PRO C 54 " pdb=" N PRO C 55 " ideal model delta sigma weight residual 121.31 117.11 4.20 4.60e-01 4.73e+00 8.32e+01 angle pdb=" N PRO B 68 " pdb=" CA PRO B 68 " pdb=" CB PRO B 68 " ideal model delta sigma weight residual 102.81 96.80 6.01 6.70e-01 2.23e+00 8.04e+01 angle pdb=" CA ASP A 297 " pdb=" CB ASP A 297 " pdb=" CG ASP A 297 " ideal model delta sigma weight residual 112.60 121.15 -8.55 1.00e+00 1.00e+00 7.30e+01 angle pdb=" C PRO A 473 " pdb=" CA PRO A 473 " pdb=" CB PRO A 473 " ideal model delta sigma weight residual 111.56 100.82 10.74 1.27e+00 6.20e-01 7.16e+01 ... (remaining 21934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8468 17.96 - 35.91: 713 35.91 - 53.86: 166 53.86 - 71.81: 28 71.81 - 89.77: 10 Dihedral angle restraints: 9385 sinusoidal: 3631 harmonic: 5754 Sorted by residual: dihedral pdb=" CA ARG F 90 " pdb=" C ARG F 90 " pdb=" N GLY F 91 " pdb=" CA GLY F 91 " ideal model delta harmonic sigma weight residual -180.00 -150.61 -29.39 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ALA A 333 " pdb=" C ALA A 333 " pdb=" N PHE A 334 " pdb=" CA PHE A 334 " ideal model delta harmonic sigma weight residual -180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ASP C 111 " pdb=" C ASP C 111 " pdb=" N GLU C 112 " pdb=" CA GLU C 112 " ideal model delta harmonic sigma weight residual 180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 9382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1723 0.093 - 0.186: 725 0.186 - 0.278: 159 0.278 - 0.371: 25 0.371 - 0.464: 1 Chirality restraints: 2633 Sorted by residual: chirality pdb=" CA PRO A 265 " pdb=" N PRO A 265 " pdb=" C PRO A 265 " pdb=" CB PRO A 265 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA ARG F 90 " pdb=" N ARG F 90 " pdb=" C ARG F 90 " pdb=" CB ARG F 90 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA TYR A 113 " pdb=" N TYR A 113 " pdb=" C TYR A 113 " pdb=" CB TYR A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 2630 not shown) Planarity restraints: 2637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE e 18 " 0.099 2.00e-02 2.50e+03 6.98e-02 8.54e+01 pdb=" CG PHE e 18 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE e 18 " -0.102 2.00e-02 2.50e+03 pdb=" CD2 PHE e 18 " -0.090 2.00e-02 2.50e+03 pdb=" CE1 PHE e 18 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 PHE e 18 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE e 18 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 28 " -0.122 2.00e-02 2.50e+03 6.32e-02 7.98e+01 pdb=" CG TYR B 28 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B 28 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR B 28 " 0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR B 28 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR B 28 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 28 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR B 28 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 431 " -0.078 2.00e-02 2.50e+03 5.32e-02 7.07e+01 pdb=" CG TRP D 431 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 TRP D 431 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 431 " 0.078 2.00e-02 2.50e+03 pdb=" NE1 TRP D 431 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TRP D 431 " -0.050 2.00e-02 2.50e+03 pdb=" CE3 TRP D 431 " -0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 431 " -0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 431 " 0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP D 431 " -0.008 2.00e-02 2.50e+03 ... (remaining 2634 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 410 2.63 - 3.20: 15982 3.20 - 3.76: 28312 3.76 - 4.33: 41114 4.33 - 4.90: 64094 Nonbonded interactions: 149912 Sorted by model distance: nonbonded pdb=" OD1 ASP A 678 " pdb=" O HOH A1001 " model vdw 2.058 2.440 nonbonded pdb=" CE2APHE B 41 " pdb=" CD1 LEU B 45 " model vdw 2.083 3.760 nonbonded pdb=" NH1 ARG D 231 " pdb=" O HOH D 501 " model vdw 2.106 2.520 nonbonded pdb=" O HOH A1002 " pdb=" O HOH A1008 " model vdw 2.117 2.440 nonbonded pdb=" OG1 THR E 113 " pdb=" O HOH E 301 " model vdw 2.181 2.440 ... (remaining 149907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.24 max=1.00 mean=0.98 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: 4.590 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: 13.570 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 58.210 Find NCS groups from input model: 0.490 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:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 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 : 0.020 0.232 16137 Z= 1.301 Angle : 2.179 13.447 21939 Z= 1.477 Chirality : 0.102 0.464 2633 Planarity : 0.022 0.249 2637 Dihedral : 14.727 89.768 5707 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 2.50 % Allowed : 6.60 % Favored : 90.90 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.16), residues: 2010 helix: -0.87 (0.11), residues: 1509 sheet: -0.81 (0.71), residues: 48 loop : -1.15 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.024 TRP A 273 HIS 0.074 0.013 HIS A 349 PHE 0.102 0.022 PHE e 18 TYR 0.122 0.023 TYR B 28 ARG 0.059 0.007 ARG F 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 256 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 40 MET cc_start: 0.9295 (mtp) cc_final: 0.9010 (mtp) REVERT: D 103 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8601 (mm-30) REVERT: D 189 MET cc_start: 0.9283 (mtt) cc_final: 0.9028 (mtp) REVERT: D 283 MET cc_start: 0.9419 (mtm) cc_final: 0.9203 (mtm) REVERT: D 311 MET cc_start: 0.9389 (mtt) cc_final: 0.8988 (mtt) REVERT: D 396 ILE cc_start: 0.8857 (pt) cc_final: 0.8506 (mt) REVERT: D 439 GLN cc_start: 0.8928 (tt0) cc_final: 0.8159 (pm20) REVERT: D 467 GLU cc_start: 0.9242 (tp30) cc_final: 0.9005 (tp30) REVERT: D 488 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8749 (mm-30) REVERT: A 207 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8329 (mp0) REVERT: A 314 MET cc_start: 0.9301 (tpp) cc_final: 0.8782 (tpp) REVERT: A 382 MET cc_start: 0.9371 (mtt) cc_final: 0.9160 (mtp) REVERT: A 421 MET cc_start: 0.9216 (mtp) cc_final: 0.8879 (mtm) REVERT: A 459 LYS cc_start: 0.8326 (tttt) cc_final: 0.8107 (mtmm) REVERT: A 461 LYS cc_start: 0.8174 (mmtp) cc_final: 0.7797 (mtpt) REVERT: A 496 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8886 (mt) REVERT: A 518 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7951 (mt-10) REVERT: A 551 MET cc_start: 0.9057 (ttp) cc_final: 0.8802 (ttt) REVERT: A 561 MET cc_start: 0.8463 (mmt) cc_final: 0.8116 (mmm) REVERT: A 563 GLU cc_start: 0.8587 (pt0) cc_final: 0.8177 (pm20) REVERT: A 706 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7640 (tttm) REVERT: A 715 ILE cc_start: 0.8589 (mt) cc_final: 0.8319 (tp) REVERT: B 69 PHE cc_start: 0.8861 (m-80) cc_final: 0.8587 (m-10) REVERT: B 74 MET cc_start: 0.9392 (ttm) cc_final: 0.9159 (ttp) REVERT: B 102 GLU cc_start: 0.8403 (tt0) cc_final: 0.8180 (tp30) REVERT: B 142 ASP cc_start: 0.8977 (t0) cc_final: 0.8756 (t0) REVERT: C 1 MET cc_start: 0.8863 (tpp) cc_final: 0.8569 (tpt) REVERT: C 14 MET cc_start: 0.9259 (ttp) cc_final: 0.8953 (ttp) REVERT: C 46 MET cc_start: 0.9510 (mmp) cc_final: 0.9050 (mmp) REVERT: C 80 SER cc_start: 0.9224 (t) cc_final: 0.8882 (p) REVERT: E 51 MET cc_start: 0.8878 (mmm) cc_final: 0.8659 (mmm) REVERT: E 53 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8151 (ttm-80) REVERT: E 146 HIS cc_start: 0.8496 (m90) cc_final: 0.8224 (m170) REVERT: G 1 MET cc_start: 0.8251 (ttt) cc_final: 0.7987 (ttm) REVERT: G 92 TYR cc_start: 0.9363 (t80) cc_final: 0.8842 (t80) REVERT: G 109 LYS cc_start: 0.7978 (mmtm) cc_final: 0.7745 (mmmt) REVERT: e 19 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.7142 (mm-40) outliers start: 37 outliers final: 14 residues processed: 285 average time/residue: 1.3494 time to fit residues: 423.7297 Evaluate side-chains 239 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 222 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 PRO Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 385 PRO Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 401 PRO Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 94 PRO Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain e residue 19 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 175 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN E 8 ASN E 137 ASN F 43 ASN e 8 ASN e 19 GLN e 20 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16137 Z= 0.257 Angle : 0.641 8.199 21939 Z= 0.350 Chirality : 0.044 0.188 2633 Planarity : 0.005 0.039 2637 Dihedral : 8.983 84.615 2293 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.02 % Allowed : 10.17 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.18), residues: 2010 helix: 1.38 (0.13), residues: 1524 sheet: -0.46 (0.68), residues: 58 loop : -0.64 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 431 HIS 0.012 0.002 HIS D 333 PHE 0.045 0.002 PHE A 352 TYR 0.029 0.002 TYR A 447 ARG 0.010 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 242 time to evaluate : 1.936 Fit side-chains revert: symmetry clash REVERT: D 40 MET cc_start: 0.9276 (mtp) cc_final: 0.8944 (mtp) REVERT: D 103 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8150 (mm-30) REVERT: D 311 MET cc_start: 0.9266 (mtt) cc_final: 0.8842 (mtt) REVERT: D 439 GLN cc_start: 0.8904 (tt0) cc_final: 0.8183 (pm20) REVERT: D 467 GLU cc_start: 0.9184 (tp30) cc_final: 0.8810 (tp30) REVERT: D 488 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8818 (mm-30) REVERT: A 201 ASP cc_start: 0.8945 (m-30) cc_final: 0.8277 (p0) REVERT: A 207 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8321 (mp0) REVERT: A 314 MET cc_start: 0.9079 (tpp) cc_final: 0.8782 (tpp) REVERT: A 431 ILE cc_start: 0.8371 (pp) cc_final: 0.8168 (mp) REVERT: A 459 LYS cc_start: 0.8443 (tttt) cc_final: 0.8220 (mtmm) REVERT: A 461 LYS cc_start: 0.7939 (mmtp) cc_final: 0.7583 (mtpt) REVERT: A 518 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7935 (mt-10) REVERT: A 561 MET cc_start: 0.8592 (mmt) cc_final: 0.8250 (mmm) REVERT: A 563 GLU cc_start: 0.8631 (pt0) cc_final: 0.8195 (pm20) REVERT: A 706 LYS cc_start: 0.8469 (ttmt) cc_final: 0.7875 (tttm) REVERT: B 102 GLU cc_start: 0.8155 (tt0) cc_final: 0.7865 (tp30) REVERT: C 14 MET cc_start: 0.9063 (ttp) cc_final: 0.8779 (ttp) REVERT: C 80 SER cc_start: 0.9154 (t) cc_final: 0.8901 (p) REVERT: E 51 MET cc_start: 0.8690 (mmm) cc_final: 0.8463 (mmm) REVERT: E 129 TYR cc_start: 0.9052 (m-80) cc_final: 0.8786 (m-80) REVERT: E 146 HIS cc_start: 0.8400 (m90) cc_final: 0.8018 (m170) REVERT: G 79 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8504 (p) REVERT: G 92 TYR cc_start: 0.9282 (t80) cc_final: 0.8603 (t80) REVERT: e 8 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7364 (t0) REVERT: e 46 ARG cc_start: 0.8761 (mmm-85) cc_final: 0.8481 (mtp85) outliers start: 28 outliers final: 8 residues processed: 256 average time/residue: 1.3921 time to fit residues: 393.0516 Evaluate side-chains 230 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 219 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain e residue 8 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 175 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN E 8 ASN E 137 ASN e 8 ASN e 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16137 Z= 0.241 Angle : 0.591 7.248 21939 Z= 0.319 Chirality : 0.043 0.208 2633 Planarity : 0.005 0.041 2637 Dihedral : 8.405 80.107 2271 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.96 % Allowed : 11.06 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.18), residues: 2010 helix: 1.78 (0.13), residues: 1518 sheet: 0.24 (0.75), residues: 48 loop : -0.29 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 139 HIS 0.008 0.002 HIS A 349 PHE 0.040 0.002 PHE A 352 TYR 0.026 0.002 TYR C 92 ARG 0.008 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 215 time to evaluate : 1.889 Fit side-chains REVERT: D 103 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8192 (mm-30) REVERT: D 311 MET cc_start: 0.9250 (mtt) cc_final: 0.8807 (mtt) REVERT: D 439 GLN cc_start: 0.8949 (tt0) cc_final: 0.8267 (pm20) REVERT: D 467 GLU cc_start: 0.9217 (tp30) cc_final: 0.8836 (tp30) REVERT: D 488 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8782 (mm-30) REVERT: A 201 ASP cc_start: 0.9021 (m-30) cc_final: 0.8323 (p0) REVERT: A 207 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8318 (mp0) REVERT: A 370 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7780 (mtp180) REVERT: A 459 LYS cc_start: 0.8450 (tttt) cc_final: 0.8239 (mtmm) REVERT: A 461 LYS cc_start: 0.7925 (mmtp) cc_final: 0.7527 (mtpt) REVERT: A 518 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7912 (mt-10) REVERT: A 561 MET cc_start: 0.8579 (mmt) cc_final: 0.8248 (mmm) REVERT: A 563 GLU cc_start: 0.8626 (pt0) cc_final: 0.8229 (pm20) REVERT: C 14 MET cc_start: 0.9044 (ttp) cc_final: 0.8786 (ttp) REVERT: C 80 SER cc_start: 0.9129 (t) cc_final: 0.8926 (p) REVERT: C 105 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7700 (mp10) REVERT: E 8 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8237 (m-40) REVERT: E 51 MET cc_start: 0.8659 (mmm) cc_final: 0.8456 (mmm) REVERT: E 72 ASN cc_start: 0.9214 (m-40) cc_final: 0.8887 (m110) REVERT: E 124 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8034 (p0) REVERT: F 1 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6790 (tpp) REVERT: G 79 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8426 (p) REVERT: e 46 ARG cc_start: 0.8788 (mmm-85) cc_final: 0.8566 (mtp85) outliers start: 27 outliers final: 6 residues processed: 230 average time/residue: 1.4769 time to fit residues: 372.6833 Evaluate side-chains 226 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 213 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 94 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 117 optimal weight: 0.2980 chunk 176 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN E 8 ASN E 137 ASN e 8 ASN e 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16137 Z= 0.210 Angle : 0.551 7.792 21939 Z= 0.297 Chirality : 0.041 0.198 2633 Planarity : 0.004 0.042 2637 Dihedral : 7.961 76.739 2269 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.96 % Allowed : 11.41 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.13 (0.18), residues: 2010 helix: 1.93 (0.13), residues: 1518 sheet: 0.19 (0.74), residues: 48 loop : -0.18 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 139 HIS 0.008 0.001 HIS D 333 PHE 0.037 0.002 PHE A 352 TYR 0.025 0.002 TYR C 92 ARG 0.009 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 213 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: D 103 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8178 (mm-30) REVERT: D 311 MET cc_start: 0.9227 (mtt) cc_final: 0.8802 (mtt) REVERT: D 439 GLN cc_start: 0.8944 (tt0) cc_final: 0.8260 (pm20) REVERT: D 488 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8769 (mm-30) REVERT: A 201 ASP cc_start: 0.9032 (m-30) cc_final: 0.8314 (p0) REVERT: A 207 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8319 (mp0) REVERT: A 370 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7713 (mtp180) REVERT: A 461 LYS cc_start: 0.7880 (mmtp) cc_final: 0.7496 (mtpt) REVERT: A 518 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7940 (mt-10) REVERT: A 561 MET cc_start: 0.8607 (mmt) cc_final: 0.8313 (mmm) REVERT: A 563 GLU cc_start: 0.8610 (pt0) cc_final: 0.8223 (pm20) REVERT: C 14 MET cc_start: 0.9021 (ttp) cc_final: 0.8786 (ttp) REVERT: C 105 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7686 (mp10) REVERT: E 51 MET cc_start: 0.8619 (mmm) cc_final: 0.8415 (mmm) REVERT: E 72 ASN cc_start: 0.9190 (m-40) cc_final: 0.8882 (m110) REVERT: E 124 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8050 (p0) REVERT: E 128 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8829 (tp) REVERT: F 1 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6742 (tpp) REVERT: e 17 ASN cc_start: 0.7591 (t0) cc_final: 0.7368 (t0) outliers start: 27 outliers final: 10 residues processed: 228 average time/residue: 1.5527 time to fit residues: 388.4074 Evaluate side-chains 228 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 212 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 94 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN C 50 GLN E 8 ASN E 137 ASN e 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16137 Z= 0.268 Angle : 0.581 7.223 21939 Z= 0.314 Chirality : 0.043 0.200 2633 Planarity : 0.004 0.044 2637 Dihedral : 7.867 75.181 2268 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.08 % Allowed : 11.89 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.07 (0.18), residues: 2010 helix: 1.86 (0.13), residues: 1519 sheet: 0.24 (0.75), residues: 48 loop : -0.11 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 139 HIS 0.008 0.002 HIS A 349 PHE 0.034 0.002 PHE A 352 TYR 0.026 0.002 TYR C 92 ARG 0.008 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 213 time to evaluate : 2.021 Fit side-chains REVERT: D 103 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8264 (mm-30) REVERT: D 311 MET cc_start: 0.9262 (mtt) cc_final: 0.8823 (mtt) REVERT: D 439 GLN cc_start: 0.8939 (tt0) cc_final: 0.8261 (pm20) REVERT: D 488 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8781 (mm-30) REVERT: A 201 ASP cc_start: 0.9028 (m-30) cc_final: 0.8300 (p0) REVERT: A 207 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8314 (mp0) REVERT: A 461 LYS cc_start: 0.7838 (mmtp) cc_final: 0.7482 (mtpt) REVERT: A 518 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7938 (mt-10) REVERT: A 561 MET cc_start: 0.8606 (mmt) cc_final: 0.8295 (mmm) REVERT: A 563 GLU cc_start: 0.8602 (pt0) cc_final: 0.8197 (pm20) REVERT: C 105 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7662 (mp10) REVERT: E 19 GLN cc_start: 0.4962 (OUTLIER) cc_final: 0.4636 (mm-40) REVERT: E 51 MET cc_start: 0.8672 (mmm) cc_final: 0.8451 (mmm) REVERT: E 72 ASN cc_start: 0.9201 (m-40) cc_final: 0.8911 (m110) REVERT: E 124 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8062 (p0) REVERT: E 128 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8845 (tp) REVERT: F 1 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6786 (tpp) REVERT: G 92 TYR cc_start: 0.9295 (t80) cc_final: 0.8675 (t80) outliers start: 29 outliers final: 14 residues processed: 231 average time/residue: 1.5292 time to fit residues: 386.5902 Evaluate side-chains 232 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 212 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 94 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 186 optimal weight: 0.0970 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN E 8 ASN E 137 ASN e 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16137 Z= 0.242 Angle : 0.563 7.117 21939 Z= 0.304 Chirality : 0.042 0.194 2633 Planarity : 0.004 0.044 2637 Dihedral : 7.762 75.252 2268 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.08 % Allowed : 12.07 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.11 (0.18), residues: 2010 helix: 1.90 (0.13), residues: 1518 sheet: 0.25 (0.75), residues: 48 loop : -0.12 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 139 HIS 0.007 0.001 HIS A 349 PHE 0.035 0.002 PHE A 352 TYR 0.026 0.002 TYR C 92 ARG 0.008 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 215 time to evaluate : 1.746 Fit side-chains REVERT: D 103 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8262 (mm-30) REVERT: D 311 MET cc_start: 0.9252 (mtt) cc_final: 0.8819 (mtt) REVERT: D 439 GLN cc_start: 0.8933 (tt0) cc_final: 0.8261 (pm20) REVERT: A 201 ASP cc_start: 0.9060 (m-30) cc_final: 0.8325 (p0) REVERT: A 207 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8320 (mp0) REVERT: A 461 LYS cc_start: 0.7826 (mmtp) cc_final: 0.7469 (mtpt) REVERT: A 518 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7912 (mt-10) REVERT: A 561 MET cc_start: 0.8606 (mmt) cc_final: 0.8286 (mmm) REVERT: A 563 GLU cc_start: 0.8664 (pt0) cc_final: 0.8239 (pm20) REVERT: B 59 ASP cc_start: 0.8964 (p0) cc_final: 0.8742 (p0) REVERT: C 105 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: E 19 GLN cc_start: 0.4942 (OUTLIER) cc_final: 0.4619 (mm-40) REVERT: E 72 ASN cc_start: 0.9191 (m-40) cc_final: 0.8907 (m110) REVERT: E 124 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8061 (p0) REVERT: E 128 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8845 (tp) REVERT: F 1 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6755 (tpp) REVERT: G 92 TYR cc_start: 0.9289 (t80) cc_final: 0.8669 (t80) REVERT: e 17 ASN cc_start: 0.7579 (t0) cc_final: 0.7374 (t0) outliers start: 29 outliers final: 17 residues processed: 231 average time/residue: 1.4850 time to fit residues: 375.7086 Evaluate side-chains 233 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 94 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 136 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 186 optimal weight: 0.0970 chunk 116 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN E 8 ASN E 137 ASN e 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16137 Z= 0.205 Angle : 0.542 9.467 21939 Z= 0.292 Chirality : 0.041 0.184 2633 Planarity : 0.004 0.045 2637 Dihedral : 7.586 75.093 2268 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.96 % Allowed : 12.54 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.22 (0.18), residues: 2010 helix: 1.99 (0.13), residues: 1518 sheet: 0.20 (0.75), residues: 48 loop : -0.09 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 139 HIS 0.007 0.001 HIS D 333 PHE 0.034 0.002 PHE A 352 TYR 0.024 0.002 TYR C 92 ARG 0.010 0.001 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 213 time to evaluate : 1.862 Fit side-chains REVERT: D 103 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8261 (mm-30) REVERT: D 311 MET cc_start: 0.9230 (mtt) cc_final: 0.8820 (mtt) REVERT: D 439 GLN cc_start: 0.8930 (tt0) cc_final: 0.8268 (pm20) REVERT: A 201 ASP cc_start: 0.9049 (m-30) cc_final: 0.8300 (p0) REVERT: A 207 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8319 (mp0) REVERT: A 461 LYS cc_start: 0.7798 (mmtp) cc_final: 0.7446 (mtpt) REVERT: A 518 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7808 (mt-10) REVERT: A 561 MET cc_start: 0.8604 (mmt) cc_final: 0.8281 (mmm) REVERT: A 563 GLU cc_start: 0.8659 (pt0) cc_final: 0.8249 (pm20) REVERT: A 714 ASN cc_start: 0.8579 (m110) cc_final: 0.8322 (m110) REVERT: B 59 ASP cc_start: 0.8975 (p0) cc_final: 0.8740 (p0) REVERT: C 105 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: E 19 GLN cc_start: 0.4942 (OUTLIER) cc_final: 0.4621 (mm-40) REVERT: E 72 ASN cc_start: 0.9159 (m-40) cc_final: 0.8878 (m110) REVERT: E 128 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8840 (tp) REVERT: F 1 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6728 (tpp) outliers start: 27 outliers final: 17 residues processed: 228 average time/residue: 1.4516 time to fit residues: 363.4535 Evaluate side-chains 234 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 212 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain e residue 8 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN E 8 ASN E 137 ASN e 8 ASN e 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16137 Z= 0.241 Angle : 0.553 6.730 21939 Z= 0.300 Chirality : 0.042 0.189 2633 Planarity : 0.004 0.045 2637 Dihedral : 7.585 75.151 2268 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.02 % Allowed : 12.72 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.16 (0.18), residues: 2010 helix: 1.93 (0.13), residues: 1519 sheet: 0.21 (0.75), residues: 48 loop : -0.08 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 101 HIS 0.007 0.001 HIS A 349 PHE 0.033 0.002 PHE A 352 TYR 0.025 0.002 TYR C 92 ARG 0.009 0.001 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 215 time to evaluate : 1.917 Fit side-chains REVERT: D 103 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8291 (mm-30) REVERT: D 311 MET cc_start: 0.9247 (mtt) cc_final: 0.8829 (mtt) REVERT: D 422 MET cc_start: 0.9234 (mmp) cc_final: 0.8992 (mmp) REVERT: D 439 GLN cc_start: 0.8930 (tt0) cc_final: 0.8270 (pm20) REVERT: A 201 ASP cc_start: 0.9047 (m-30) cc_final: 0.8296 (p0) REVERT: A 207 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8329 (mp0) REVERT: A 461 LYS cc_start: 0.7810 (mmtp) cc_final: 0.7452 (mtpt) REVERT: A 518 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7784 (mt-10) REVERT: A 561 MET cc_start: 0.8600 (mmt) cc_final: 0.8314 (mmm) REVERT: A 563 GLU cc_start: 0.8698 (pt0) cc_final: 0.8237 (pm20) REVERT: A 714 ASN cc_start: 0.8583 (m110) cc_final: 0.8337 (m110) REVERT: B 36 ASN cc_start: 0.9180 (m-40) cc_final: 0.8966 (m-40) REVERT: B 59 ASP cc_start: 0.8991 (p0) cc_final: 0.8752 (p0) REVERT: C 105 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: E 19 GLN cc_start: 0.5008 (OUTLIER) cc_final: 0.4694 (mm-40) REVERT: E 72 ASN cc_start: 0.9172 (m-40) cc_final: 0.8895 (m110) REVERT: E 124 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8045 (p0) REVERT: E 128 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8847 (tp) REVERT: F 1 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6735 (tpp) REVERT: G 92 TYR cc_start: 0.9255 (t80) cc_final: 0.8646 (t80) outliers start: 28 outliers final: 18 residues processed: 231 average time/residue: 1.4759 time to fit residues: 373.9544 Evaluate side-chains 237 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 213 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain e residue 8 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 75 optimal weight: 0.0670 chunk 136 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 172 optimal weight: 0.1980 chunk 113 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN E 8 ASN E 137 ASN e 8 ASN e 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16137 Z= 0.202 Angle : 0.533 8.908 21939 Z= 0.289 Chirality : 0.041 0.180 2633 Planarity : 0.004 0.047 2637 Dihedral : 7.469 75.316 2268 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 0.93 % Favored : 99.02 % Rotamer: Outliers : 1.84 % Allowed : 13.08 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.24 (0.18), residues: 2010 helix: 1.98 (0.13), residues: 1523 sheet: 0.22 (0.75), residues: 48 loop : -0.02 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 101 HIS 0.007 0.001 HIS D 333 PHE 0.033 0.001 PHE A 352 TYR 0.024 0.002 TYR C 92 ARG 0.008 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 213 time to evaluate : 1.848 Fit side-chains REVERT: D 103 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8270 (mm-30) REVERT: D 311 MET cc_start: 0.9227 (mtt) cc_final: 0.8825 (mtt) REVERT: D 439 GLN cc_start: 0.8945 (tt0) cc_final: 0.8303 (pm20) REVERT: A 201 ASP cc_start: 0.9046 (m-30) cc_final: 0.8296 (p0) REVERT: A 207 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8331 (mp0) REVERT: A 461 LYS cc_start: 0.7784 (mmtp) cc_final: 0.7431 (mtpt) REVERT: A 518 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7804 (mt-10) REVERT: A 561 MET cc_start: 0.8588 (mmt) cc_final: 0.8299 (mmm) REVERT: A 563 GLU cc_start: 0.8692 (pt0) cc_final: 0.8247 (pm20) REVERT: A 714 ASN cc_start: 0.8561 (m110) cc_final: 0.8305 (m110) REVERT: B 36 ASN cc_start: 0.9172 (m-40) cc_final: 0.8965 (m-40) REVERT: B 59 ASP cc_start: 0.8989 (p0) cc_final: 0.8755 (p0) REVERT: C 62 THR cc_start: 0.8771 (p) cc_final: 0.8526 (m) REVERT: C 105 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: E 19 GLN cc_start: 0.4963 (OUTLIER) cc_final: 0.4647 (mm-40) REVERT: E 72 ASN cc_start: 0.9145 (m-40) cc_final: 0.8866 (m110) REVERT: E 128 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8842 (tp) REVERT: F 1 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6756 (tpp) REVERT: F 52 MET cc_start: 0.9094 (mtm) cc_final: 0.8824 (mtp) REVERT: G 92 TYR cc_start: 0.9249 (t80) cc_final: 0.8649 (t80) outliers start: 25 outliers final: 17 residues processed: 228 average time/residue: 1.4718 time to fit residues: 368.8023 Evaluate side-chains 231 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 209 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain e residue 8 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 0.0870 chunk 86 optimal weight: 0.4980 chunk 127 optimal weight: 0.7980 chunk 192 optimal weight: 0.7980 chunk 176 optimal weight: 0.3980 chunk 153 optimal weight: 3.9990 chunk 15 optimal weight: 0.0670 chunk 118 optimal weight: 0.3980 chunk 93 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN E 8 ASN E 137 ASN e 8 ASN e 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16137 Z= 0.168 Angle : 0.509 8.760 21939 Z= 0.275 Chirality : 0.040 0.209 2633 Planarity : 0.004 0.048 2637 Dihedral : 7.250 75.725 2268 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.49 % Allowed : 13.50 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.39 (0.18), residues: 2010 helix: 2.09 (0.13), residues: 1522 sheet: 0.25 (0.75), residues: 48 loop : 0.01 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 101 HIS 0.009 0.001 HIS D 333 PHE 0.033 0.001 PHE A 352 TYR 0.024 0.001 TYR A 447 ARG 0.011 0.000 ARG A 587 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 214 time to evaluate : 1.716 Fit side-chains REVERT: D 103 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8226 (mm-30) REVERT: D 311 MET cc_start: 0.9169 (mtt) cc_final: 0.8781 (mtt) REVERT: D 439 GLN cc_start: 0.8933 (tt0) cc_final: 0.8290 (pm20) REVERT: A 201 ASP cc_start: 0.9045 (m-30) cc_final: 0.8296 (p0) REVERT: A 207 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8234 (mp0) REVERT: A 461 LYS cc_start: 0.7744 (mmtp) cc_final: 0.7362 (mtpt) REVERT: A 518 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7802 (mt-10) REVERT: A 561 MET cc_start: 0.8583 (mmt) cc_final: 0.8291 (mmm) REVERT: A 563 GLU cc_start: 0.8643 (pt0) cc_final: 0.8231 (pm20) REVERT: A 714 ASN cc_start: 0.8582 (m110) cc_final: 0.8353 (m110) REVERT: B 36 ASN cc_start: 0.9090 (m-40) cc_final: 0.8885 (m-40) REVERT: B 59 ASP cc_start: 0.8987 (p0) cc_final: 0.8750 (p0) REVERT: C 62 THR cc_start: 0.8762 (p) cc_final: 0.8519 (m) REVERT: C 105 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7672 (mp10) REVERT: E 72 ASN cc_start: 0.9096 (m-40) cc_final: 0.8806 (m110) REVERT: F 52 MET cc_start: 0.9003 (mtm) cc_final: 0.8787 (mtp) outliers start: 19 outliers final: 13 residues processed: 225 average time/residue: 1.5451 time to fit residues: 380.5949 Evaluate side-chains 225 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain e residue 8 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 0.2980 chunk 46 optimal weight: 0.1980 chunk 141 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 134 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN E 8 ASN E 137 ASN e 8 ASN e 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.076777 restraints weight = 97828.589| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.72 r_work: 0.2668 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16137 Z= 0.212 Angle : 0.532 8.824 21939 Z= 0.288 Chirality : 0.041 0.197 2633 Planarity : 0.004 0.046 2637 Dihedral : 7.271 76.466 2268 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.55 % Allowed : 13.44 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.33 (0.18), residues: 2010 helix: 2.04 (0.13), residues: 1523 sheet: 0.30 (0.75), residues: 48 loop : 0.01 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 101 HIS 0.006 0.001 HIS A 349 PHE 0.032 0.002 PHE A 352 TYR 0.023 0.002 TYR C 92 ARG 0.010 0.001 ARG A 587 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6873.79 seconds wall clock time: 122 minutes 45.20 seconds (7365.20 seconds total)