Starting phenix.real_space_refine on Wed Feb 21 09:04:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z16_11027/02_2024/6z16_11027_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z16_11027/02_2024/6z16_11027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z16_11027/02_2024/6z16_11027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z16_11027/02_2024/6z16_11027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z16_11027/02_2024/6z16_11027_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z16_11027/02_2024/6z16_11027_updated.pdb" } resolution = 2.98 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= 0.001 sd= 0.006 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 26 5.49 5 S 142 5.16 5 C 20386 2.51 5 N 4594 2.21 5 O 5098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "F ARG 20": "NH1" <-> "NH2" Residue "G ARG 103": "NH1" <-> "NH2" Residue "a PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 183": "NH1" <-> "NH2" Residue "a ARG 187": "NH1" <-> "NH2" Residue "a PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 473": "NH1" <-> "NH2" Residue "a ARG 644": "NH1" <-> "NH2" Residue "a ARG 789": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "d ARG 258": "NH1" <-> "NH2" Residue "f ARG 20": "NH1" <-> "NH2" Residue "g ARG 103": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30250 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6221 Classifications: {'peptide': 788} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 758} Chain: "B" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1070 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "D" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3796 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 470} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1274 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 648 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "a" Number of atoms: 6221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6221 Classifications: {'peptide': 788} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 758} Chain: "b" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1070 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain: "c" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "d" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3796 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 470} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1274 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "f" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 648 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "g" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "A" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 276 Unusual residues: {' K': 1, 'PTY': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 75 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'PTY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "a" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 276 Unusual residues: {' K': 1, 'PTY': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 75 Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'PTY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "f" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Time building chain proxies: 16.99, per 1000 atoms: 0.56 Number of scatterers: 30250 At special positions: 0 Unit cell: (221.76, 225.12, 95.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 142 16.00 P 26 15.00 O 5098 8.00 N 4594 7.00 C 20386 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: 11.70 Conformation dependent library (CDL) restraints added in 6.0 seconds 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 150 helices and 8 sheets defined 70.8% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.15 Creating SS restraints... Processing helix chain 'A' and resid 32 through 35 No H-bonds generated for 'chain 'A' and resid 32 through 35' Processing helix chain 'A' and resid 37 through 51 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 57 through 73 Proline residue: A 63 - end of helix removed outlier: 3.946A pdb=" N ILE A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 105 through 128 Processing helix chain 'A' and resid 136 through 154 Processing helix chain 'A' and resid 159 through 177 Processing helix chain 'A' and resid 184 through 214 Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 234 through 248 Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 266 through 274 Processing helix chain 'A' and resid 280 through 292 Proline residue: A 290 - end of helix Processing helix chain 'A' and resid 296 through 318 removed outlier: 4.693A pdb=" N SER A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 349 removed outlier: 4.419A pdb=" N PHE A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 359 through 391 Processing helix chain 'A' and resid 407 through 421 Processing helix chain 'A' and resid 427 through 440 removed outlier: 3.629A pdb=" N SER A 431 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 433 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 434 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 436 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 440 " --> pdb=" O THR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 473 Proline residue: A 453 - end of helix Processing helix chain 'A' and resid 493 through 511 removed outlier: 4.857A pdb=" N ALA A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 514 through 528 removed outlier: 5.170A pdb=" N ALA A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) Proline residue: A 523 - end of helix Processing helix chain 'A' and resid 537 through 543 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.817A pdb=" N MET A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 587 through 608 Processing helix chain 'A' and resid 613 through 634 Processing helix chain 'A' and resid 650 through 667 Processing helix chain 'A' and resid 672 through 692 Processing helix chain 'A' and resid 696 through 717 Processing helix chain 'A' and resid 734 through 755 Processing helix chain 'A' and resid 765 through 769 Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 793 through 812 Processing helix chain 'B' and resid 6 through 28 Proline residue: B 17 - end of helix Processing helix chain 'B' and resid 37 through 54 Processing helix chain 'B' and resid 58 through 63 Processing helix chain 'B' and resid 68 through 88 Processing helix chain 'B' and resid 114 through 137 Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.986A pdb=" N CYS C 11 " --> pdb=" O VAL C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 47 Processing helix chain 'C' and resid 68 through 97 Processing helix chain 'D' and resid 2 through 19 removed outlier: 4.214A pdb=" N LEU D 5 " --> pdb=" O SER D 2 " (cutoff:3.500A) Proline residue: D 8 - end of helix removed outlier: 4.960A pdb=" N ILE D 11 " --> pdb=" O PRO D 8 " (cutoff:3.500A) Proline residue: D 12 - end of helix Processing helix chain 'D' and resid 26 through 53 Processing helix chain 'D' and resid 76 through 99 Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 109 through 124 Processing helix chain 'D' and resid 129 through 148 Processing helix chain 'D' and resid 153 through 183 Processing helix chain 'D' and resid 189 through 198 Processing helix chain 'D' and resid 203 through 219 Processing helix chain 'D' and resid 229 through 235 Processing helix chain 'D' and resid 238 through 262 removed outlier: 5.388A pdb=" N THR D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS D 250 " --> pdb=" O GLY D 246 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 253 " --> pdb=" O THR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 292 Processing helix chain 'D' and resid 296 through 315 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 367 through 381 Processing helix chain 'D' and resid 387 through 401 removed outlier: 4.209A pdb=" N ILE D 390 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY D 391 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D 392 " --> pdb=" O PHE D 389 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP D 401 " --> pdb=" O ALA D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 429 Processing helix chain 'D' and resid 446 through 461 Processing helix chain 'D' and resid 463 through 477 Proline residue: D 468 - end of helix Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'E' and resid 3 through 18 Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 51 through 79 Processing helix chain 'E' and resid 100 through 111 Processing helix chain 'E' and resid 141 through 156 Processing helix chain 'F' and resid 3 through 22 Processing helix chain 'F' and resid 27 through 52 Processing helix chain 'F' and resid 58 through 79 Processing helix chain 'G' and resid 11 through 33 Processing helix chain 'G' and resid 37 through 66 Processing helix chain 'G' and resid 72 through 98 Proline residue: G 86 - end of helix Processing helix chain 'a' and resid 32 through 35 No H-bonds generated for 'chain 'a' and resid 32 through 35' Processing helix chain 'a' and resid 37 through 51 Proline residue: a 46 - end of helix Processing helix chain 'a' and resid 57 through 73 Proline residue: a 63 - end of helix removed outlier: 3.942A pdb=" N ILE a 66 " --> pdb=" O PHE a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 80 Processing helix chain 'a' and resid 105 through 128 Processing helix chain 'a' and resid 136 through 155 Processing helix chain 'a' and resid 159 through 177 Processing helix chain 'a' and resid 184 through 214 Processing helix chain 'a' and resid 220 through 223 No H-bonds generated for 'chain 'a' and resid 220 through 223' Processing helix chain 'a' and resid 234 through 248 Processing helix chain 'a' and resid 255 through 257 No H-bonds generated for 'chain 'a' and resid 255 through 257' Processing helix chain 'a' and resid 261 through 263 No H-bonds generated for 'chain 'a' and resid 261 through 263' Processing helix chain 'a' and resid 266 through 275 Processing helix chain 'a' and resid 280 through 294 Proline residue: a 290 - end of helix removed outlier: 5.981A pdb=" N VAL a 294 " --> pdb=" O PRO a 290 " (cutoff:3.500A) Processing helix chain 'a' and resid 296 through 318 removed outlier: 4.667A pdb=" N SER a 318 " --> pdb=" O SER a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 323 through 349 removed outlier: 4.400A pdb=" N PHE a 349 " --> pdb=" O GLY a 345 " (cutoff:3.500A) Processing helix chain 'a' and resid 353 through 355 No H-bonds generated for 'chain 'a' and resid 353 through 355' Processing helix chain 'a' and resid 359 through 391 removed outlier: 3.852A pdb=" N VAL a 363 " --> pdb=" O PHE a 359 " (cutoff:3.500A) Processing helix chain 'a' and resid 407 through 421 Processing helix chain 'a' and resid 427 through 440 removed outlier: 3.654A pdb=" N SER a 431 " --> pdb=" O GLY a 428 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET a 434 " --> pdb=" O SER a 431 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE a 436 " --> pdb=" O GLU a 433 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU a 440 " --> pdb=" O THR a 437 " (cutoff:3.500A) Processing helix chain 'a' and resid 448 through 473 Proline residue: a 453 - end of helix Processing helix chain 'a' and resid 493 through 511 removed outlier: 4.875A pdb=" N ALA a 498 " --> pdb=" O GLY a 494 " (cutoff:3.500A) Proline residue: a 499 - end of helix Processing helix chain 'a' and resid 514 through 528 removed outlier: 5.207A pdb=" N ALA a 522 " --> pdb=" O ASP a 518 " (cutoff:3.500A) Proline residue: a 523 - end of helix Processing helix chain 'a' and resid 537 through 543 Processing helix chain 'a' and resid 552 through 567 Processing helix chain 'a' and resid 574 through 583 Processing helix chain 'a' and resid 587 through 608 Processing helix chain 'a' and resid 613 through 634 Processing helix chain 'a' and resid 650 through 667 Processing helix chain 'a' and resid 672 through 692 Processing helix chain 'a' and resid 696 through 717 Processing helix chain 'a' and resid 734 through 755 Processing helix chain 'a' and resid 765 through 769 Processing helix chain 'a' and resid 781 through 786 Processing helix chain 'a' and resid 793 through 812 Processing helix chain 'b' and resid 6 through 28 Proline residue: b 17 - end of helix Processing helix chain 'b' and resid 37 through 54 Processing helix chain 'b' and resid 58 through 63 Processing helix chain 'b' and resid 68 through 88 Processing helix chain 'b' and resid 114 through 137 Processing helix chain 'c' and resid 2 through 20 Processing helix chain 'c' and resid 25 through 47 Processing helix chain 'c' and resid 67 through 97 Processing helix chain 'd' and resid 2 through 19 removed outlier: 4.209A pdb=" N LEU d 5 " --> pdb=" O SER d 2 " (cutoff:3.500A) Proline residue: d 8 - end of helix removed outlier: 5.027A pdb=" N ILE d 11 " --> pdb=" O PRO d 8 " (cutoff:3.500A) Proline residue: d 12 - end of helix Processing helix chain 'd' and resid 26 through 53 Processing helix chain 'd' and resid 76 through 99 Processing helix chain 'd' and resid 102 through 106 Processing helix chain 'd' and resid 109 through 124 Processing helix chain 'd' and resid 129 through 148 Processing helix chain 'd' and resid 153 through 183 Processing helix chain 'd' and resid 189 through 198 Processing helix chain 'd' and resid 203 through 219 Processing helix chain 'd' and resid 229 through 235 Processing helix chain 'd' and resid 238 through 262 removed outlier: 5.409A pdb=" N THR d 249 " --> pdb=" O GLY d 245 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LYS d 250 " --> pdb=" O GLY d 246 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL d 251 " --> pdb=" O LEU d 247 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY d 252 " --> pdb=" O LEU d 248 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL d 253 " --> pdb=" O THR d 249 " (cutoff:3.500A) Processing helix chain 'd' and resid 268 through 292 Processing helix chain 'd' and resid 296 through 315 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 367 through 381 Processing helix chain 'd' and resid 387 through 401 removed outlier: 4.217A pdb=" N ILE d 390 " --> pdb=" O SER d 387 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY d 391 " --> pdb=" O GLY d 388 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS d 392 " --> pdb=" O PHE d 389 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU d 393 " --> pdb=" O ILE d 390 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP d 401 " --> pdb=" O ALA d 398 " (cutoff:3.500A) Processing helix chain 'd' and resid 405 through 429 Processing helix chain 'd' and resid 446 through 461 Processing helix chain 'd' and resid 463 through 477 Proline residue: d 468 - end of helix Processing helix chain 'd' and resid 481 through 487 Processing helix chain 'e' and resid 3 through 18 Processing helix chain 'e' and resid 24 through 40 Processing helix chain 'e' and resid 51 through 79 Processing helix chain 'e' and resid 100 through 111 Processing helix chain 'e' and resid 141 through 156 Processing helix chain 'f' and resid 3 through 22 Processing helix chain 'f' and resid 27 through 51 Processing helix chain 'f' and resid 58 through 79 Processing helix chain 'g' and resid 11 through 33 Processing helix chain 'g' and resid 37 through 66 Processing helix chain 'g' and resid 72 through 98 Proline residue: g 86 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 85 through 92 removed outlier: 6.969A pdb=" N ILE A 97 " --> pdb=" O TRP A 91 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 98 through 101 Processing sheet with id= C, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= D, first strand: chain 'E' and resid 89 through 94 Processing sheet with id= E, first strand: chain 'a' and resid 85 through 92 removed outlier: 7.014A pdb=" N ILE a 97 " --> pdb=" O TRP a 91 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'b' and resid 98 through 101 Processing sheet with id= G, first strand: chain 'd' and resid 57 through 60 Processing sheet with id= H, first strand: chain 'e' and resid 89 through 94 2003 hydrogen bonds defined for protein. 5649 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: 10.07 Time building geometry restraints manager: 12.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4572 1.32 - 1.45: 8315 1.45 - 1.57: 17759 1.57 - 1.69: 46 1.69 - 1.82: 270 Bond restraints: 30962 Sorted by residual: bond pdb=" O14 PTY B 201 " pdb=" P1 PTY B 201 " ideal model delta sigma weight residual 1.646 1.462 0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" O14 PTY E 201 " pdb=" P1 PTY E 201 " ideal model delta sigma weight residual 1.646 1.466 0.180 2.00e-02 2.50e+03 8.13e+01 bond pdb=" O14 PTY a 906 " pdb=" P1 PTY a 906 " ideal model delta sigma weight residual 1.646 1.466 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" O14 PTY A 906 " pdb=" P1 PTY A 906 " ideal model delta sigma weight residual 1.646 1.470 0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" O14 PTY a 902 " pdb=" P1 PTY a 902 " ideal model delta sigma weight residual 1.646 1.470 0.176 2.00e-02 2.50e+03 7.73e+01 ... (remaining 30957 not shown) Histogram of bond angle deviations from ideal: 96.73 - 105.11: 547 105.11 - 113.49: 17619 113.49 - 121.87: 18386 121.87 - 130.25: 5195 130.25 - 138.63: 195 Bond angle restraints: 41942 Sorted by residual: angle pdb=" N PRO D 384 " pdb=" CA PRO D 384 " pdb=" C PRO D 384 " ideal model delta sigma weight residual 110.70 117.69 -6.99 1.22e+00 6.72e-01 3.28e+01 angle pdb=" N PRO d 384 " pdb=" CA PRO d 384 " pdb=" C PRO d 384 " ideal model delta sigma weight residual 110.70 117.34 -6.64 1.22e+00 6.72e-01 2.96e+01 angle pdb=" C ASN a 81 " pdb=" N ASP a 82 " pdb=" CA ASP a 82 " ideal model delta sigma weight residual 121.54 131.02 -9.48 1.91e+00 2.74e-01 2.46e+01 angle pdb=" C VAL G 108 " pdb=" N ARG G 109 " pdb=" CA ARG G 109 " ideal model delta sigma weight residual 121.31 128.61 -7.30 1.49e+00 4.50e-01 2.40e+01 angle pdb=" N ALA D 235 " pdb=" CA ALA D 235 " pdb=" C ALA D 235 " ideal model delta sigma weight residual 112.17 118.78 -6.61 1.36e+00 5.41e-01 2.36e+01 ... (remaining 41937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.92: 17819 34.92 - 69.84: 209 69.84 - 104.77: 37 104.77 - 139.69: 10 139.69 - 174.61: 5 Dihedral angle restraints: 18080 sinusoidal: 7240 harmonic: 10840 Sorted by residual: dihedral pdb=" CA ASP E 120 " pdb=" C ASP E 120 " pdb=" N VAL E 121 " pdb=" CA VAL E 121 " ideal model delta harmonic sigma weight residual 180.00 148.77 31.23 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA ASP e 120 " pdb=" C ASP e 120 " pdb=" N VAL e 121 " pdb=" CA VAL e 121 " ideal model delta harmonic sigma weight residual 180.00 150.83 29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA PHE e 49 " pdb=" C PHE e 49 " pdb=" N TYR e 50 " pdb=" CA TYR e 50 " ideal model delta harmonic sigma weight residual -180.00 -152.35 -27.65 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 18077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4100 0.074 - 0.147: 762 0.147 - 0.221: 108 0.221 - 0.295: 10 0.295 - 0.369: 8 Chirality restraints: 4988 Sorted by residual: chirality pdb=" C6 PTY A 906 " pdb=" C1 PTY A 906 " pdb=" C5 PTY A 906 " pdb=" O7 PTY A 906 " both_signs ideal model delta sigma weight residual False 2.49 2.12 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C6 PTY B 201 " pdb=" C1 PTY B 201 " pdb=" C5 PTY B 201 " pdb=" O7 PTY B 201 " both_signs ideal model delta sigma weight residual False 2.49 2.13 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C6 PTY a 907 " pdb=" C1 PTY a 907 " pdb=" C5 PTY a 907 " pdb=" O7 PTY a 907 " both_signs ideal model delta sigma weight residual False 2.49 2.13 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 4985 not shown) Planarity restraints: 4948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 374 " 0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C ALA A 374 " -0.088 2.00e-02 2.50e+03 pdb=" O ALA A 374 " 0.033 2.00e-02 2.50e+03 pdb=" N THR A 375 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA a 374 " -0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ALA a 374 " 0.086 2.00e-02 2.50e+03 pdb=" O ALA a 374 " -0.033 2.00e-02 2.50e+03 pdb=" N THR a 375 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 373 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C HIS A 373 " 0.073 2.00e-02 2.50e+03 pdb=" O HIS A 373 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA A 374 " -0.025 2.00e-02 2.50e+03 ... (remaining 4945 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 8482 2.82 - 3.40: 33370 3.40 - 3.98: 57533 3.98 - 4.56: 81369 4.56 - 5.14: 121687 Nonbonded interactions: 302441 Sorted by model distance: nonbonded pdb=" O TYR A 767 " pdb=" OG1 THR A 771 " model vdw 2.238 2.440 nonbonded pdb=" O GLN d 155 " pdb=" OG1 THR d 159 " model vdw 2.242 2.440 nonbonded pdb=" O GLN D 155 " pdb=" OG1 THR D 159 " model vdw 2.243 2.440 nonbonded pdb=" O TYR a 767 " pdb=" OG1 THR a 771 " model vdw 2.249 2.440 nonbonded pdb=" O PHE A 315 " pdb=" OH TYR A 577 " model vdw 2.261 2.440 ... (remaining 302436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = (chain 'B' and resid 3 through 140) selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = (chain 'E' and resid 1 through 158) selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.030 Extract box with map and model: 3.620 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 86.880 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.280 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:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.008 0.184 30962 Z= 0.526 Angle : 1.135 15.316 41942 Z= 0.579 Chirality : 0.060 0.369 4988 Planarity : 0.009 0.063 4948 Dihedral : 13.193 174.609 11120 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.64 (0.11), residues: 3716 helix: -1.12 (0.08), residues: 2742 sheet: -1.47 (0.57), residues: 70 loop : -3.36 (0.16), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP a 166 HIS 0.013 0.002 HIS D 272 PHE 0.047 0.004 PHE c 87 TYR 0.040 0.003 TYR A 619 ARG 0.010 0.001 ARG a 473 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 773 time to evaluate : 6.076 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7753 (t0) cc_final: 0.7550 (t0) REVERT: A 131 LYS cc_start: 0.6419 (ttpp) cc_final: 0.5842 (tttt) REVERT: A 319 LYS cc_start: 0.8005 (tmtm) cc_final: 0.7766 (tptp) REVERT: A 357 ASN cc_start: 0.5945 (t0) cc_final: 0.5733 (p0) REVERT: A 372 ASN cc_start: 0.8244 (t0) cc_final: 0.7994 (t0) REVERT: A 440 LEU cc_start: 0.7946 (mt) cc_final: 0.7280 (tm) REVERT: A 514 ASN cc_start: 0.7088 (m-40) cc_final: 0.6580 (p0) REVERT: A 568 ARG cc_start: 0.8046 (tpp-160) cc_final: 0.6839 (mpt-90) REVERT: C 60 LYS cc_start: 0.7381 (mttt) cc_final: 0.6699 (ttpp) REVERT: C 63 ARG cc_start: 0.8979 (ptm160) cc_final: 0.8519 (ptm-80) REVERT: D 293 TYR cc_start: 0.8076 (m-80) cc_final: 0.7809 (m-80) REVERT: D 318 MET cc_start: 0.6703 (mmp) cc_final: 0.5449 (pmt) REVERT: E 102 GLU cc_start: 0.7866 (pt0) cc_final: 0.6156 (mp0) REVERT: E 126 SER cc_start: 0.6689 (p) cc_final: 0.6384 (p) REVERT: F 86 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7198 (mm-30) REVERT: G 100 ASN cc_start: 0.7430 (m-40) cc_final: 0.6922 (t0) REVERT: a 48 PHE cc_start: 0.7566 (t80) cc_final: 0.7358 (t80) REVERT: a 89 MET cc_start: 0.7482 (ttm) cc_final: 0.7248 (ttm) REVERT: a 514 ASN cc_start: 0.7425 (m-40) cc_final: 0.7073 (m110) REVERT: a 568 ARG cc_start: 0.8218 (tpp-160) cc_final: 0.7020 (mpt-90) REVERT: c 60 LYS cc_start: 0.7501 (mttt) cc_final: 0.7051 (ttpp) REVERT: c 63 ARG cc_start: 0.9081 (ptm160) cc_final: 0.8649 (ptm-80) REVERT: d 113 PHE cc_start: 0.8675 (t80) cc_final: 0.8416 (t80) REVERT: d 197 ASN cc_start: 0.8528 (m-40) cc_final: 0.8149 (t0) REVERT: e 77 LYS cc_start: 0.7547 (pttm) cc_final: 0.7281 (mttm) REVERT: e 83 SER cc_start: 0.7017 (m) cc_final: 0.6678 (t) REVERT: e 99 LYS cc_start: 0.8159 (ptpt) cc_final: 0.7819 (ptmt) REVERT: e 102 GLU cc_start: 0.7868 (pt0) cc_final: 0.6143 (mp0) REVERT: e 126 SER cc_start: 0.6744 (p) cc_final: 0.6524 (p) REVERT: f 86 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7220 (mm-30) REVERT: g 94 ARG cc_start: 0.7600 (ttp-110) cc_final: 0.7230 (ttp80) REVERT: g 100 ASN cc_start: 0.7833 (m-40) cc_final: 0.7278 (t0) outliers start: 3 outliers final: 1 residues processed: 776 average time/residue: 1.1439 time to fit residues: 1081.8167 Evaluate side-chains 492 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 491 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 153 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 285 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 330 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 320 GLN A 547 HIS ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN A 733 HIS C 102 HIS D 155 GLN D 266 HIS ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 HIS ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 158 HIS a 191 GLN a 610 ASN a 733 HIS ** a 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 155 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 90 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30962 Z= 0.266 Angle : 0.681 8.665 41942 Z= 0.354 Chirality : 0.043 0.216 4988 Planarity : 0.006 0.052 4948 Dihedral : 13.578 144.714 4808 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 3.48 % Allowed : 11.17 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 3716 helix: 0.65 (0.09), residues: 2728 sheet: -0.39 (0.57), residues: 90 loop : -3.08 (0.17), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 371 HIS 0.007 0.001 HIS D 272 PHE 0.031 0.002 PHE a 376 TYR 0.021 0.002 TYR A 619 ARG 0.006 0.001 ARG A 644 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 542 time to evaluate : 3.650 Fit side-chains revert: symmetry clash REVERT: A 94 SER cc_start: 0.8243 (m) cc_final: 0.7575 (p) REVERT: A 131 LYS cc_start: 0.6426 (ttpp) cc_final: 0.5857 (tttt) REVERT: A 319 LYS cc_start: 0.7960 (tmtm) cc_final: 0.7669 (tptp) REVERT: A 440 LEU cc_start: 0.7935 (mt) cc_final: 0.6999 (tm) REVERT: A 568 ARG cc_start: 0.8067 (tpp-160) cc_final: 0.6847 (mpt-90) REVERT: A 722 LYS cc_start: 0.8151 (mmpt) cc_final: 0.7160 (mmtm) REVERT: B 31 HIS cc_start: 0.8803 (OUTLIER) cc_final: 0.8547 (m170) REVERT: B 78 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6872 (t80) REVERT: C 60 LYS cc_start: 0.7374 (mttt) cc_final: 0.6691 (ttpp) REVERT: C 63 ARG cc_start: 0.8954 (ptm160) cc_final: 0.8510 (ptm-80) REVERT: D 5 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7976 (tt) REVERT: D 293 TYR cc_start: 0.8122 (m-80) cc_final: 0.7816 (m-80) REVERT: D 318 MET cc_start: 0.6833 (mmp) cc_final: 0.5577 (pmt) REVERT: E 110 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7086 (pt) REVERT: E 157 SER cc_start: 0.6694 (t) cc_final: 0.6349 (m) REVERT: F 86 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7134 (mm-30) REVERT: G 100 ASN cc_start: 0.7404 (m-40) cc_final: 0.6854 (t0) REVERT: a 48 PHE cc_start: 0.7748 (t80) cc_final: 0.7427 (t80) REVERT: a 372 ASN cc_start: 0.8552 (t0) cc_final: 0.8289 (m110) REVERT: a 440 LEU cc_start: 0.8095 (mm) cc_final: 0.7327 (tm) REVERT: a 567 TYR cc_start: 0.8116 (t80) cc_final: 0.7883 (t80) REVERT: a 568 ARG cc_start: 0.8211 (tpp-160) cc_final: 0.7096 (mpt-90) REVERT: c 60 LYS cc_start: 0.7521 (mttt) cc_final: 0.6986 (ttpp) REVERT: c 63 ARG cc_start: 0.9062 (ptm160) cc_final: 0.8601 (ptm-80) REVERT: d 5 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8016 (tt) REVERT: d 197 ASN cc_start: 0.8551 (m-40) cc_final: 0.8173 (t0) REVERT: d 461 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8596 (mp) REVERT: e 108 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8171 (tmm) REVERT: f 86 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7191 (mm-30) REVERT: g 71 ASN cc_start: 0.8558 (m110) cc_final: 0.8093 (m-40) REVERT: g 94 ARG cc_start: 0.7607 (ttp-110) cc_final: 0.7353 (ttm170) REVERT: g 100 ASN cc_start: 0.7828 (m-40) cc_final: 0.7259 (t0) outliers start: 109 outliers final: 42 residues processed: 601 average time/residue: 1.0873 time to fit residues: 802.9419 Evaluate side-chains 530 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 481 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain a residue 33 ILE Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 194 MET Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 618 MET Chi-restraints excluded: chain a residue 697 ASP Chi-restraints excluded: chain a residue 701 THR Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain c residue 62 SER Chi-restraints excluded: chain c residue 97 GLU Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain d residue 255 SER Chi-restraints excluded: chain d residue 461 ILE Chi-restraints excluded: chain d residue 476 VAL Chi-restraints excluded: chain d residue 489 LYS Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 90 ILE Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 153 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 225 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 331 optimal weight: 2.9990 chunk 357 optimal weight: 20.0000 chunk 294 optimal weight: 9.9990 chunk 328 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 265 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 191 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30962 Z= 0.214 Angle : 0.628 10.078 41942 Z= 0.325 Chirality : 0.042 0.227 4988 Planarity : 0.005 0.054 4948 Dihedral : 12.837 150.199 4808 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.02 % Allowed : 13.40 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.14), residues: 3716 helix: 1.27 (0.10), residues: 2724 sheet: -0.11 (0.60), residues: 90 loop : -2.80 (0.18), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 371 HIS 0.007 0.001 HIS D 272 PHE 0.031 0.002 PHE a 376 TYR 0.019 0.002 TYR a 466 ARG 0.005 0.001 ARG a 394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 534 time to evaluate : 3.491 Fit side-chains revert: symmetry clash REVERT: A 94 SER cc_start: 0.8058 (m) cc_final: 0.7453 (p) REVERT: A 123 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8779 (tm) REVERT: A 131 LYS cc_start: 0.6431 (ttpp) cc_final: 0.5839 (tttt) REVERT: A 319 LYS cc_start: 0.7936 (tmtm) cc_final: 0.7634 (tptp) REVERT: A 354 MET cc_start: 0.7056 (pmm) cc_final: 0.6323 (tpp) REVERT: A 440 LEU cc_start: 0.7924 (mt) cc_final: 0.7406 (tp) REVERT: A 567 TYR cc_start: 0.7793 (t80) cc_final: 0.7512 (t80) REVERT: A 568 ARG cc_start: 0.8050 (tpp-160) cc_final: 0.6809 (mpt-90) REVERT: A 688 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8587 (tt) REVERT: A 722 LYS cc_start: 0.8078 (mmpt) cc_final: 0.7124 (mmtm) REVERT: B 78 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.6935 (t80) REVERT: C 60 LYS cc_start: 0.7251 (mttt) cc_final: 0.6571 (ttpp) REVERT: C 63 ARG cc_start: 0.8925 (ptm160) cc_final: 0.8476 (ptm-80) REVERT: D 293 TYR cc_start: 0.8072 (m-80) cc_final: 0.7747 (m-80) REVERT: D 318 MET cc_start: 0.6913 (mmp) cc_final: 0.5487 (pmt) REVERT: E 110 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7092 (pt) REVERT: E 157 SER cc_start: 0.6679 (t) cc_final: 0.6320 (m) REVERT: F 86 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7116 (mm-30) REVERT: G 100 ASN cc_start: 0.7404 (m-40) cc_final: 0.6718 (t0) REVERT: a 48 PHE cc_start: 0.7720 (t80) cc_final: 0.7365 (t80) REVERT: a 440 LEU cc_start: 0.8094 (mm) cc_final: 0.7228 (tm) REVERT: a 567 TYR cc_start: 0.8224 (t80) cc_final: 0.8005 (t80) REVERT: a 568 ARG cc_start: 0.8146 (tpp-160) cc_final: 0.7015 (mpt-90) REVERT: a 722 LYS cc_start: 0.8256 (mmpt) cc_final: 0.7280 (mmtm) REVERT: b 78 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7190 (t80) REVERT: c 60 LYS cc_start: 0.7448 (mttt) cc_final: 0.6798 (ttpp) REVERT: c 63 ARG cc_start: 0.9022 (ptm160) cc_final: 0.8559 (ptm-80) REVERT: d 5 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7950 (tt) REVERT: d 76 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8226 (m) REVERT: d 197 ASN cc_start: 0.8575 (m-40) cc_final: 0.8202 (t0) REVERT: d 405 ILE cc_start: 0.8506 (mm) cc_final: 0.8263 (mt) REVERT: d 461 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8538 (mp) REVERT: d 466 VAL cc_start: 0.8253 (p) cc_final: 0.8010 (m) REVERT: e 108 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8099 (tmm) REVERT: e 110 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7135 (pt) REVERT: f 86 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7205 (mm-30) REVERT: g 71 ASN cc_start: 0.8542 (m110) cc_final: 0.8103 (m-40) REVERT: g 94 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7267 (ttp80) REVERT: g 100 ASN cc_start: 0.7818 (m-40) cc_final: 0.7270 (t0) outliers start: 126 outliers final: 45 residues processed: 605 average time/residue: 1.0748 time to fit residues: 803.9036 Evaluate side-chains 530 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 475 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain a residue 33 ILE Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 184 ASP Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 194 MET Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain a residue 697 ASP Chi-restraints excluded: chain a residue 701 THR Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain b residue 85 SER Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain c residue 62 SER Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 461 ILE Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 158 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 chunk 332 optimal weight: 9.9990 chunk 351 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 314 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN A 727 GLN D 3 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 138 ASN a 191 GLN a 372 ASN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 0.074 30962 Z= 0.259 Angle : 0.648 9.819 41942 Z= 0.334 Chirality : 0.043 0.258 4988 Planarity : 0.005 0.055 4948 Dihedral : 12.568 152.452 4808 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.21 % Allowed : 14.36 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.14), residues: 3716 helix: 1.44 (0.10), residues: 2742 sheet: -0.04 (0.60), residues: 90 loop : -2.63 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 298 HIS 0.008 0.001 HIS D 272 PHE 0.030 0.002 PHE a 376 TYR 0.020 0.002 TYR A 767 ARG 0.006 0.001 ARG A 644 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 503 time to evaluate : 3.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 SER cc_start: 0.8016 (m) cc_final: 0.7364 (p) REVERT: A 131 LYS cc_start: 0.6422 (ttpp) cc_final: 0.5845 (tttt) REVERT: A 319 LYS cc_start: 0.7892 (tmtm) cc_final: 0.7646 (tptp) REVERT: A 440 LEU cc_start: 0.7884 (mt) cc_final: 0.7622 (tp) REVERT: A 567 TYR cc_start: 0.7861 (t80) cc_final: 0.7598 (t80) REVERT: A 568 ARG cc_start: 0.8068 (tpp-160) cc_final: 0.6806 (mpt-90) REVERT: A 688 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8606 (tt) REVERT: A 722 LYS cc_start: 0.8088 (mmpt) cc_final: 0.7141 (mmtm) REVERT: B 78 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.7048 (t80) REVERT: C 60 LYS cc_start: 0.7275 (mttt) cc_final: 0.6595 (ttpp) REVERT: C 63 ARG cc_start: 0.8898 (ptm160) cc_final: 0.8455 (ptm-80) REVERT: D 229 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8071 (tt) REVERT: D 293 TYR cc_start: 0.8101 (m-80) cc_final: 0.7793 (m-80) REVERT: E 110 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.7052 (pt) REVERT: E 154 MET cc_start: 0.7175 (mmm) cc_final: 0.6975 (mmm) REVERT: E 157 SER cc_start: 0.6523 (t) cc_final: 0.6171 (m) REVERT: F 86 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7165 (mm-30) REVERT: G 100 ASN cc_start: 0.7392 (m-40) cc_final: 0.6731 (t0) REVERT: a 48 PHE cc_start: 0.7721 (t80) cc_final: 0.7363 (t80) REVERT: a 440 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7129 (tm) REVERT: a 567 TYR cc_start: 0.8281 (t80) cc_final: 0.8020 (t80) REVERT: a 568 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7032 (mpt-90) REVERT: a 594 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: a 651 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.6530 (m-80) REVERT: a 722 LYS cc_start: 0.8354 (mmpt) cc_final: 0.7386 (mmtm) REVERT: b 62 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8056 (ttpp) REVERT: b 78 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7204 (t80) REVERT: c 60 LYS cc_start: 0.7504 (mttt) cc_final: 0.6820 (ttpp) REVERT: c 63 ARG cc_start: 0.9020 (ptm160) cc_final: 0.8529 (ptm-80) REVERT: d 5 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8011 (tt) REVERT: d 197 ASN cc_start: 0.8500 (m-40) cc_final: 0.8128 (t0) REVERT: d 405 ILE cc_start: 0.8559 (mm) cc_final: 0.8315 (mt) REVERT: d 466 VAL cc_start: 0.8257 (p) cc_final: 0.7991 (m) REVERT: e 108 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8209 (tmm) REVERT: e 110 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7199 (pt) REVERT: f 86 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7219 (mm-30) REVERT: g 71 ASN cc_start: 0.8571 (m110) cc_final: 0.8132 (m-40) REVERT: g 94 ARG cc_start: 0.7640 (ttp-110) cc_final: 0.7327 (ttp80) REVERT: g 100 ASN cc_start: 0.7805 (m-40) cc_final: 0.7236 (t0) outliers start: 132 outliers final: 67 residues processed: 573 average time/residue: 1.1041 time to fit residues: 776.5273 Evaluate side-chains 546 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 467 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain a residue 33 ILE Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 184 ASP Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 194 MET Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 469 LEU Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 594 PHE Chi-restraints excluded: chain a residue 618 MET Chi-restraints excluded: chain a residue 651 TYR Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain a residue 697 ASP Chi-restraints excluded: chain a residue 701 THR Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 62 LYS Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain b residue 85 SER Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 75 ASP Chi-restraints excluded: chain d residue 137 GLU Chi-restraints excluded: chain d residue 155 GLN Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain d residue 323 VAL Chi-restraints excluded: chain d residue 476 VAL Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 77 LYS Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 SER Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain g residue 98 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 chunk 243 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 315 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 191 GLN a 727 GLN b 96 HIS d 303 ASN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30962 Z= 0.240 Angle : 0.628 9.971 41942 Z= 0.324 Chirality : 0.043 0.240 4988 Planarity : 0.005 0.056 4948 Dihedral : 12.356 154.703 4808 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.40 % Allowed : 15.19 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.14), residues: 3716 helix: 1.53 (0.10), residues: 2744 sheet: -0.21 (0.59), residues: 94 loop : -2.51 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 298 HIS 0.007 0.001 HIS D 272 PHE 0.030 0.002 PHE a 376 TYR 0.019 0.002 TYR A 466 ARG 0.006 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 498 time to evaluate : 3.655 Fit side-chains revert: symmetry clash REVERT: A 94 SER cc_start: 0.7973 (m) cc_final: 0.7342 (p) REVERT: A 131 LYS cc_start: 0.6394 (ttpp) cc_final: 0.5831 (tttt) REVERT: A 319 LYS cc_start: 0.7903 (tmtm) cc_final: 0.7649 (tptp) REVERT: A 354 MET cc_start: 0.6906 (pmm) cc_final: 0.6379 (tpp) REVERT: A 440 LEU cc_start: 0.7861 (mt) cc_final: 0.7622 (tp) REVERT: A 567 TYR cc_start: 0.7949 (t80) cc_final: 0.7660 (t80) REVERT: A 568 ARG cc_start: 0.8052 (tpp-160) cc_final: 0.6802 (mpt-90) REVERT: A 688 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8586 (tt) REVERT: A 722 LYS cc_start: 0.8085 (mmpt) cc_final: 0.7127 (mmtm) REVERT: B 78 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.7029 (t80) REVERT: B 134 GLU cc_start: 0.8333 (pt0) cc_final: 0.7987 (tt0) REVERT: C 60 LYS cc_start: 0.7252 (mttt) cc_final: 0.6565 (ttpp) REVERT: C 63 ARG cc_start: 0.8878 (ptm160) cc_final: 0.8439 (ptm-80) REVERT: D 189 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8023 (mmt) REVERT: D 229 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8055 (tt) REVERT: D 293 TYR cc_start: 0.8082 (m-80) cc_final: 0.7754 (m-80) REVERT: E 108 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8482 (tmm) REVERT: E 110 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.6992 (pt) REVERT: E 119 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7802 (pp) REVERT: E 157 SER cc_start: 0.6541 (t) cc_final: 0.6190 (m) REVERT: F 86 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7125 (mm-30) REVERT: G 100 ASN cc_start: 0.7404 (m-40) cc_final: 0.6727 (t0) REVERT: a 48 PHE cc_start: 0.7757 (t80) cc_final: 0.7413 (t80) REVERT: a 440 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7256 (tp) REVERT: a 567 TYR cc_start: 0.8383 (t80) cc_final: 0.8130 (t80) REVERT: a 568 ARG cc_start: 0.8177 (tpp-160) cc_final: 0.7050 (mpt-90) REVERT: a 594 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: a 701 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8521 (m) REVERT: a 722 LYS cc_start: 0.8315 (mmpt) cc_final: 0.7418 (mmtm) REVERT: b 78 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7252 (t80) REVERT: c 60 LYS cc_start: 0.7522 (mttt) cc_final: 0.6824 (ttpp) REVERT: c 63 ARG cc_start: 0.9012 (ptm160) cc_final: 0.8512 (ptm-80) REVERT: d 5 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7991 (tt) REVERT: d 197 ASN cc_start: 0.8480 (m-40) cc_final: 0.8117 (t0) REVERT: d 405 ILE cc_start: 0.8551 (mm) cc_final: 0.8317 (mt) REVERT: d 407 GLU cc_start: 0.7508 (mp0) cc_final: 0.7280 (mp0) REVERT: d 466 VAL cc_start: 0.8234 (p) cc_final: 0.7968 (m) REVERT: e 67 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7538 (tp30) REVERT: e 108 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8167 (tmm) REVERT: e 110 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7213 (pt) REVERT: f 86 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7225 (mm-30) REVERT: g 64 PHE cc_start: 0.8826 (t80) cc_final: 0.8181 (t80) REVERT: g 71 ASN cc_start: 0.8597 (m110) cc_final: 0.8161 (m-40) REVERT: g 94 ARG cc_start: 0.7603 (ttp-110) cc_final: 0.7286 (ttp80) REVERT: g 100 ASN cc_start: 0.7815 (m-40) cc_final: 0.7255 (t0) outliers start: 138 outliers final: 68 residues processed: 575 average time/residue: 1.1033 time to fit residues: 780.0774 Evaluate side-chains 544 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 461 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain a residue 33 ILE Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 184 ASP Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 194 MET Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 469 LEU Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 594 PHE Chi-restraints excluded: chain a residue 618 MET Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain a residue 697 ASP Chi-restraints excluded: chain a residue 701 THR Chi-restraints excluded: chain a residue 715 LEU Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain b residue 85 SER Chi-restraints excluded: chain b residue 90 ASP Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain c residue 57 LEU Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain d residue 137 GLU Chi-restraints excluded: chain d residue 155 GLN Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain d residue 296 MET Chi-restraints excluded: chain d residue 476 VAL Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 67 GLU Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 SER Chi-restraints excluded: chain f residue 37 MET Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain g residue 98 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 4.9990 chunk 316 optimal weight: 7.9990 chunk 69 optimal weight: 0.0570 chunk 206 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 352 optimal weight: 1.9990 chunk 292 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 184 optimal weight: 20.0000 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 3 ASN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 30962 Z= 0.212 Angle : 0.612 10.098 41942 Z= 0.316 Chirality : 0.042 0.238 4988 Planarity : 0.005 0.055 4948 Dihedral : 12.063 156.703 4808 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.96 % Allowed : 15.95 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 1.01 (0.14), residues: 3716 helix: 1.63 (0.10), residues: 2730 sheet: -0.14 (0.58), residues: 94 loop : -2.39 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 298 HIS 0.006 0.001 HIS D 272 PHE 0.030 0.001 PHE a 376 TYR 0.019 0.002 TYR A 466 ARG 0.008 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 498 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 SER cc_start: 0.7914 (m) cc_final: 0.7296 (p) REVERT: A 123 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8866 (tm) REVERT: A 131 LYS cc_start: 0.6416 (ttpp) cc_final: 0.5849 (tttt) REVERT: A 277 MET cc_start: 0.7716 (tpt) cc_final: 0.7373 (tpt) REVERT: A 319 LYS cc_start: 0.7923 (tmtm) cc_final: 0.7652 (tptp) REVERT: A 440 LEU cc_start: 0.7934 (mt) cc_final: 0.7654 (tp) REVERT: A 567 TYR cc_start: 0.7999 (t80) cc_final: 0.7691 (t80) REVERT: A 568 ARG cc_start: 0.8005 (tpp-160) cc_final: 0.6750 (mpt-90) REVERT: A 722 LYS cc_start: 0.8077 (mmpt) cc_final: 0.7110 (mmtm) REVERT: B 78 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6988 (t80) REVERT: B 134 GLU cc_start: 0.8283 (pt0) cc_final: 0.7973 (tt0) REVERT: C 60 LYS cc_start: 0.7167 (mttt) cc_final: 0.6491 (ttpp) REVERT: C 63 ARG cc_start: 0.8855 (ptm160) cc_final: 0.8414 (ptm-80) REVERT: D 229 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8078 (tt) REVERT: D 293 TYR cc_start: 0.8056 (m-80) cc_final: 0.7737 (m-80) REVERT: D 461 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8534 (mp) REVERT: E 108 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8137 (tmm) REVERT: E 110 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.7000 (pt) REVERT: E 119 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7827 (pp) REVERT: E 157 SER cc_start: 0.6578 (t) cc_final: 0.6236 (m) REVERT: F 86 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7117 (mm-30) REVERT: G 98 TYR cc_start: 0.5943 (OUTLIER) cc_final: 0.5692 (m-80) REVERT: G 100 ASN cc_start: 0.7391 (m-40) cc_final: 0.6884 (t0) REVERT: a 48 PHE cc_start: 0.7773 (t80) cc_final: 0.7558 (t80) REVERT: a 52 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6716 (pt) REVERT: a 440 LEU cc_start: 0.8052 (mm) cc_final: 0.7239 (tp) REVERT: a 567 TYR cc_start: 0.8408 (t80) cc_final: 0.8135 (t80) REVERT: a 568 ARG cc_start: 0.8122 (tpp-160) cc_final: 0.6956 (mpt-90) REVERT: a 594 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: a 651 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.6348 (m-80) REVERT: a 701 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8540 (m) REVERT: a 722 LYS cc_start: 0.8302 (mmpt) cc_final: 0.7420 (mmtm) REVERT: b 78 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.7236 (t80) REVERT: c 60 LYS cc_start: 0.7492 (mttt) cc_final: 0.6795 (ttpp) REVERT: c 63 ARG cc_start: 0.9005 (ptm160) cc_final: 0.8490 (ptm-80) REVERT: d 197 ASN cc_start: 0.8469 (m-40) cc_final: 0.8103 (t0) REVERT: d 405 ILE cc_start: 0.8477 (mm) cc_final: 0.8260 (mt) REVERT: d 466 VAL cc_start: 0.8175 (p) cc_final: 0.7905 (m) REVERT: e 108 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8223 (tmm) REVERT: e 110 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7212 (pt) REVERT: f 86 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7212 (mm-30) REVERT: g 64 PHE cc_start: 0.8869 (t80) cc_final: 0.8227 (t80) REVERT: g 71 ASN cc_start: 0.8588 (m110) cc_final: 0.8149 (m-40) REVERT: g 94 ARG cc_start: 0.7614 (ttp-110) cc_final: 0.7316 (ttp80) REVERT: g 100 ASN cc_start: 0.7820 (m-40) cc_final: 0.7236 (t0) outliers start: 124 outliers final: 67 residues processed: 565 average time/residue: 1.0802 time to fit residues: 749.0460 Evaluate side-chains 551 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 469 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain a residue 33 ILE Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 184 ASP Chi-restraints excluded: chain a residue 194 MET Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 469 LEU Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 594 PHE Chi-restraints excluded: chain a residue 618 MET Chi-restraints excluded: chain a residue 651 TYR Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain a residue 701 THR Chi-restraints excluded: chain a residue 715 LEU Chi-restraints excluded: chain a residue 768 VAL Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain b residue 85 SER Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain c residue 57 LEU Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 75 ASP Chi-restraints excluded: chain d residue 137 GLU Chi-restraints excluded: chain d residue 155 GLN Chi-restraints excluded: chain d residue 161 LYS Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain d residue 296 MET Chi-restraints excluded: chain d residue 476 VAL Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 SER Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain g residue 98 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 257 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 296 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 350 optimal weight: 0.9990 chunk 219 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30962 Z= 0.284 Angle : 0.662 9.588 41942 Z= 0.339 Chirality : 0.044 0.240 4988 Planarity : 0.005 0.055 4948 Dihedral : 12.176 157.678 4808 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.99 % Allowed : 16.11 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.14), residues: 3716 helix: 1.55 (0.10), residues: 2742 sheet: -0.15 (0.58), residues: 94 loop : -2.38 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 298 HIS 0.009 0.001 HIS D 272 PHE 0.028 0.002 PHE a 376 TYR 0.018 0.002 TYR a 466 ARG 0.006 0.001 ARG a 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 489 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7345 (t80) REVERT: A 94 SER cc_start: 0.7936 (m) cc_final: 0.7311 (p) REVERT: A 123 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8866 (tm) REVERT: A 131 LYS cc_start: 0.6400 (ttpp) cc_final: 0.5856 (tttt) REVERT: A 277 MET cc_start: 0.7732 (tpt) cc_final: 0.7391 (tpt) REVERT: A 319 LYS cc_start: 0.7906 (tmtm) cc_final: 0.7635 (tptp) REVERT: A 354 MET cc_start: 0.6881 (pmm) cc_final: 0.6388 (tpp) REVERT: A 440 LEU cc_start: 0.7915 (mt) cc_final: 0.7655 (tp) REVERT: A 568 ARG cc_start: 0.8042 (tpp-160) cc_final: 0.6789 (mpt-90) REVERT: A 594 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: A 688 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8597 (tt) REVERT: A 722 LYS cc_start: 0.8076 (mmpt) cc_final: 0.7136 (mmtm) REVERT: B 78 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6958 (t80) REVERT: B 134 GLU cc_start: 0.8316 (pt0) cc_final: 0.8005 (tt0) REVERT: C 60 LYS cc_start: 0.7222 (mttt) cc_final: 0.6523 (ttpp) REVERT: C 63 ARG cc_start: 0.8846 (ptm160) cc_final: 0.8402 (ptm-80) REVERT: D 189 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8015 (mmt) REVERT: D 229 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8101 (tt) REVERT: D 293 TYR cc_start: 0.8063 (m-80) cc_final: 0.7740 (m-80) REVERT: D 438 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: D 461 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8533 (mp) REVERT: E 67 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7377 (tp30) REVERT: E 108 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8117 (tmm) REVERT: E 110 ILE cc_start: 0.7345 (OUTLIER) cc_final: 0.7039 (pt) REVERT: E 119 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7794 (pp) REVERT: F 86 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7108 (mm-30) REVERT: G 98 TYR cc_start: 0.5970 (OUTLIER) cc_final: 0.5700 (m-80) REVERT: G 100 ASN cc_start: 0.7427 (m-40) cc_final: 0.6904 (t0) REVERT: a 52 ILE cc_start: 0.6983 (OUTLIER) cc_final: 0.6761 (pt) REVERT: a 131 LYS cc_start: 0.6868 (ttpp) cc_final: 0.6336 (tttt) REVERT: a 440 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7277 (tp) REVERT: a 567 TYR cc_start: 0.8444 (t80) cc_final: 0.8100 (t80) REVERT: a 568 ARG cc_start: 0.8122 (tpp-160) cc_final: 0.6944 (mpt-90) REVERT: a 594 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: a 701 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8536 (m) REVERT: a 722 LYS cc_start: 0.8289 (mmpt) cc_final: 0.7423 (mmtm) REVERT: b 62 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8050 (ttpp) REVERT: b 78 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7261 (t80) REVERT: c 60 LYS cc_start: 0.7535 (mttt) cc_final: 0.6816 (ttpp) REVERT: c 63 ARG cc_start: 0.8993 (ptm160) cc_final: 0.8490 (ptm-80) REVERT: d 197 ASN cc_start: 0.8476 (m-40) cc_final: 0.8105 (t0) REVERT: d 405 ILE cc_start: 0.8564 (mm) cc_final: 0.8315 (mt) REVERT: d 466 VAL cc_start: 0.8184 (p) cc_final: 0.7899 (m) REVERT: e 67 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7592 (tp30) REVERT: e 108 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8246 (tmm) REVERT: e 110 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7239 (pt) REVERT: f 75 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: f 86 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7195 (mm-30) REVERT: g 64 PHE cc_start: 0.8874 (t80) cc_final: 0.8189 (t80) REVERT: g 71 ASN cc_start: 0.8641 (m110) cc_final: 0.8217 (m-40) REVERT: g 94 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.7324 (ttp80) REVERT: g 100 ASN cc_start: 0.7812 (m-40) cc_final: 0.7225 (t0) outliers start: 125 outliers final: 73 residues processed: 555 average time/residue: 1.0847 time to fit residues: 739.5014 Evaluate side-chains 562 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 465 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain a residue 33 ILE Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 184 ASP Chi-restraints excluded: chain a residue 194 MET Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 469 LEU Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 504 SER Chi-restraints excluded: chain a residue 555 MET Chi-restraints excluded: chain a residue 594 PHE Chi-restraints excluded: chain a residue 618 MET Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain a residue 701 THR Chi-restraints excluded: chain a residue 715 LEU Chi-restraints excluded: chain a residue 768 VAL Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 62 LYS Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain b residue 85 SER Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain c residue 57 LEU Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 137 GLU Chi-restraints excluded: chain d residue 155 GLN Chi-restraints excluded: chain d residue 161 LYS Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain d residue 296 MET Chi-restraints excluded: chain d residue 476 VAL Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 67 GLU Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 119 LEU Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 SER Chi-restraints excluded: chain f residue 37 MET Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 75 PHE Chi-restraints excluded: chain g residue 98 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 223 optimal weight: 30.0000 chunk 239 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 275 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN a 191 GLN c 96 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30962 Z= 0.318 Angle : 0.690 11.920 41942 Z= 0.353 Chirality : 0.045 0.245 4988 Planarity : 0.005 0.064 4948 Dihedral : 12.333 159.513 4808 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.99 % Allowed : 16.40 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.14), residues: 3716 helix: 1.49 (0.10), residues: 2732 sheet: -0.15 (0.57), residues: 94 loop : -2.35 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 104 HIS 0.010 0.001 HIS D 272 PHE 0.027 0.002 PHE a 376 TYR 0.019 0.002 TYR A 466 ARG 0.007 0.001 ARG a 394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 485 time to evaluate : 3.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7360 (t80) REVERT: A 94 SER cc_start: 0.7959 (m) cc_final: 0.7318 (p) REVERT: A 123 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8865 (tm) REVERT: A 131 LYS cc_start: 0.6396 (ttpp) cc_final: 0.5856 (tttt) REVERT: A 277 MET cc_start: 0.7806 (tpt) cc_final: 0.7403 (tpt) REVERT: A 319 LYS cc_start: 0.7901 (tmtm) cc_final: 0.7625 (tptp) REVERT: A 440 LEU cc_start: 0.7951 (mt) cc_final: 0.7672 (tp) REVERT: A 567 TYR cc_start: 0.8217 (t80) cc_final: 0.7977 (t80) REVERT: A 568 ARG cc_start: 0.7952 (tpp-160) cc_final: 0.6723 (mpt-90) REVERT: A 594 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: A 688 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8580 (tt) REVERT: A 722 LYS cc_start: 0.8079 (mmpt) cc_final: 0.7090 (mmtm) REVERT: B 78 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6939 (t80) REVERT: B 134 GLU cc_start: 0.8348 (pt0) cc_final: 0.8035 (tt0) REVERT: C 60 LYS cc_start: 0.7213 (mttt) cc_final: 0.6466 (ttpp) REVERT: C 63 ARG cc_start: 0.8856 (ptm160) cc_final: 0.8406 (ptm-80) REVERT: D 189 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8055 (mmt) REVERT: D 229 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8138 (tt) REVERT: D 293 TYR cc_start: 0.8088 (m-80) cc_final: 0.7764 (m-80) REVERT: D 438 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: D 461 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8537 (mp) REVERT: E 67 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7402 (tp30) REVERT: E 108 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8161 (tmm) REVERT: E 110 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7049 (pt) REVERT: E 119 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7841 (pp) REVERT: F 86 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7010 (mm-30) REVERT: G 98 TYR cc_start: 0.5984 (OUTLIER) cc_final: 0.5650 (m-80) REVERT: G 100 ASN cc_start: 0.7423 (m-40) cc_final: 0.6926 (t0) REVERT: a 131 LYS cc_start: 0.6733 (ttpp) cc_final: 0.6213 (tttt) REVERT: a 440 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7288 (tp) REVERT: a 567 TYR cc_start: 0.8471 (t80) cc_final: 0.8119 (t80) REVERT: a 568 ARG cc_start: 0.8123 (tpp-160) cc_final: 0.6961 (mpt-90) REVERT: a 594 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7486 (m-80) REVERT: a 652 GLU cc_start: 0.7904 (mp0) cc_final: 0.7688 (mp0) REVERT: a 701 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8531 (m) REVERT: a 722 LYS cc_start: 0.8293 (mmpt) cc_final: 0.7436 (mmtm) REVERT: b 62 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8016 (ttpp) REVERT: b 78 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.7273 (t80) REVERT: c 60 LYS cc_start: 0.7557 (mttt) cc_final: 0.6843 (ttpp) REVERT: c 63 ARG cc_start: 0.9016 (ptm160) cc_final: 0.8512 (ptm-80) REVERT: d 197 ASN cc_start: 0.8484 (m-40) cc_final: 0.8104 (t0) REVERT: d 293 TYR cc_start: 0.7915 (m-80) cc_final: 0.7690 (m-80) REVERT: d 401 ASP cc_start: 0.8557 (t0) cc_final: 0.8314 (t0) REVERT: d 405 ILE cc_start: 0.8638 (mm) cc_final: 0.8380 (mt) REVERT: d 466 VAL cc_start: 0.8200 (p) cc_final: 0.7909 (m) REVERT: e 67 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7590 (tp30) REVERT: e 108 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8291 (tmm) REVERT: e 110 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7252 (pt) REVERT: f 75 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: f 86 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7204 (mm-30) REVERT: g 64 PHE cc_start: 0.8842 (t80) cc_final: 0.8150 (t80) REVERT: g 71 ASN cc_start: 0.8702 (m110) cc_final: 0.8270 (m-40) REVERT: g 94 ARG cc_start: 0.7662 (ttp-110) cc_final: 0.7327 (ttp80) REVERT: g 100 ASN cc_start: 0.7822 (m-40) cc_final: 0.7228 (t0) outliers start: 125 outliers final: 72 residues processed: 554 average time/residue: 1.1008 time to fit residues: 747.5503 Evaluate side-chains 560 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 465 time to evaluate : 3.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 184 ASP Chi-restraints excluded: chain a residue 194 MET Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 454 VAL Chi-restraints excluded: chain a residue 469 LEU Chi-restraints excluded: chain a residue 504 SER Chi-restraints excluded: chain a residue 555 MET Chi-restraints excluded: chain a residue 594 PHE Chi-restraints excluded: chain a residue 618 MET Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain a residue 701 THR Chi-restraints excluded: chain a residue 715 LEU Chi-restraints excluded: chain a residue 768 VAL Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 62 LYS Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain c residue 57 LEU Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 137 GLU Chi-restraints excluded: chain d residue 155 GLN Chi-restraints excluded: chain d residue 161 LYS Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain d residue 186 THR Chi-restraints excluded: chain d residue 251 VAL Chi-restraints excluded: chain d residue 296 MET Chi-restraints excluded: chain d residue 476 VAL Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 67 GLU Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 119 LEU Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 SER Chi-restraints excluded: chain f residue 37 MET Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 75 PHE Chi-restraints excluded: chain g residue 98 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 3.9990 chunk 336 optimal weight: 6.9990 chunk 306 optimal weight: 9.9990 chunk 326 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 256 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 chunk 295 optimal weight: 7.9990 chunk 309 optimal weight: 2.9990 chunk 325 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30962 Z= 0.241 Angle : 0.650 12.049 41942 Z= 0.332 Chirality : 0.043 0.295 4988 Planarity : 0.005 0.059 4948 Dihedral : 12.100 162.730 4808 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.67 % Allowed : 16.85 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3716 helix: 1.53 (0.10), residues: 2760 sheet: -0.06 (0.57), residues: 94 loop : -2.51 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 104 HIS 0.007 0.001 HIS D 272 PHE 0.028 0.002 PHE a 376 TYR 0.020 0.002 TYR A 466 ARG 0.008 0.000 ARG a 394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 500 time to evaluate : 3.702 Fit side-chains revert: symmetry clash REVERT: A 48 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.7306 (t80) REVERT: A 94 SER cc_start: 0.7909 (m) cc_final: 0.7309 (p) REVERT: A 123 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8875 (tm) REVERT: A 131 LYS cc_start: 0.6429 (ttpp) cc_final: 0.5868 (tttt) REVERT: A 277 MET cc_start: 0.7735 (tpt) cc_final: 0.7334 (tpt) REVERT: A 319 LYS cc_start: 0.7890 (tmtm) cc_final: 0.7600 (tptp) REVERT: A 354 MET cc_start: 0.6827 (pmm) cc_final: 0.6321 (tpp) REVERT: A 440 LEU cc_start: 0.7945 (mt) cc_final: 0.7589 (tp) REVERT: A 567 TYR cc_start: 0.8226 (t80) cc_final: 0.7971 (t80) REVERT: A 568 ARG cc_start: 0.7944 (tpp-160) cc_final: 0.6710 (mpt-90) REVERT: A 594 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: A 688 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8603 (tt) REVERT: A 722 LYS cc_start: 0.8070 (mmpt) cc_final: 0.7094 (mmtm) REVERT: B 78 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6946 (t80) REVERT: B 134 GLU cc_start: 0.8315 (pt0) cc_final: 0.8021 (tt0) REVERT: C 60 LYS cc_start: 0.7143 (mttt) cc_final: 0.6404 (ttpp) REVERT: C 63 ARG cc_start: 0.8850 (ptm160) cc_final: 0.8403 (ptm-80) REVERT: D 189 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7991 (mmt) REVERT: D 229 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8108 (tt) REVERT: D 293 TYR cc_start: 0.8036 (m-80) cc_final: 0.7723 (m-80) REVERT: D 438 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: D 461 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8519 (mp) REVERT: E 67 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7360 (tp30) REVERT: E 110 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.6979 (pt) REVERT: E 119 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7888 (pp) REVERT: F 86 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6985 (mm-30) REVERT: G 98 TYR cc_start: 0.5923 (OUTLIER) cc_final: 0.5599 (m-80) REVERT: G 100 ASN cc_start: 0.7407 (m-40) cc_final: 0.6900 (t0) REVERT: a 131 LYS cc_start: 0.6807 (ttpp) cc_final: 0.6273 (tttt) REVERT: a 440 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7248 (tp) REVERT: a 567 TYR cc_start: 0.8466 (t80) cc_final: 0.8146 (t80) REVERT: a 568 ARG cc_start: 0.8039 (tpp-160) cc_final: 0.6936 (mpt-90) REVERT: a 594 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7475 (m-80) REVERT: a 701 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8518 (m) REVERT: a 722 LYS cc_start: 0.8357 (mmpt) cc_final: 0.7494 (mmtm) REVERT: b 78 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7246 (t80) REVERT: b 136 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8664 (mp) REVERT: c 11 CYS cc_start: 0.8163 (m) cc_final: 0.7960 (t) REVERT: c 60 LYS cc_start: 0.7519 (mttt) cc_final: 0.6797 (ttpp) REVERT: c 63 ARG cc_start: 0.8966 (ptm160) cc_final: 0.8458 (ptm-80) REVERT: d 197 ASN cc_start: 0.8502 (m-40) cc_final: 0.8118 (t0) REVERT: d 466 VAL cc_start: 0.8176 (p) cc_final: 0.7900 (m) REVERT: e 67 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7570 (tp30) REVERT: e 108 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8270 (tmm) REVERT: e 110 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7247 (pt) REVERT: f 75 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: f 86 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7181 (mm-30) REVERT: g 64 PHE cc_start: 0.8829 (t80) cc_final: 0.8146 (t80) REVERT: g 71 ASN cc_start: 0.8691 (m110) cc_final: 0.8248 (m-40) REVERT: g 94 ARG cc_start: 0.7611 (ttp-110) cc_final: 0.7297 (ttp80) REVERT: g 100 ASN cc_start: 0.7826 (m-40) cc_final: 0.7210 (t0) outliers start: 115 outliers final: 70 residues processed: 560 average time/residue: 1.0968 time to fit residues: 752.5586 Evaluate side-chains 571 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 479 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 184 ASP Chi-restraints excluded: chain a residue 194 MET Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 389 HIS Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 454 VAL Chi-restraints excluded: chain a residue 469 LEU Chi-restraints excluded: chain a residue 594 PHE Chi-restraints excluded: chain a residue 618 MET Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain a residue 697 ASP Chi-restraints excluded: chain a residue 701 THR Chi-restraints excluded: chain a residue 715 LEU Chi-restraints excluded: chain a residue 768 VAL Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain b residue 136 ILE Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain c residue 57 LEU Chi-restraints excluded: chain c residue 62 SER Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 137 GLU Chi-restraints excluded: chain d residue 155 GLN Chi-restraints excluded: chain d residue 161 LYS Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain d residue 186 THR Chi-restraints excluded: chain d residue 255 SER Chi-restraints excluded: chain d residue 476 VAL Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 67 GLU Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 123 ASP Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain f residue 37 MET Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 75 PHE Chi-restraints excluded: chain g residue 98 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 20.0000 chunk 345 optimal weight: 0.9980 chunk 211 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 chunk 362 optimal weight: 8.9990 chunk 333 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 223 optimal weight: 30.0000 chunk 177 optimal weight: 4.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN a 702 GLN c 96 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30962 Z= 0.313 Angle : 0.706 12.710 41942 Z= 0.360 Chirality : 0.045 0.289 4988 Planarity : 0.005 0.058 4948 Dihedral : 12.252 164.527 4808 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.32 % Allowed : 17.71 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3716 helix: 1.45 (0.10), residues: 2750 sheet: -0.10 (0.56), residues: 94 loop : -2.39 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 104 HIS 0.010 0.001 HIS D 272 PHE 0.027 0.002 PHE d 373 TYR 0.019 0.002 TYR A 755 ARG 0.008 0.001 ARG a 394 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 488 time to evaluate : 3.407 Fit side-chains revert: symmetry clash REVERT: A 48 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7328 (t80) REVERT: A 94 SER cc_start: 0.7928 (m) cc_final: 0.7288 (p) REVERT: A 123 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8854 (tm) REVERT: A 131 LYS cc_start: 0.6404 (ttpp) cc_final: 0.5861 (tttt) REVERT: A 277 MET cc_start: 0.7753 (tpt) cc_final: 0.7356 (tpt) REVERT: A 319 LYS cc_start: 0.7900 (tmtm) cc_final: 0.7612 (tptp) REVERT: A 354 MET cc_start: 0.6884 (pmm) cc_final: 0.6369 (tpp) REVERT: A 439 MET cc_start: 0.7017 (ppp) cc_final: 0.6322 (ptm) REVERT: A 440 LEU cc_start: 0.8078 (mt) cc_final: 0.7581 (pt) REVERT: A 567 TYR cc_start: 0.8248 (t80) cc_final: 0.8034 (t80) REVERT: A 568 ARG cc_start: 0.7956 (tpp-160) cc_final: 0.6732 (mpt-90) REVERT: A 594 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: A 688 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8597 (tt) REVERT: A 722 LYS cc_start: 0.8065 (mmpt) cc_final: 0.7082 (mmtm) REVERT: B 78 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6938 (t80) REVERT: B 134 GLU cc_start: 0.8357 (pt0) cc_final: 0.8053 (tt0) REVERT: C 60 LYS cc_start: 0.7212 (mttt) cc_final: 0.6470 (ttpp) REVERT: C 63 ARG cc_start: 0.8809 (ptm160) cc_final: 0.8382 (ptm-80) REVERT: D 189 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8044 (mmt) REVERT: D 229 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8136 (tt) REVERT: D 293 TYR cc_start: 0.8074 (m-80) cc_final: 0.7763 (m-80) REVERT: D 438 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: D 461 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8559 (mp) REVERT: D 464 GLU cc_start: 0.8745 (tp30) cc_final: 0.8540 (tp30) REVERT: E 67 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: E 110 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.7031 (pt) REVERT: E 119 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7977 (pp) REVERT: E 154 MET cc_start: 0.7006 (mtm) cc_final: 0.6669 (mmm) REVERT: F 86 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6988 (mm-30) REVERT: G 81 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8250 (mp) REVERT: G 98 TYR cc_start: 0.5995 (OUTLIER) cc_final: 0.5676 (m-80) REVERT: G 100 ASN cc_start: 0.7399 (m-40) cc_final: 0.6906 (t0) REVERT: a 131 LYS cc_start: 0.6736 (ttpp) cc_final: 0.6211 (tttt) REVERT: a 440 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7252 (tp) REVERT: a 567 TYR cc_start: 0.8500 (t80) cc_final: 0.8208 (t80) REVERT: a 568 ARG cc_start: 0.8014 (tpp-160) cc_final: 0.6918 (mpt-90) REVERT: a 594 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7508 (m-80) REVERT: a 652 GLU cc_start: 0.7959 (mp0) cc_final: 0.7719 (mp0) REVERT: a 701 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8463 (m) REVERT: a 722 LYS cc_start: 0.8317 (mmpt) cc_final: 0.7457 (mmtm) REVERT: b 78 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.7272 (t80) REVERT: b 87 MET cc_start: 0.7165 (ptp) cc_final: 0.6911 (ptm) REVERT: c 60 LYS cc_start: 0.7530 (mttt) cc_final: 0.6823 (ttpp) REVERT: c 63 ARG cc_start: 0.9010 (ptm160) cc_final: 0.8490 (ptm-80) REVERT: d 197 ASN cc_start: 0.8503 (m-40) cc_final: 0.8120 (t0) REVERT: d 466 VAL cc_start: 0.8206 (p) cc_final: 0.7915 (m) REVERT: e 13 PHE cc_start: 0.8057 (m-80) cc_final: 0.7847 (m-80) REVERT: e 67 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7557 (tp30) REVERT: e 108 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8345 (tmm) REVERT: e 110 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7276 (pt) REVERT: f 75 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: f 86 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7190 (mm-30) REVERT: g 64 PHE cc_start: 0.8844 (t80) cc_final: 0.8152 (t80) REVERT: g 71 ASN cc_start: 0.8692 (m110) cc_final: 0.8255 (m-40) REVERT: g 81 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8283 (mp) REVERT: g 94 ARG cc_start: 0.7636 (ttp-110) cc_final: 0.7315 (ttp80) REVERT: g 100 ASN cc_start: 0.7842 (m-40) cc_final: 0.7210 (t0) outliers start: 104 outliers final: 67 residues processed: 542 average time/residue: 1.1236 time to fit residues: 745.8608 Evaluate side-chains 567 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 477 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 184 ASP Chi-restraints excluded: chain a residue 194 MET Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 454 VAL Chi-restraints excluded: chain a residue 469 LEU Chi-restraints excluded: chain a residue 504 SER Chi-restraints excluded: chain a residue 555 MET Chi-restraints excluded: chain a residue 594 PHE Chi-restraints excluded: chain a residue 618 MET Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain a residue 697 ASP Chi-restraints excluded: chain a residue 701 THR Chi-restraints excluded: chain a residue 715 LEU Chi-restraints excluded: chain a residue 768 VAL Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain c residue 62 SER Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 137 GLU Chi-restraints excluded: chain d residue 155 GLN Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain d residue 186 THR Chi-restraints excluded: chain d residue 251 VAL Chi-restraints excluded: chain d residue 255 SER Chi-restraints excluded: chain d residue 476 VAL Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 67 GLU Chi-restraints excluded: chain e residue 77 LYS Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 123 ASP Chi-restraints excluded: chain f residue 37 MET Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 75 PHE Chi-restraints excluded: chain g residue 81 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 6.9990 chunk 307 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 266 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 289 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 296 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114011 restraints weight = 43230.351| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.87 r_work: 0.3298 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 30962 Z= 0.314 Angle : 0.710 12.754 41942 Z= 0.363 Chirality : 0.046 0.264 4988 Planarity : 0.005 0.056 4948 Dihedral : 12.335 168.665 4806 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.38 % Allowed : 18.09 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 3716 helix: 1.46 (0.10), residues: 2732 sheet: -0.12 (0.56), residues: 94 loop : -2.41 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 104 HIS 0.009 0.001 HIS D 272 PHE 0.028 0.002 PHE A 371 TYR 0.019 0.002 TYR A 755 ARG 0.008 0.001 ARG a 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11641.13 seconds wall clock time: 208 minutes 59.00 seconds (12539.00 seconds total)