Starting phenix.real_space_refine on Wed May 21 00:26:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7b_61200/05_2025/9j7b_61200.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7b_61200/05_2025/9j7b_61200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j7b_61200/05_2025/9j7b_61200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7b_61200/05_2025/9j7b_61200.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7b_61200/05_2025/9j7b_61200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7b_61200/05_2025/9j7b_61200.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12893 2.51 5 N 3684 2.21 5 O 3889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20578 Number of models: 1 Model: "" Number of chains: 11 Chain: "J" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4932 Classifications: {'peptide': 627} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "A" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4932 Classifications: {'peptide': 627} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "B" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 564 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 6, 'TRANS': 65} Chain: "G" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 54 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 9} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4562 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 577} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "P" Number of atoms: 4308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4308 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 548} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "Q" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 524 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "R" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "S" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 296 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 4, 'TRANS': 55} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 100 Chain: "C" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 301 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 4, 'TRANS': 56} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 100 Time building chain proxies: 15.39, per 1000 atoms: 0.75 Number of scatterers: 20578 At special positions: 0 Unit cell: (139.4, 143.5, 168.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3889 8.00 N 3684 7.00 C 12893 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 - 3.00 Amino acid : True - 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: 5.36 Conformation dependent library (CDL) restraints added in 2.9 seconds 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5118 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 3 sheets defined 69.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'J' and resid 1 through 15 Processing helix chain 'J' and resid 16 through 23 Processing helix chain 'J' and resid 28 through 37 removed outlier: 3.864A pdb=" N ILE J 32 " --> pdb=" O SER J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 56 removed outlier: 4.023A pdb=" N ASN J 56 " --> pdb=" O ILE J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 69 removed outlier: 3.655A pdb=" N VAL J 62 " --> pdb=" O HIS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 99 removed outlier: 3.555A pdb=" N CYS J 94 " --> pdb=" O THR J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 110 Processing helix chain 'J' and resid 123 through 132 Processing helix chain 'J' and resid 133 through 143 removed outlier: 3.539A pdb=" N VAL J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 164 removed outlier: 4.075A pdb=" N LYS J 164 " --> pdb=" O ILE J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 176 Processing helix chain 'J' and resid 189 through 198 Processing helix chain 'J' and resid 199 through 210 removed outlier: 3.643A pdb=" N TRP J 209 " --> pdb=" O GLU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 227 Processing helix chain 'J' and resid 231 through 242 Processing helix chain 'J' and resid 245 through 262 removed outlier: 3.509A pdb=" N PHE J 260 " --> pdb=" O LEU J 256 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN J 262 " --> pdb=" O ALA J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 285 Processing helix chain 'J' and resid 310 through 318 removed outlier: 3.687A pdb=" N LEU J 314 " --> pdb=" O ASN J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 337 Processing helix chain 'J' and resid 344 through 357 Processing helix chain 'J' and resid 359 through 377 Processing helix chain 'J' and resid 382 through 398 Processing helix chain 'J' and resid 403 through 428 Processing helix chain 'J' and resid 432 through 457 Processing helix chain 'J' and resid 460 through 478 Processing helix chain 'J' and resid 486 through 493 Processing helix chain 'J' and resid 502 through 507 removed outlier: 3.912A pdb=" N VAL J 506 " --> pdb=" O HIS J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 511 through 522 Processing helix chain 'J' and resid 534 through 541 Processing helix chain 'J' and resid 548 through 563 removed outlier: 3.524A pdb=" N LEU J 552 " --> pdb=" O ASP J 548 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 592 Processing helix chain 'J' and resid 596 through 609 Processing helix chain 'J' and resid 617 through 627 Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 17 through 24 Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 58 through 68 removed outlier: 3.562A pdb=" N VAL A 62 " --> pdb=" O HIS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 199 through 209 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 245 through 262 removed outlier: 3.541A pdb=" N ASN A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 284 Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 320 through 337 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.040A pdb=" N ILE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 378 Processing helix chain 'A' and resid 381 through 398 Processing helix chain 'A' and resid 403 through 428 Processing helix chain 'A' and resid 432 through 457 removed outlier: 3.769A pdb=" N ALA A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 478 Processing helix chain 'A' and resid 486 through 493 Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.708A pdb=" N VAL A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 521 Processing helix chain 'A' and resid 534 through 541 removed outlier: 3.504A pdb=" N GLN A 541 " --> pdb=" O HIS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.628A pdb=" N ILE A 557 " --> pdb=" O HIS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 removed outlier: 4.332A pdb=" N THR A 581 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 593 Processing helix chain 'A' and resid 602 through 608 Processing helix chain 'A' and resid 617 through 627 removed outlier: 3.725A pdb=" N GLU A 622 " --> pdb=" O ARG A 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 84 removed outlier: 3.788A pdb=" N LEU B 71 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 74 " --> pdb=" O PHE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 100 removed outlier: 3.574A pdb=" N ALA B 96 " --> pdb=" O HIS B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 115 through 125 removed outlier: 4.290A pdb=" N GLN B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 123 " --> pdb=" O PHE B 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 8 removed outlier: 4.366A pdb=" N SER G 8 " --> pdb=" O ALA G 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'O' and resid 2 through 14 removed outlier: 3.515A pdb=" N GLU O 14 " --> pdb=" O LYS O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 25 removed outlier: 3.550A pdb=" N LEU O 20 " --> pdb=" O LYS O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 38 removed outlier: 3.512A pdb=" N TYR O 34 " --> pdb=" O SER O 30 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR O 38 " --> pdb=" O TYR O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 45 removed outlier: 3.508A pdb=" N GLY O 44 " --> pdb=" O GLN O 41 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN O 45 " --> pdb=" O GLN O 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 41 through 45' Processing helix chain 'O' and resid 48 through 56 Processing helix chain 'O' and resid 58 through 69 removed outlier: 3.554A pdb=" N LEU O 64 " --> pdb=" O LYS O 60 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU O 65 " --> pdb=" O VAL O 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU O 66 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS O 68 " --> pdb=" O LEU O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 98 Processing helix chain 'O' and resid 100 through 111 removed outlier: 3.664A pdb=" N VAL O 104 " --> pdb=" O HIS O 100 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU O 106 " --> pdb=" O GLU O 102 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER O 109 " --> pdb=" O LYS O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 132 Processing helix chain 'O' and resid 133 through 143 removed outlier: 3.561A pdb=" N VAL O 141 " --> pdb=" O VAL O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 156 through 162 Processing helix chain 'O' and resid 166 through 176 removed outlier: 3.683A pdb=" N ARG O 171 " --> pdb=" O THR O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 197 removed outlier: 3.865A pdb=" N ALA O 197 " --> pdb=" O PHE O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 199 through 210 removed outlier: 3.523A pdb=" N ARG O 210 " --> pdb=" O LEU O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 221 through 228 Processing helix chain 'O' and resid 232 through 241 removed outlier: 3.589A pdb=" N SER O 240 " --> pdb=" O GLU O 236 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS O 241 " --> pdb=" O LEU O 237 " (cutoff:3.500A) Processing helix chain 'O' and resid 245 through 260 removed outlier: 3.757A pdb=" N LEU O 253 " --> pdb=" O ARG O 249 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA O 258 " --> pdb=" O GLU O 254 " (cutoff:3.500A) Processing helix chain 'O' and resid 268 through 284 Processing helix chain 'O' and resid 312 through 317 removed outlier: 3.510A pdb=" N SER O 316 " --> pdb=" O GLN O 312 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE O 317 " --> pdb=" O GLU O 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 312 through 317' Processing helix chain 'O' and resid 320 through 337 removed outlier: 3.573A pdb=" N LEU O 324 " --> pdb=" O ASP O 320 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL O 331 " --> pdb=" O GLU O 327 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG O 332 " --> pdb=" O GLY O 328 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE O 335 " --> pdb=" O VAL O 331 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 357 Proline residue: O 346 - end of helix removed outlier: 3.541A pdb=" N TYR O 349 " --> pdb=" O HIS O 345 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY O 351 " --> pdb=" O ILE O 347 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 378 removed outlier: 4.132A pdb=" N HIS O 369 " --> pdb=" O LYS O 365 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA O 370 " --> pdb=" O LEU O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 381 through 398 removed outlier: 3.575A pdb=" N ILE O 396 " --> pdb=" O PHE O 392 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS O 397 " --> pdb=" O SER O 393 " (cutoff:3.500A) Processing helix chain 'O' and resid 403 through 428 removed outlier: 3.546A pdb=" N LEU O 416 " --> pdb=" O ARG O 412 " (cutoff:3.500A) Processing helix chain 'O' and resid 432 through 457 removed outlier: 3.710A pdb=" N GLU O 441 " --> pdb=" O MET O 437 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS O 442 " --> pdb=" O ASP O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 460 through 478 removed outlier: 3.510A pdb=" N LYS O 466 " --> pdb=" O GLU O 462 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN O 470 " --> pdb=" O LYS O 466 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE O 471 " --> pdb=" O ILE O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 486 through 493 Processing helix chain 'O' and resid 502 through 507 Processing helix chain 'O' and resid 511 through 521 removed outlier: 3.534A pdb=" N ASP O 520 " --> pdb=" O LYS O 516 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS O 521 " --> pdb=" O LEU O 517 " (cutoff:3.500A) Processing helix chain 'O' and resid 534 through 541 Processing helix chain 'O' and resid 548 through 563 removed outlier: 3.620A pdb=" N ILE O 557 " --> pdb=" O HIS O 553 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL O 560 " --> pdb=" O ILE O 556 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY O 563 " --> pdb=" O LEU O 559 " (cutoff:3.500A) Processing helix chain 'O' and resid 582 through 592 Processing helix chain 'P' and resid 2 through 14 Processing helix chain 'P' and resid 16 through 25 removed outlier: 3.936A pdb=" N LEU P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU P 23 " --> pdb=" O THR P 19 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 38 removed outlier: 3.621A pdb=" N LEU P 36 " --> pdb=" O ILE P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 57 removed outlier: 3.605A pdb=" N ALA P 54 " --> pdb=" O LEU P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 65 removed outlier: 4.022A pdb=" N VAL P 62 " --> pdb=" O HIS P 58 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU P 65 " --> pdb=" O VAL P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 84 removed outlier: 3.624A pdb=" N TYR P 84 " --> pdb=" O PHE P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 98 Processing helix chain 'P' and resid 100 through 111 removed outlier: 4.791A pdb=" N LEU P 106 " --> pdb=" O GLU P 102 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL P 108 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER P 109 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 123 through 132 Processing helix chain 'P' and resid 133 through 144 removed outlier: 3.618A pdb=" N VAL P 137 " --> pdb=" O ARG P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 164 Processing helix chain 'P' and resid 166 through 174 Processing helix chain 'P' and resid 199 through 209 Processing helix chain 'P' and resid 221 through 229 Processing helix chain 'P' and resid 231 through 240 removed outlier: 3.503A pdb=" N VAL P 235 " --> pdb=" O LYS P 231 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU P 236 " --> pdb=" O ALA P 232 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU P 237 " --> pdb=" O ASP P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 245 through 261 removed outlier: 3.622A pdb=" N GLU P 251 " --> pdb=" O ARG P 247 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU P 253 " --> pdb=" O ARG P 249 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER P 259 " --> pdb=" O LEU P 255 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE P 260 " --> pdb=" O LEU P 256 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA P 261 " --> pdb=" O GLY P 257 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 284 removed outlier: 3.576A pdb=" N THR P 272 " --> pdb=" O ASP P 268 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR P 273 " --> pdb=" O ILE P 269 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE P 284 " --> pdb=" O MET P 280 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 317 removed outlier: 3.565A pdb=" N LEU P 314 " --> pdb=" O ASN P 310 " (cutoff:3.500A) Processing helix chain 'P' and resid 320 through 337 removed outlier: 3.532A pdb=" N LEU P 324 " --> pdb=" O ASP P 320 " (cutoff:3.500A) Processing helix chain 'P' and resid 340 through 357 removed outlier: 4.178A pdb=" N SER P 344 " --> pdb=" O ASN P 340 " (cutoff:3.500A) Proline residue: P 346 - end of helix Processing helix chain 'P' and resid 359 through 377 removed outlier: 3.936A pdb=" N ILE P 364 " --> pdb=" O PHE P 360 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS P 365 " --> pdb=" O GLU P 361 " (cutoff:3.500A) Processing helix chain 'P' and resid 381 through 398 Processing helix chain 'P' and resid 403 through 428 removed outlier: 3.619A pdb=" N VAL P 410 " --> pdb=" O ASP P 406 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG P 424 " --> pdb=" O GLN P 420 " (cutoff:3.500A) Processing helix chain 'P' and resid 433 through 457 Processing helix chain 'P' and resid 460 through 478 removed outlier: 3.637A pdb=" N ILE P 471 " --> pdb=" O ILE P 467 " (cutoff:3.500A) Processing helix chain 'P' and resid 486 through 491 Processing helix chain 'P' and resid 501 through 505 Processing helix chain 'P' and resid 511 through 522 removed outlier: 3.562A pdb=" N LEU P 517 " --> pdb=" O LEU P 513 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU P 518 " --> pdb=" O VAL P 514 " (cutoff:3.500A) Processing helix chain 'P' and resid 534 through 542 Processing helix chain 'P' and resid 543 through 548 removed outlier: 3.510A pdb=" N SER P 547 " --> pdb=" O ASN P 543 " (cutoff:3.500A) Processing helix chain 'P' and resid 548 through 555 removed outlier: 3.510A pdb=" N ILE P 555 " --> pdb=" O THR P 551 " (cutoff:3.500A) Processing helix chain 'P' and resid 555 through 560 Processing helix chain 'Q' and resid 63 through 84 removed outlier: 3.704A pdb=" N LYS Q 68 " --> pdb=" O GLU Q 64 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU Q 71 " --> pdb=" O GLN Q 67 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU Q 73 " --> pdb=" O PHE Q 69 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU Q 78 " --> pdb=" O ILE Q 74 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU Q 79 " --> pdb=" O GLN Q 75 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU Q 80 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 95 removed outlier: 3.725A pdb=" N ASN Q 95 " --> pdb=" O ASP Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 114 removed outlier: 3.903A pdb=" N VAL Q 109 " --> pdb=" O GLN Q 105 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLN Q 112 " --> pdb=" O GLN Q 108 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU Q 114 " --> pdb=" O LEU Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 126 removed outlier: 3.672A pdb=" N GLN Q 120 " --> pdb=" O PRO Q 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 77 Processing helix chain 'S' and resid 78 through 84 Processing helix chain 'S' and resid 85 through 100 removed outlier: 3.617A pdb=" N GLY S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP S 91 " --> pdb=" O GLU S 87 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS S 92 " --> pdb=" O LYS S 88 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN S 95 " --> pdb=" O ASP S 91 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA S 98 " --> pdb=" O THR S 94 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 114 Processing helix chain 'S' and resid 115 through 125 removed outlier: 3.902A pdb=" N GLN S 120 " --> pdb=" O PRO S 116 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET S 121 " --> pdb=" O PRO S 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 removed outlier: 3.643A pdb=" N GLU C 73 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 76 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 100 removed outlier: 3.899A pdb=" N HIS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.693A pdb=" N PHE C 119 " --> pdb=" O PRO C 115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 77 through 80 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 42 Processing sheet with id=AA3, first strand: chain 'O' and resid 79 through 80 removed outlier: 3.615A pdb=" N ILE O 86 " --> pdb=" O VAL O 79 " (cutoff:3.500A) 1139 hydrogen bonds defined for protein. 3393 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.99 Time building geometry restraints manager: 6.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7101 1.34 - 1.46: 3997 1.46 - 1.58: 9663 1.58 - 1.70: 0 1.70 - 1.81: 156 Bond restraints: 20917 Sorted by residual: bond pdb=" N SER P 259 " pdb=" CA SER P 259 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.33e-02 5.65e+03 5.57e+00 bond pdb=" CA SER P 259 " pdb=" CB SER P 259 " ideal model delta sigma weight residual 1.530 1.507 0.023 1.68e-02 3.54e+03 1.92e+00 bond pdb=" CB PHE J 388 " pdb=" CG PHE J 388 " ideal model delta sigma weight residual 1.502 1.471 0.031 2.30e-02 1.89e+03 1.77e+00 bond pdb=" C THR P 48 " pdb=" N PRO P 49 " ideal model delta sigma weight residual 1.334 1.354 -0.020 1.51e-02 4.39e+03 1.70e+00 bond pdb=" CB PHE J 392 " pdb=" CG PHE J 392 " ideal model delta sigma weight residual 1.502 1.476 0.026 2.30e-02 1.89e+03 1.25e+00 ... (remaining 20912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 27658 1.62 - 3.24: 592 3.24 - 4.86: 101 4.86 - 6.48: 44 6.48 - 8.11: 7 Bond angle restraints: 28402 Sorted by residual: angle pdb=" N PRO G 11 " pdb=" CA PRO G 11 " pdb=" CB PRO G 11 " ideal model delta sigma weight residual 103.00 110.30 -7.30 1.10e+00 8.26e-01 4.40e+01 angle pdb=" N ILE A 616 " pdb=" CA ILE A 616 " pdb=" C ILE A 616 " ideal model delta sigma weight residual 109.19 104.77 4.42 8.20e-01 1.49e+00 2.90e+01 angle pdb=" C ILE A 616 " pdb=" CA ILE A 616 " pdb=" CB ILE A 616 " ideal model delta sigma weight residual 109.33 114.17 -4.84 9.80e-01 1.04e+00 2.44e+01 angle pdb=" N VAL A 39 " pdb=" CA VAL A 39 " pdb=" C VAL A 39 " ideal model delta sigma weight residual 112.29 108.57 3.72 9.40e-01 1.13e+00 1.57e+01 angle pdb=" CA ILE A 616 " pdb=" C ILE A 616 " pdb=" N PRO A 617 " ideal model delta sigma weight residual 116.57 120.20 -3.63 9.80e-01 1.04e+00 1.37e+01 ... (remaining 28397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11330 17.98 - 35.96: 1043 35.96 - 53.94: 181 53.94 - 71.92: 53 71.92 - 89.90: 20 Dihedral angle restraints: 12627 sinusoidal: 4729 harmonic: 7898 Sorted by residual: dihedral pdb=" CA LYS A 598 " pdb=" C LYS A 598 " pdb=" N CYS A 599 " pdb=" CA CYS A 599 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA MET A 595 " pdb=" C MET A 595 " pdb=" N SER A 596 " pdb=" CA SER A 596 " ideal model delta harmonic sigma weight residual 180.00 -159.88 -20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA THR B 113 " pdb=" C THR B 113 " pdb=" N LEU B 114 " pdb=" CA LEU B 114 " ideal model delta harmonic sigma weight residual 180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 12624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2784 0.057 - 0.114: 489 0.114 - 0.171: 32 0.171 - 0.228: 4 0.228 - 0.285: 3 Chirality restraints: 3312 Sorted by residual: chirality pdb=" CB VAL P 39 " pdb=" CA VAL P 39 " pdb=" CG1 VAL P 39 " pdb=" CG2 VAL P 39 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CG LEU A 35 " pdb=" CB LEU A 35 " pdb=" CD1 LEU A 35 " pdb=" CD2 LEU A 35 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA PRO G 11 " pdb=" N PRO G 11 " pdb=" C PRO G 11 " pdb=" CB PRO G 11 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3309 not shown) Planarity restraints: 3719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR P 48 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.13e+00 pdb=" N PRO P 49 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO P 49 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO P 49 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 616 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 617 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 617 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 617 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 392 " 0.024 2.00e-02 2.50e+03 1.90e-02 6.31e+00 pdb=" CG PHE J 392 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE J 392 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE J 392 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE J 392 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE J 392 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE J 392 " 0.011 2.00e-02 2.50e+03 ... (remaining 3716 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1076 2.73 - 3.27: 22979 3.27 - 3.82: 36942 3.82 - 4.36: 43297 4.36 - 4.90: 68559 Nonbonded interactions: 172853 Sorted by model distance: nonbonded pdb=" O ILE J 546 " pdb=" OH TYR A 275 " model vdw 2.190 3.040 nonbonded pdb=" O THR O 73 " pdb=" OG1 THR O 90 " model vdw 2.195 3.040 nonbonded pdb=" O ALA J 227 " pdb=" OG SER J 259 " model vdw 2.232 3.040 nonbonded pdb=" OG SER A 580 " pdb=" OG SER A 585 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR A 449 " pdb=" O PRO A 497 " model vdw 2.250 3.040 ... (remaining 172848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 523 or (resid 524 through 531 and ( \ name N or name CA or name C or name O or name CB )) or resid 532 or (resid 533 t \ hrough 562 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 523 or (resid 524 through 531 and ( \ name N or name CA or name C or name O or name CB )) or resid 532 or (resid 533 t \ hrough 562 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'O' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 523 or (resid 524 through 531 and ( \ name N or name CA or name C or name O or name CB )) or resid 532 or (resid 533 t \ hrough 562 and (name N or name CA or name C or name O or name CB )))) selection = chain 'P' } ncs_group { reference = (chain 'B' and resid 62 through 128) selection = chain 'Q' } ncs_group { reference = (chain 'C' and resid 66 through 125) selection = chain 'S' } 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 group one per residue 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: 15.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.390 Process input model: 52.170 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 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 : 0.003 0.037 20917 Z= 0.135 Angle : 0.613 8.106 28402 Z= 0.333 Chirality : 0.042 0.285 3312 Planarity : 0.004 0.067 3719 Dihedral : 14.972 89.896 7509 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -1.08 (0.15), residues: 2661 helix: -0.29 (0.12), residues: 1676 sheet: None (None), residues: 0 loop : -1.31 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 93 HIS 0.009 0.001 HIS A 627 PHE 0.040 0.002 PHE J 392 TYR 0.012 0.001 TYR J 542 ARG 0.006 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.21457 ( 1139) hydrogen bonds : angle 6.85342 ( 3393) covalent geometry : bond 0.00275 (20917) covalent geometry : angle 0.61289 (28402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 177 ARG cc_start: 0.9024 (mmt180) cc_final: 0.8605 (ptt-90) REVERT: J 220 MET cc_start: 0.7714 (ptp) cc_final: 0.7455 (ptp) REVERT: J 326 MET cc_start: 0.9022 (mmt) cc_final: 0.8635 (mmt) REVERT: J 342 ASP cc_start: 0.7934 (t70) cc_final: 0.7168 (t0) REVERT: A 16 LYS cc_start: 0.8076 (mmpt) cc_final: 0.7518 (pttm) REVERT: A 157 CYS cc_start: 0.8519 (p) cc_final: 0.8237 (t) REVERT: A 280 MET cc_start: 0.9158 (mmp) cc_final: 0.8668 (tpp) REVERT: A 333 GLU cc_start: 0.8703 (tp30) cc_final: 0.8469 (tp30) REVERT: A 424 ARG cc_start: 0.8428 (mtm180) cc_final: 0.7880 (ptp-170) REVERT: A 441 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8642 (mt-10) REVERT: A 521 CYS cc_start: 0.8329 (t) cc_final: 0.7921 (t) REVERT: A 587 ILE cc_start: 0.9156 (mt) cc_final: 0.8932 (mm) REVERT: A 590 LYS cc_start: 0.8861 (mttp) cc_final: 0.8369 (mtpt) REVERT: O 326 MET cc_start: 0.5412 (tmm) cc_final: 0.4308 (tpt) REVERT: P 210 ARG cc_start: 0.8614 (tpp80) cc_final: 0.8333 (ttp80) REVERT: P 360 PHE cc_start: 0.6590 (m-80) cc_final: 0.5887 (m-80) REVERT: Q 78 GLU cc_start: 0.8507 (tt0) cc_final: 0.7226 (tm-30) REVERT: Q 119 PHE cc_start: 0.8393 (t80) cc_final: 0.7616 (t80) REVERT: Q 121 MET cc_start: 0.9015 (tmm) cc_final: 0.7932 (tmm) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.3176 time to fit residues: 178.9366 Evaluate side-chains 189 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 5.9990 chunk 201 optimal weight: 0.7980 chunk 111 optimal weight: 0.1980 chunk 68 optimal weight: 0.9980 chunk 135 optimal weight: 30.0000 chunk 107 optimal weight: 0.0270 chunk 208 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 241 optimal weight: 10.0000 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN A 553 HIS A 592 GLN B 75 GLN ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 ASN O 375 GLN O 397 HIS O 443 ASN O 476 HIS O 541 GLN O 553 HIS P 56 ASN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 369 HIS ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.102464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.081526 restraints weight = 120314.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.079049 restraints weight = 81443.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.079464 restraints weight = 70952.303| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20917 Z= 0.141 Angle : 0.580 11.024 28402 Z= 0.313 Chirality : 0.039 0.168 3312 Planarity : 0.004 0.062 3719 Dihedral : 4.396 19.405 2912 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.14 % Allowed : 5.11 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.62 (0.16), residues: 2661 helix: 0.13 (0.12), residues: 1781 sheet: -3.19 (1.35), residues: 10 loop : -1.35 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 367 HIS 0.010 0.001 HIS P 476 PHE 0.038 0.002 PHE O 549 TYR 0.026 0.001 TYR O 472 ARG 0.005 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.05138 ( 1139) hydrogen bonds : angle 4.91677 ( 3393) covalent geometry : bond 0.00291 (20917) covalent geometry : angle 0.58000 (28402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 248 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 220 MET cc_start: 0.6875 (ptp) cc_final: 0.6654 (ptp) REVERT: J 280 MET cc_start: 0.8436 (ttt) cc_final: 0.8235 (tmm) REVERT: J 326 MET cc_start: 0.9071 (mmt) cc_final: 0.8725 (mmt) REVERT: J 381 THR cc_start: 0.9006 (p) cc_final: 0.8577 (t) REVERT: J 438 ASP cc_start: 0.8773 (m-30) cc_final: 0.8516 (m-30) REVERT: J 586 GLU cc_start: 0.8844 (tt0) cc_final: 0.8639 (tm-30) REVERT: A 280 MET cc_start: 0.9136 (mmp) cc_final: 0.8787 (tpp) REVERT: A 358 MET cc_start: 0.9215 (mmt) cc_final: 0.8778 (mmm) REVERT: A 384 ASP cc_start: 0.8473 (m-30) cc_final: 0.8258 (m-30) REVERT: A 587 ILE cc_start: 0.8852 (mt) cc_final: 0.8640 (mm) REVERT: A 590 LYS cc_start: 0.8658 (mttp) cc_final: 0.8320 (mtpt) REVERT: O 14 GLU cc_start: 0.8540 (pt0) cc_final: 0.7799 (tm-30) REVERT: O 56 ASN cc_start: 0.8923 (m-40) cc_final: 0.8704 (m-40) REVERT: O 133 ARG cc_start: 0.8560 (tpm170) cc_final: 0.8331 (tpm170) REVERT: O 326 MET cc_start: 0.5436 (tmm) cc_final: 0.4407 (tpt) REVERT: O 422 MET cc_start: 0.6784 (mmt) cc_final: 0.6502 (mmm) REVERT: O 502 HIS cc_start: 0.6817 (m170) cc_final: 0.6490 (m170) REVERT: O 550 LEU cc_start: 0.8083 (mt) cc_final: 0.7711 (mm) REVERT: P 210 ARG cc_start: 0.8829 (tpp80) cc_final: 0.8362 (ttp80) REVERT: P 358 MET cc_start: 0.8059 (mmm) cc_final: 0.7824 (tpt) REVERT: Q 120 GLN cc_start: 0.9020 (mp-120) cc_final: 0.8793 (mm-40) REVERT: Q 121 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8525 (tmm) outliers start: 3 outliers final: 0 residues processed: 250 average time/residue: 0.3129 time to fit residues: 121.4005 Evaluate side-chains 176 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 83 optimal weight: 0.8980 chunk 239 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 253 optimal weight: 0.7980 chunk 237 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 ASN O 116 HIS ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 443 ASN ** P 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.100002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.072587 restraints weight = 110188.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.072859 restraints weight = 62391.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.072248 restraints weight = 47138.230| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20917 Z= 0.144 Angle : 0.567 9.867 28402 Z= 0.303 Chirality : 0.039 0.155 3312 Planarity : 0.004 0.057 3719 Dihedral : 4.312 19.997 2912 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.19 % Allowed : 3.79 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.34 (0.16), residues: 2661 helix: 0.36 (0.12), residues: 1791 sheet: None (None), residues: 0 loop : -1.33 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP P 209 HIS 0.010 0.001 HIS A 627 PHE 0.019 0.002 PHE A 626 TYR 0.034 0.001 TYR P 445 ARG 0.012 0.000 ARG P 46 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 1139) hydrogen bonds : angle 4.62688 ( 3393) covalent geometry : bond 0.00306 (20917) covalent geometry : angle 0.56657 (28402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 159 MET cc_start: 0.8258 (mmt) cc_final: 0.7592 (mmm) REVERT: J 220 MET cc_start: 0.7481 (ptp) cc_final: 0.7213 (ptp) REVERT: J 280 MET cc_start: 0.8788 (ttt) cc_final: 0.8531 (tmm) REVERT: J 326 MET cc_start: 0.9189 (mmt) cc_final: 0.8904 (mmm) REVERT: J 438 ASP cc_start: 0.8834 (m-30) cc_final: 0.8581 (m-30) REVERT: J 586 GLU cc_start: 0.8913 (tt0) cc_final: 0.8685 (tm-30) REVERT: A 16 LYS cc_start: 0.8381 (mmpt) cc_final: 0.7685 (pttm) REVERT: A 280 MET cc_start: 0.9214 (mmp) cc_final: 0.8790 (tpp) REVERT: A 384 ASP cc_start: 0.8675 (m-30) cc_final: 0.8417 (m-30) REVERT: A 441 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8272 (mt-10) REVERT: A 587 ILE cc_start: 0.8937 (mt) cc_final: 0.8710 (mm) REVERT: A 590 LYS cc_start: 0.8756 (mttp) cc_final: 0.8414 (mtpt) REVERT: O 14 GLU cc_start: 0.8561 (pt0) cc_final: 0.7952 (tm-30) REVERT: O 56 ASN cc_start: 0.8893 (m-40) cc_final: 0.8674 (m-40) REVERT: O 133 ARG cc_start: 0.8422 (tpm170) cc_final: 0.8199 (tpm170) REVERT: O 265 GLU cc_start: 0.6451 (mp0) cc_final: 0.5804 (tt0) REVERT: O 422 MET cc_start: 0.6915 (mmt) cc_final: 0.6557 (mmm) REVERT: P 210 ARG cc_start: 0.8987 (tpp80) cc_final: 0.8434 (ttp80) REVERT: P 384 ASP cc_start: 0.8088 (m-30) cc_final: 0.7771 (m-30) REVERT: P 445 TYR cc_start: 0.7962 (m-80) cc_final: 0.7519 (m-10) REVERT: Q 119 PHE cc_start: 0.7866 (t80) cc_final: 0.7659 (t80) REVERT: Q 121 MET cc_start: 0.8790 (ttp) cc_final: 0.8360 (ttt) outliers start: 4 outliers final: 2 residues processed: 226 average time/residue: 0.3108 time to fit residues: 110.1236 Evaluate side-chains 165 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 27 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 chunk 218 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 154 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 380 ASN O 443 ASN O 476 HIS ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 511 ASN Q 102 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.101569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.081255 restraints weight = 121357.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.079094 restraints weight = 87123.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.079183 restraints weight = 82599.166| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20917 Z= 0.131 Angle : 0.562 10.248 28402 Z= 0.297 Chirality : 0.039 0.165 3312 Planarity : 0.004 0.058 3719 Dihedral : 4.276 20.749 2912 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.15 (0.16), residues: 2661 helix: 0.53 (0.12), residues: 1786 sheet: None (None), residues: 0 loop : -1.31 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP P 209 HIS 0.008 0.001 HIS P 476 PHE 0.015 0.001 PHE B 70 TYR 0.021 0.001 TYR P 445 ARG 0.003 0.000 ARG J 332 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 1139) hydrogen bonds : angle 4.47777 ( 3393) covalent geometry : bond 0.00282 (20917) covalent geometry : angle 0.56207 (28402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 159 MET cc_start: 0.8352 (mmt) cc_final: 0.7747 (mmm) REVERT: J 220 MET cc_start: 0.6831 (ptp) cc_final: 0.6558 (ptp) REVERT: J 326 MET cc_start: 0.9053 (mmt) cc_final: 0.8811 (mmm) REVERT: J 438 ASP cc_start: 0.8744 (m-30) cc_final: 0.8495 (m-30) REVERT: A 16 LYS cc_start: 0.8370 (mmpt) cc_final: 0.7819 (pttm) REVERT: A 280 MET cc_start: 0.9100 (mmp) cc_final: 0.8821 (tpp) REVERT: A 384 ASP cc_start: 0.8688 (m-30) cc_final: 0.8418 (m-30) REVERT: A 587 ILE cc_start: 0.8830 (mt) cc_final: 0.8620 (mm) REVERT: A 590 LYS cc_start: 0.8701 (mttp) cc_final: 0.8405 (mtpt) REVERT: O 14 GLU cc_start: 0.8538 (pt0) cc_final: 0.7758 (tm-30) REVERT: O 265 GLU cc_start: 0.6466 (mp0) cc_final: 0.5799 (tt0) REVERT: O 422 MET cc_start: 0.6720 (mmt) cc_final: 0.6277 (mmm) REVERT: O 502 HIS cc_start: 0.7013 (m170) cc_final: 0.6691 (m170) REVERT: P 204 LYS cc_start: 0.8821 (tppp) cc_final: 0.8518 (tppt) REVERT: P 210 ARG cc_start: 0.8726 (tpp80) cc_final: 0.8303 (ttp80) REVERT: P 445 TYR cc_start: 0.7718 (m-80) cc_final: 0.7319 (m-10) REVERT: P 450 LEU cc_start: 0.8985 (mt) cc_final: 0.8743 (mt) REVERT: P 468 ASN cc_start: 0.9104 (p0) cc_final: 0.8361 (t0) REVERT: Q 120 GLN cc_start: 0.8903 (mp-120) cc_final: 0.8675 (mm-40) REVERT: Q 121 MET cc_start: 0.8803 (ttp) cc_final: 0.8554 (ttt) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.3118 time to fit residues: 111.5517 Evaluate side-chains 158 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 144 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 382 HIS A 420 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.101501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.081009 restraints weight = 121965.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.078716 restraints weight = 82789.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.079118 restraints weight = 74850.981| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20917 Z= 0.125 Angle : 0.561 10.148 28402 Z= 0.296 Chirality : 0.039 0.234 3312 Planarity : 0.004 0.058 3719 Dihedral : 4.243 22.269 2912 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.02 (0.16), residues: 2661 helix: 0.63 (0.12), residues: 1791 sheet: None (None), residues: 0 loop : -1.27 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 209 HIS 0.009 0.001 HIS P 476 PHE 0.034 0.002 PHE O 549 TYR 0.020 0.001 TYR B 86 ARG 0.004 0.000 ARG J 332 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 1139) hydrogen bonds : angle 4.38322 ( 3393) covalent geometry : bond 0.00269 (20917) covalent geometry : angle 0.56070 (28402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 159 MET cc_start: 0.8371 (mmt) cc_final: 0.7783 (mmm) REVERT: J 220 MET cc_start: 0.6766 (ptp) cc_final: 0.6554 (ptp) REVERT: J 326 MET cc_start: 0.9044 (mmt) cc_final: 0.8606 (mmt) REVERT: J 438 ASP cc_start: 0.8769 (m-30) cc_final: 0.8533 (m-30) REVERT: J 586 GLU cc_start: 0.8431 (pp20) cc_final: 0.8217 (tm-30) REVERT: A 16 LYS cc_start: 0.8414 (mmpt) cc_final: 0.7841 (pttm) REVERT: A 255 LEU cc_start: 0.9422 (tp) cc_final: 0.9186 (tt) REVERT: A 280 MET cc_start: 0.9183 (mmp) cc_final: 0.8916 (tpp) REVERT: A 384 ASP cc_start: 0.8643 (m-30) cc_final: 0.8397 (m-30) REVERT: A 590 LYS cc_start: 0.8751 (mttp) cc_final: 0.8503 (mtpt) REVERT: O 14 GLU cc_start: 0.8509 (pt0) cc_final: 0.7743 (tm-30) REVERT: O 56 ASN cc_start: 0.8785 (m-40) cc_final: 0.8576 (m-40) REVERT: O 265 GLU cc_start: 0.6479 (mp0) cc_final: 0.5772 (tt0) REVERT: O 422 MET cc_start: 0.6820 (mmt) cc_final: 0.6394 (mmm) REVERT: O 502 HIS cc_start: 0.7011 (m170) cc_final: 0.6670 (m170) REVERT: P 144 ASN cc_start: 0.7540 (m-40) cc_final: 0.7235 (m-40) REVERT: P 210 ARG cc_start: 0.8716 (tpp80) cc_final: 0.8289 (ttp80) REVERT: P 445 TYR cc_start: 0.7897 (m-80) cc_final: 0.7358 (m-10) REVERT: Q 120 GLN cc_start: 0.8980 (mp-120) cc_final: 0.8769 (mm-40) REVERT: Q 121 MET cc_start: 0.8833 (ttp) cc_final: 0.8532 (ttp) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.3240 time to fit residues: 114.6313 Evaluate side-chains 155 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 242 optimal weight: 9.9990 chunk 244 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 208 optimal weight: 0.2980 chunk 11 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 166 optimal weight: 0.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 382 HIS A 420 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.101952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.081190 restraints weight = 120750.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.079052 restraints weight = 80296.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.079488 restraints weight = 73342.485| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20917 Z= 0.117 Angle : 0.561 10.954 28402 Z= 0.295 Chirality : 0.039 0.163 3312 Planarity : 0.004 0.056 3719 Dihedral : 4.208 21.580 2912 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: 0.09 (0.16), residues: 2661 helix: 0.71 (0.12), residues: 1800 sheet: None (None), residues: 0 loop : -1.23 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 209 HIS 0.009 0.001 HIS P 476 PHE 0.018 0.001 PHE O 549 TYR 0.027 0.001 TYR O 440 ARG 0.005 0.000 ARG J 210 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 1139) hydrogen bonds : angle 4.30223 ( 3393) covalent geometry : bond 0.00247 (20917) covalent geometry : angle 0.56056 (28402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 159 MET cc_start: 0.8379 (mmt) cc_final: 0.7830 (mmm) REVERT: J 220 MET cc_start: 0.6684 (ptp) cc_final: 0.6481 (ptp) REVERT: J 326 MET cc_start: 0.8988 (mmt) cc_final: 0.8680 (mmt) REVERT: J 438 ASP cc_start: 0.8726 (m-30) cc_final: 0.8500 (m-30) REVERT: A 213 ILE cc_start: 0.8706 (tt) cc_final: 0.8457 (mt) REVERT: A 255 LEU cc_start: 0.9408 (tp) cc_final: 0.9136 (tt) REVERT: A 280 MET cc_start: 0.9200 (mmp) cc_final: 0.8918 (tpp) REVERT: A 329 LEU cc_start: 0.9284 (mt) cc_final: 0.9021 (mt) REVERT: A 384 ASP cc_start: 0.8560 (m-30) cc_final: 0.8324 (m-30) REVERT: A 590 LYS cc_start: 0.8791 (mttp) cc_final: 0.8546 (mtmt) REVERT: O 14 GLU cc_start: 0.8515 (pt0) cc_final: 0.7734 (tm-30) REVERT: O 56 ASN cc_start: 0.8790 (m-40) cc_final: 0.8548 (m110) REVERT: O 265 GLU cc_start: 0.6394 (mp0) cc_final: 0.5697 (tt0) REVERT: O 422 MET cc_start: 0.6684 (mmt) cc_final: 0.6212 (mmm) REVERT: O 502 HIS cc_start: 0.6802 (m170) cc_final: 0.6581 (m170) REVERT: P 144 ASN cc_start: 0.7497 (m-40) cc_final: 0.7189 (m-40) REVERT: P 210 ARG cc_start: 0.8709 (tpp80) cc_final: 0.8288 (ttp80) REVERT: P 220 MET cc_start: 0.4891 (mmt) cc_final: 0.4638 (mmt) REVERT: P 420 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7350 (tp40) REVERT: P 445 TYR cc_start: 0.7826 (m-80) cc_final: 0.7375 (m-10) REVERT: P 468 ASN cc_start: 0.9098 (p0) cc_final: 0.8233 (t0) REVERT: Q 80 LEU cc_start: 0.7184 (tp) cc_final: 0.6960 (tp) REVERT: Q 121 MET cc_start: 0.8847 (ttp) cc_final: 0.8580 (ttp) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.2911 time to fit residues: 99.8055 Evaluate side-chains 160 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 25 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 180 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN B 92 HIS ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.098995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.069336 restraints weight = 112806.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.070946 restraints weight = 68255.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.071245 restraints weight = 45755.336| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20917 Z= 0.166 Angle : 0.607 9.114 28402 Z= 0.320 Chirality : 0.040 0.249 3312 Planarity : 0.004 0.057 3719 Dihedral : 4.265 21.297 2912 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: 0.07 (0.16), residues: 2661 helix: 0.71 (0.12), residues: 1802 sheet: None (None), residues: 0 loop : -1.29 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 209 HIS 0.013 0.001 HIS A 241 PHE 0.023 0.002 PHE J 392 TYR 0.040 0.001 TYR P 449 ARG 0.008 0.000 ARG J 46 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 1139) hydrogen bonds : angle 4.42921 ( 3393) covalent geometry : bond 0.00360 (20917) covalent geometry : angle 0.60651 (28402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 159 MET cc_start: 0.8261 (mmt) cc_final: 0.7761 (mmm) REVERT: J 220 MET cc_start: 0.7742 (ptp) cc_final: 0.7392 (ptp) REVERT: J 280 MET cc_start: 0.8728 (tmm) cc_final: 0.8461 (tpt) REVERT: J 326 MET cc_start: 0.9158 (mmt) cc_final: 0.8819 (mmt) REVERT: J 371 LEU cc_start: 0.9338 (tp) cc_final: 0.9126 (tt) REVERT: J 438 ASP cc_start: 0.8806 (m-30) cc_final: 0.8581 (m-30) REVERT: A 213 ILE cc_start: 0.8727 (tt) cc_final: 0.8505 (mt) REVERT: A 280 MET cc_start: 0.9153 (mmp) cc_final: 0.8922 (tpp) REVERT: A 503 THR cc_start: 0.9218 (p) cc_final: 0.8950 (p) REVERT: O 14 GLU cc_start: 0.8484 (pt0) cc_final: 0.7999 (tm-30) REVERT: O 56 ASN cc_start: 0.8670 (m-40) cc_final: 0.8443 (m110) REVERT: O 265 GLU cc_start: 0.6326 (mp0) cc_final: 0.5606 (tt0) REVERT: O 422 MET cc_start: 0.6968 (mmt) cc_final: 0.6609 (mmm) REVERT: P 144 ASN cc_start: 0.7704 (m-40) cc_final: 0.7442 (m-40) REVERT: P 210 ARG cc_start: 0.8997 (tpp80) cc_final: 0.8475 (ttp80) REVERT: P 326 MET cc_start: 0.8707 (ptm) cc_final: 0.8463 (ppp) REVERT: P 445 TYR cc_start: 0.8211 (m-80) cc_final: 0.7835 (m-10) REVERT: Q 121 MET cc_start: 0.8947 (ttp) cc_final: 0.8655 (ttp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2951 time to fit residues: 96.0847 Evaluate side-chains 154 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 63 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 173 optimal weight: 0.4980 chunk 177 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 100 HIS ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 HIS A 289 ASN ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 ASN O 489 HIS ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 511 ASN ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.094390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.064779 restraints weight = 115645.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.065855 restraints weight = 76483.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.065668 restraints weight = 47694.128| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 20917 Z= 0.383 Angle : 0.883 14.685 28402 Z= 0.459 Chirality : 0.047 0.347 3312 Planarity : 0.006 0.068 3719 Dihedral : 5.039 25.867 2912 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 25.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.96 (0.16), residues: 2661 helix: -0.13 (0.12), residues: 1795 sheet: None (None), residues: 0 loop : -1.52 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 209 HIS 0.021 0.003 HIS A 241 PHE 0.049 0.003 PHE P 388 TYR 0.027 0.003 TYR J 277 ARG 0.007 0.001 ARG P 309 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 1139) hydrogen bonds : angle 5.21291 ( 3393) covalent geometry : bond 0.00798 (20917) covalent geometry : angle 0.88316 (28402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 220 MET cc_start: 0.8597 (ptp) cc_final: 0.8063 (ptp) REVERT: J 326 MET cc_start: 0.9299 (mmt) cc_final: 0.8875 (mmp) REVERT: J 438 ASP cc_start: 0.8815 (m-30) cc_final: 0.8570 (m-30) REVERT: A 16 LYS cc_start: 0.8386 (mmpt) cc_final: 0.7521 (pttm) REVERT: A 326 MET cc_start: 0.9301 (mmp) cc_final: 0.8875 (mmm) REVERT: A 413 CYS cc_start: 0.9133 (m) cc_final: 0.8910 (m) REVERT: A 503 THR cc_start: 0.9281 (p) cc_final: 0.8981 (p) REVERT: A 561 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7931 (tm-30) REVERT: O 14 GLU cc_start: 0.8532 (pt0) cc_final: 0.8101 (tm-30) REVERT: O 56 ASN cc_start: 0.8587 (m-40) cc_final: 0.8362 (m110) REVERT: O 133 ARG cc_start: 0.8390 (tpm170) cc_final: 0.8177 (tpp-160) REVERT: O 395 MET cc_start: 0.7758 (ptp) cc_final: 0.7389 (ptp) REVERT: O 422 MET cc_start: 0.7374 (mmt) cc_final: 0.7055 (mmm) REVERT: O 472 TYR cc_start: 0.8447 (t80) cc_final: 0.7742 (m-80) REVERT: O 476 HIS cc_start: 0.8567 (m-70) cc_final: 0.8187 (m-70) REVERT: P 326 MET cc_start: 0.8821 (ptm) cc_final: 0.8450 (ppp) REVERT: P 445 TYR cc_start: 0.8469 (m-80) cc_final: 0.8106 (m-10) REVERT: Q 121 MET cc_start: 0.8902 (ttp) cc_final: 0.8638 (ptm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.3137 time to fit residues: 92.1412 Evaluate side-chains 136 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 182 optimal weight: 0.0770 chunk 80 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 chunk 206 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 chunk 240 optimal weight: 0.0020 chunk 187 optimal weight: 0.0870 chunk 193 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN A 397 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 HIS ** P 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 372 HIS ** P 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.098197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.069095 restraints weight = 115481.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.070820 restraints weight = 77593.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.071321 restraints weight = 46031.833| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20917 Z= 0.134 Angle : 0.641 14.093 28402 Z= 0.333 Chirality : 0.041 0.221 3312 Planarity : 0.004 0.054 3719 Dihedral : 4.657 21.363 2912 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.34 (0.16), residues: 2661 helix: 0.37 (0.12), residues: 1813 sheet: None (None), residues: 0 loop : -1.40 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 367 HIS 0.014 0.001 HIS A 241 PHE 0.027 0.002 PHE J 623 TYR 0.038 0.001 TYR P 354 ARG 0.007 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 1139) hydrogen bonds : angle 4.56089 ( 3393) covalent geometry : bond 0.00290 (20917) covalent geometry : angle 0.64057 (28402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 220 MET cc_start: 0.8093 (ptp) cc_final: 0.7844 (ptp) REVERT: J 326 MET cc_start: 0.9201 (mmt) cc_final: 0.8845 (mmt) REVERT: J 438 ASP cc_start: 0.8716 (m-30) cc_final: 0.8488 (m-30) REVERT: A 422 MET cc_start: 0.8705 (ppp) cc_final: 0.8499 (ppp) REVERT: A 503 THR cc_start: 0.8945 (p) cc_final: 0.8696 (p) REVERT: A 561 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7452 (tm-30) REVERT: O 14 GLU cc_start: 0.8470 (pt0) cc_final: 0.7994 (tm-30) REVERT: O 56 ASN cc_start: 0.8605 (m-40) cc_final: 0.8361 (m110) REVERT: O 395 MET cc_start: 0.7674 (ptp) cc_final: 0.7358 (ptp) REVERT: O 422 MET cc_start: 0.7281 (mmt) cc_final: 0.6945 (mmm) REVERT: P 254 GLU cc_start: 0.9116 (pt0) cc_final: 0.8745 (mm-30) REVERT: P 326 MET cc_start: 0.8704 (ptm) cc_final: 0.8366 (ppp) REVERT: P 445 TYR cc_start: 0.8411 (m-80) cc_final: 0.8015 (m-10) REVERT: P 465 CYS cc_start: 0.8694 (t) cc_final: 0.8316 (m) REVERT: P 468 ASN cc_start: 0.8904 (p0) cc_final: 0.8192 (t0) REVERT: Q 121 MET cc_start: 0.8935 (ttp) cc_final: 0.8617 (ttp) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.3041 time to fit residues: 98.8786 Evaluate side-chains 147 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 180 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 197 optimal weight: 4.9990 chunk 252 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 219 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.098038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.067325 restraints weight = 109661.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.069279 restraints weight = 58179.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.070353 restraints weight = 37429.063| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20917 Z= 0.134 Angle : 0.617 11.659 28402 Z= 0.323 Chirality : 0.040 0.192 3312 Planarity : 0.004 0.055 3719 Dihedral : 4.483 21.782 2912 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.05 % Allowed : 0.24 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.09 (0.16), residues: 2661 helix: 0.58 (0.12), residues: 1810 sheet: None (None), residues: 0 loop : -1.35 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 209 HIS 0.014 0.001 HIS A 241 PHE 0.020 0.002 PHE B 70 TYR 0.026 0.001 TYR P 449 ARG 0.005 0.000 ARG A 482 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 1139) hydrogen bonds : angle 4.49071 ( 3393) covalent geometry : bond 0.00294 (20917) covalent geometry : angle 0.61668 (28402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 326 MET cc_start: 0.9107 (mmt) cc_final: 0.8798 (mmt) REVERT: A 51 ILE cc_start: 0.9465 (mm) cc_final: 0.9185 (pt) REVERT: A 280 MET cc_start: 0.8606 (tpp) cc_final: 0.8328 (tpp) REVERT: A 384 ASP cc_start: 0.8144 (m-30) cc_final: 0.7935 (m-30) REVERT: A 413 CYS cc_start: 0.8662 (m) cc_final: 0.8320 (m) REVERT: A 503 THR cc_start: 0.8922 (p) cc_final: 0.8621 (p) REVERT: A 568 MET cc_start: 0.7199 (mmm) cc_final: 0.6658 (mmt) REVERT: B 87 GLU cc_start: 0.8871 (mp0) cc_final: 0.8358 (tm-30) REVERT: B 88 LYS cc_start: 0.9058 (tttp) cc_final: 0.8702 (ttmt) REVERT: O 14 GLU cc_start: 0.8302 (pt0) cc_final: 0.7992 (tm-30) REVERT: O 56 ASN cc_start: 0.8519 (m-40) cc_final: 0.8298 (m110) REVERT: O 265 GLU cc_start: 0.6345 (mm-30) cc_final: 0.5199 (tt0) REVERT: O 395 MET cc_start: 0.7669 (ptp) cc_final: 0.7371 (ptp) REVERT: O 422 MET cc_start: 0.7261 (mmt) cc_final: 0.6947 (mmm) REVERT: P 159 MET cc_start: 0.2028 (mmm) cc_final: 0.1594 (mmt) REVERT: P 254 GLU cc_start: 0.9140 (pt0) cc_final: 0.8842 (mm-30) REVERT: P 326 MET cc_start: 0.8666 (ptm) cc_final: 0.8365 (ppp) REVERT: P 445 TYR cc_start: 0.8436 (m-80) cc_final: 0.8013 (m-10) REVERT: P 465 CYS cc_start: 0.8595 (t) cc_final: 0.8261 (m) REVERT: P 468 ASN cc_start: 0.8984 (p0) cc_final: 0.8228 (t0) REVERT: Q 121 MET cc_start: 0.8935 (ttp) cc_final: 0.8656 (ptm) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.3197 time to fit residues: 101.8908 Evaluate side-chains 147 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 150 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 195 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 211 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 GLN ** O 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.098392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.070506 restraints weight = 113441.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.071115 restraints weight = 71932.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.071033 restraints weight = 47749.224| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20917 Z= 0.132 Angle : 0.613 11.037 28402 Z= 0.320 Chirality : 0.040 0.175 3312 Planarity : 0.004 0.055 3719 Dihedral : 4.438 22.132 2912 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: 0.01 (0.16), residues: 2661 helix: 0.67 (0.12), residues: 1809 sheet: None (None), residues: 0 loop : -1.33 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 367 HIS 0.012 0.001 HIS A 241 PHE 0.048 0.002 PHE J 193 TYR 0.033 0.001 TYR P 449 ARG 0.004 0.000 ARG P 374 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 1139) hydrogen bonds : angle 4.45277 ( 3393) covalent geometry : bond 0.00288 (20917) covalent geometry : angle 0.61290 (28402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7276.49 seconds wall clock time: 129 minutes 40.17 seconds (7780.17 seconds total)