Starting phenix.real_space_refine on Wed Jun 18 03:41:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7b_61200/06_2025/9j7b_61200.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7b_61200/06_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_61200/06_2025/9j7b_61200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7b_61200/06_2025/9j7b_61200.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7b_61200/06_2025/9j7b_61200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7b_61200/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 16.62, per 1000 atoms: 0.81 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: 4.95 Conformation dependent library (CDL) restraints added in 3.2 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: 2.14 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: 6.60 Time building geometry restraints manager: 5.88 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: 0.010 Normalize map: mean=0, sd=1: 809.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 51.690 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 867.120 ------------------------------------------------------------------------------- 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 : 2.930 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: 0.4833 time to fit residues: 275.7620 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 : 2.526 ------------------------------------------------------------------------------- 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 = 0.081527 restraints weight = 120314.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.079053 restraints weight = 81253.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.079484 restraints weight = 70958.843| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 2.344 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 326 MET cc_start: 0.9036 (mmt) cc_final: 0.8703 (mmt) REVERT: J 381 THR cc_start: 0.8974 (p) cc_final: 0.8548 (t) REVERT: J 438 ASP cc_start: 0.8728 (m-30) cc_final: 0.8483 (m-30) REVERT: A 280 MET cc_start: 0.9096 (mmp) cc_final: 0.8780 (tpp) REVERT: A 358 MET cc_start: 0.9185 (mmt) cc_final: 0.8752 (mmm) REVERT: A 384 ASP cc_start: 0.8389 (m-30) cc_final: 0.8169 (m-30) REVERT: A 587 ILE cc_start: 0.8814 (mt) cc_final: 0.8606 (mm) REVERT: A 590 LYS cc_start: 0.8621 (mttp) cc_final: 0.8294 (mtpt) REVERT: O 14 GLU cc_start: 0.8531 (pt0) cc_final: 0.7785 (tm-30) REVERT: O 56 ASN cc_start: 0.8919 (m-40) cc_final: 0.8705 (m-40) REVERT: O 133 ARG cc_start: 0.8567 (tpm170) cc_final: 0.8339 (tpm170) REVERT: O 326 MET cc_start: 0.5452 (tmm) cc_final: 0.4418 (tpt) REVERT: O 422 MET cc_start: 0.6772 (mmt) cc_final: 0.6488 (mmm) REVERT: O 502 HIS cc_start: 0.6822 (m170) cc_final: 0.6484 (m170) REVERT: O 550 LEU cc_start: 0.8079 (mt) cc_final: 0.7708 (mm) REVERT: P 210 ARG cc_start: 0.8802 (tpp80) cc_final: 0.8353 (ttp80) REVERT: P 358 MET cc_start: 0.8015 (mmm) cc_final: 0.7785 (tpt) REVERT: Q 120 GLN cc_start: 0.9017 (mp-120) cc_final: 0.8787 (mm-40) REVERT: Q 121 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8519 (tmm) outliers start: 3 outliers final: 0 residues processed: 250 average time/residue: 0.3161 time to fit residues: 122.7426 Evaluate side-chains 175 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 2.222 ------------------------------------------------------------------------------- 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: 0.2980 chunk 239 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 226 optimal weight: 0.6980 chunk 253 optimal weight: 0.9980 chunk 237 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 240 optimal weight: 4.9990 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 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 443 ASN ** P 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.100426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.076185 restraints weight = 108931.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.074356 restraints weight = 62969.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.074681 restraints weight = 52397.858| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20917 Z= 0.131 Angle : 0.562 9.896 28402 Z= 0.300 Chirality : 0.039 0.164 3312 Planarity : 0.004 0.057 3719 Dihedral : 4.308 19.595 2912 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.09 % Allowed : 3.88 % 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: -0.35 (0.16), residues: 2661 helix: 0.35 (0.12), residues: 1790 sheet: None (None), residues: 0 loop : -1.33 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 209 HIS 0.009 0.001 HIS A 627 PHE 0.018 0.002 PHE A 626 TYR 0.033 0.001 TYR P 445 ARG 0.005 0.000 ARG J 332 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 1139) hydrogen bonds : angle 4.63029 ( 3393) covalent geometry : bond 0.00277 (20917) covalent geometry : angle 0.56218 (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 231 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 2.289 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: J 159 MET cc_start: 0.8273 (mmt) cc_final: 0.7766 (mmm) REVERT: J 326 MET cc_start: 0.9073 (mmt) cc_final: 0.8576 (mmt) REVERT: J 438 ASP cc_start: 0.8704 (m-30) cc_final: 0.8490 (m-30) REVERT: A 16 LYS cc_start: 0.8379 (mmpt) cc_final: 0.7793 (pttm) REVERT: A 280 MET cc_start: 0.9104 (mmp) cc_final: 0.8737 (tpp) REVERT: A 384 ASP cc_start: 0.8371 (m-30) cc_final: 0.8145 (m-30) REVERT: A 441 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8085 (mt-10) REVERT: A 587 ILE cc_start: 0.8833 (mt) cc_final: 0.8618 (mm) REVERT: A 590 LYS cc_start: 0.8663 (mttp) cc_final: 0.8353 (mtpt) REVERT: O 14 GLU cc_start: 0.8556 (pt0) cc_final: 0.7803 (tm-30) REVERT: O 56 ASN cc_start: 0.8905 (m-40) cc_final: 0.8682 (m-40) REVERT: O 133 ARG cc_start: 0.8541 (tpm170) cc_final: 0.8314 (tpm170) REVERT: O 422 MET cc_start: 0.6837 (mmt) cc_final: 0.6418 (mmm) REVERT: O 502 HIS cc_start: 0.6809 (m170) cc_final: 0.6504 (m170) REVERT: P 210 ARG cc_start: 0.8797 (tpp80) cc_final: 0.8334 (ttp80) REVERT: P 384 ASP cc_start: 0.7902 (m-30) cc_final: 0.7573 (m-30) REVERT: P 450 LEU cc_start: 0.9009 (mt) cc_final: 0.8805 (mt) REVERT: Q 121 MET cc_start: 0.8767 (ttp) cc_final: 0.8366 (ttt) outliers start: 2 outliers final: 0 residues processed: 231 average time/residue: 0.3116 time to fit residues: 113.8744 Evaluate side-chains 161 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 2.312 ------------------------------------------------------------------------------- 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: 4.9990 chunk 79 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 131 optimal weight: 0.0010 chunk 244 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 154 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- 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 289 ASN ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN A 464 GLN A 504 ASN ** A 627 HIS ** 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 443 ASN P 511 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.098477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.071118 restraints weight = 112174.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.071261 restraints weight = 64012.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.070710 restraints weight = 48693.834| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20917 Z= 0.183 Angle : 0.609 9.358 28402 Z= 0.322 Chirality : 0.040 0.166 3312 Planarity : 0.004 0.056 3719 Dihedral : 4.349 20.431 2912 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: -0.25 (0.16), residues: 2661 helix: 0.44 (0.12), residues: 1792 sheet: None (None), residues: 0 loop : -1.31 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP P 209 HIS 0.008 0.001 HIS J 369 PHE 0.019 0.002 PHE B 70 TYR 0.022 0.001 TYR P 445 ARG 0.004 0.000 ARG J 332 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 1139) hydrogen bonds : angle 4.61777 ( 3393) covalent geometry : bond 0.00389 (20917) covalent geometry : angle 0.60876 (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 218 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 2.267 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: 0.8294 (mmt) cc_final: 0.7689 (mmm) REVERT: J 326 MET cc_start: 0.9152 (mmt) cc_final: 0.8911 (mmm) REVERT: J 342 ASP cc_start: 0.8083 (t70) cc_final: 0.7781 (t0) REVERT: J 438 ASP cc_start: 0.8868 (m-30) cc_final: 0.8613 (m-30) REVERT: A 16 LYS cc_start: 0.8366 (mmpt) cc_final: 0.7625 (pttm) REVERT: A 251 GLU cc_start: 0.8710 (pt0) cc_final: 0.8502 (pt0) REVERT: A 280 MET cc_start: 0.9302 (mmp) cc_final: 0.9048 (tpp) REVERT: A 326 MET cc_start: 0.9147 (mmp) cc_final: 0.8667 (mmm) REVERT: A 441 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8322 (mt-10) REVERT: A 587 ILE cc_start: 0.8963 (mt) cc_final: 0.8751 (mm) REVERT: A 590 LYS cc_start: 0.8818 (mttp) cc_final: 0.8538 (mtmt) REVERT: O 14 GLU cc_start: 0.8558 (pt0) cc_final: 0.7960 (tm-30) REVERT: O 56 ASN cc_start: 0.8890 (m-40) cc_final: 0.8684 (m-40) REVERT: O 133 ARG cc_start: 0.8392 (tpm170) cc_final: 0.8186 (tpm170) REVERT: O 265 GLU cc_start: 0.6407 (mp0) cc_final: 0.5748 (tt0) REVERT: O 422 MET cc_start: 0.6943 (mmt) cc_final: 0.6575 (mmm) REVERT: P 204 LYS cc_start: 0.8915 (tppp) cc_final: 0.8632 (tppt) REVERT: P 210 ARG cc_start: 0.8971 (tpp80) cc_final: 0.8413 (ttp80) REVERT: P 445 TYR cc_start: 0.7908 (m-80) cc_final: 0.7569 (m-10) REVERT: P 450 LEU cc_start: 0.9174 (mt) cc_final: 0.8932 (mt) REVERT: P 464 GLN cc_start: 0.5550 (mm110) cc_final: 0.5280 (mm110) REVERT: P 468 ASN cc_start: 0.8910 (p0) cc_final: 0.8154 (t0) REVERT: Q 121 MET cc_start: 0.8912 (ttp) cc_final: 0.8547 (ttp) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3064 time to fit residues: 105.6345 Evaluate side-chains 151 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 2.291 ------------------------------------------------------------------------------- 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: 0.8980 chunk 45 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 144 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 289 ASN A 420 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN ** 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 ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.101406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.076240 restraints weight = 121672.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.076361 restraints weight = 82265.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.075799 restraints weight = 62489.889| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3132 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= 0.123 Angle : 0.567 10.423 28402 Z= 0.301 Chirality : 0.039 0.185 3312 Planarity : 0.004 0.058 3719 Dihedral : 4.292 22.870 2912 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % 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: -0.10 (0.16), residues: 2661 helix: 0.56 (0.12), residues: 1795 sheet: None (None), residues: 0 loop : -1.28 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 209 HIS 0.008 0.001 HIS P 476 PHE 0.034 0.002 PHE O 549 TYR 0.025 0.001 TYR O 440 ARG 0.004 0.000 ARG J 210 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 1139) hydrogen bonds : angle 4.40330 ( 3393) covalent geometry : bond 0.00262 (20917) covalent geometry : angle 0.56671 (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 219 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 2.330 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 159 MET cc_start: 0.8245 (mmt) cc_final: 0.7668 (mmm) REVERT: J 326 MET cc_start: 0.9172 (mmt) cc_final: 0.8785 (mmt) REVERT: J 342 ASP cc_start: 0.7963 (t70) cc_final: 0.7627 (t0) REVERT: J 438 ASP cc_start: 0.8838 (m-30) cc_final: 0.8600 (m-30) REVERT: A 51 ILE cc_start: 0.9410 (mm) cc_final: 0.9117 (pt) REVERT: A 255 LEU cc_start: 0.9257 (tp) cc_final: 0.8839 (tt) REVERT: A 280 MET cc_start: 0.9153 (mmp) cc_final: 0.8772 (tpp) REVERT: A 441 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8104 (mt-10) REVERT: A 503 THR cc_start: 0.9137 (p) cc_final: 0.8904 (p) REVERT: A 590 LYS cc_start: 0.8792 (mttp) cc_final: 0.8525 (mtpt) REVERT: O 14 GLU cc_start: 0.8521 (pt0) cc_final: 0.7952 (tm-30) REVERT: O 56 ASN cc_start: 0.8849 (m-40) cc_final: 0.8647 (m-40) REVERT: O 265 GLU cc_start: 0.6379 (mp0) cc_final: 0.5680 (tt0) REVERT: O 422 MET cc_start: 0.7020 (mmt) cc_final: 0.6648 (mmm) REVERT: O 472 TYR cc_start: 0.7854 (t80) cc_final: 0.7352 (m-80) REVERT: P 144 ASN cc_start: 0.7704 (m-40) cc_final: 0.7441 (m-40) REVERT: P 210 ARG cc_start: 0.9008 (tpp80) cc_final: 0.8439 (ttp80) REVERT: P 358 MET cc_start: 0.8102 (tpt) cc_final: 0.7741 (tpt) REVERT: P 445 TYR cc_start: 0.8148 (m-80) cc_final: 0.7641 (m-10) REVERT: Q 119 PHE cc_start: 0.8014 (t80) cc_final: 0.7796 (t80) REVERT: Q 121 MET cc_start: 0.8873 (ttp) cc_final: 0.8575 (ttp) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.3124 time to fit residues: 109.7676 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 : 2.437 ------------------------------------------------------------------------------- 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: 3.9990 chunk 244 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 213 optimal weight: 0.0770 chunk 132 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN ** 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 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.099894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.071086 restraints weight = 111298.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.071997 restraints weight = 75763.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.072102 restraints weight = 50377.170| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20917 Z= 0.126 Angle : 0.563 10.885 28402 Z= 0.297 Chirality : 0.039 0.169 3312 Planarity : 0.004 0.058 3719 Dihedral : 4.262 21.404 2912 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.30 % 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: 0.02 (0.16), residues: 2661 helix: 0.66 (0.12), residues: 1800 sheet: None (None), residues: 0 loop : -1.26 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 209 HIS 0.012 0.001 HIS J 325 PHE 0.017 0.001 PHE O 549 TYR 0.019 0.001 TYR O 472 ARG 0.004 0.000 ARG J 350 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 1139) hydrogen bonds : angle 4.34691 ( 3393) covalent geometry : bond 0.00271 (20917) covalent geometry : angle 0.56300 (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 215 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 2.662 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 326 MET cc_start: 0.9109 (mmt) cc_final: 0.8770 (mmt) REVERT: J 342 ASP cc_start: 0.7894 (t70) cc_final: 0.7539 (t0) REVERT: J 438 ASP cc_start: 0.8784 (m-30) cc_final: 0.8542 (m-30) REVERT: A 213 ILE cc_start: 0.8700 (tt) cc_final: 0.8464 (mt) REVERT: A 255 LEU cc_start: 0.9366 (tp) cc_final: 0.9153 (tt) REVERT: A 280 MET cc_start: 0.9054 (mmp) cc_final: 0.8814 (tpp) REVERT: A 413 CYS cc_start: 0.8709 (m) cc_final: 0.8444 (m) REVERT: A 441 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8066 (mt-10) REVERT: A 590 LYS cc_start: 0.8820 (mttp) cc_final: 0.8562 (mtmt) REVERT: O 14 GLU cc_start: 0.8527 (pt0) cc_final: 0.7963 (tm-30) REVERT: O 56 ASN cc_start: 0.8878 (m-40) cc_final: 0.8653 (m110) REVERT: O 265 GLU cc_start: 0.6382 (mp0) cc_final: 0.5659 (tt0) REVERT: O 422 MET cc_start: 0.6870 (mmt) cc_final: 0.6472 (mmm) REVERT: P 144 ASN cc_start: 0.7658 (m-40) cc_final: 0.7388 (m-40) REVERT: P 210 ARG cc_start: 0.8970 (tpp80) cc_final: 0.8423 (ttp80) REVERT: P 220 MET cc_start: 0.5290 (mmt) cc_final: 0.5017 (mmt) REVERT: P 420 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7437 (tp40) REVERT: P 445 TYR cc_start: 0.8084 (m-80) cc_final: 0.7633 (m-10) REVERT: P 464 GLN cc_start: 0.5583 (mm110) cc_final: 0.5314 (mm110) REVERT: P 468 ASN cc_start: 0.8801 (p0) cc_final: 0.8037 (t0) REVERT: Q 80 LEU cc_start: 0.7498 (tp) cc_final: 0.7265 (tp) REVERT: Q 121 MET cc_start: 0.8932 (ttp) cc_final: 0.8655 (ttp) outliers start: 2 outliers final: 0 residues processed: 215 average time/residue: 0.2898 time to fit residues: 100.7724 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 : 2.302 ------------------------------------------------------------------------------- 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: 0.9990 chunk 188 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN ** 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 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 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 = 0.4190 r_free = 0.4190 target = 0.099586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.069870 restraints weight = 111646.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.071346 restraints weight = 73510.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.071902 restraints weight = 46190.422| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20917 Z= 0.136 Angle : 0.582 9.257 28402 Z= 0.307 Chirality : 0.039 0.216 3312 Planarity : 0.004 0.057 3719 Dihedral : 4.257 21.084 2912 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: 0.10 (0.16), residues: 2661 helix: 0.73 (0.12), residues: 1796 sheet: None (None), residues: 0 loop : -1.23 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 367 HIS 0.011 0.001 HIS A 241 PHE 0.029 0.002 PHE J 392 TYR 0.039 0.001 TYR P 449 ARG 0.004 0.000 ARG J 379 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 1139) hydrogen bonds : angle 4.36214 ( 3393) covalent geometry : bond 0.00296 (20917) covalent geometry : angle 0.58186 (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 206 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.325 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 326 MET cc_start: 0.9099 (mmt) cc_final: 0.8751 (mmt) REVERT: J 438 ASP cc_start: 0.8769 (m-30) cc_final: 0.8542 (m-30) REVERT: A 213 ILE cc_start: 0.8736 (tt) cc_final: 0.8518 (mt) REVERT: A 255 LEU cc_start: 0.9443 (tp) cc_final: 0.9173 (tt) REVERT: A 280 MET cc_start: 0.9036 (mmp) cc_final: 0.8819 (tpp) REVERT: A 413 CYS cc_start: 0.8750 (m) cc_final: 0.8486 (m) REVERT: A 441 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8008 (mt-10) REVERT: A 503 THR cc_start: 0.9091 (p) cc_final: 0.8838 (p) REVERT: O 14 GLU cc_start: 0.8496 (pt0) cc_final: 0.7977 (tm-30) REVERT: O 56 ASN cc_start: 0.8858 (m-40) cc_final: 0.8639 (m110) REVERT: O 265 GLU cc_start: 0.6349 (mp0) cc_final: 0.5627 (tt0) REVERT: O 422 MET cc_start: 0.6888 (mmt) cc_final: 0.6494 (mmm) REVERT: O 472 TYR cc_start: 0.7968 (t80) cc_final: 0.7354 (m-80) REVERT: P 144 ASN cc_start: 0.7670 (m-40) cc_final: 0.7405 (m-40) REVERT: P 210 ARG cc_start: 0.8971 (tpp80) cc_final: 0.8467 (ttp80) REVERT: P 220 MET cc_start: 0.5340 (mmt) cc_final: 0.5127 (mmt) REVERT: P 445 TYR cc_start: 0.8210 (m-80) cc_final: 0.7826 (m-10) REVERT: P 464 GLN cc_start: 0.5621 (mm110) cc_final: 0.5338 (mm110) REVERT: P 468 ASN cc_start: 0.8795 (p0) cc_final: 0.7942 (t0) REVERT: Q 80 LEU cc_start: 0.7459 (tp) cc_final: 0.7247 (tp) REVERT: Q 121 MET cc_start: 0.8931 (ttp) cc_final: 0.8656 (ptm) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.3044 time to fit residues: 101.2370 Evaluate side-chains 156 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 2.272 ------------------------------------------------------------------------------- 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: 10.0000 chunk 136 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 173 optimal weight: 0.0980 chunk 177 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 124 optimal weight: 0.4980 chunk 135 optimal weight: 8.9990 chunk 262 optimal weight: 7.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- 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 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN ** A 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN 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 P 511 ASN ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 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 = 0.4133 r_free = 0.4133 target = 0.096460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.067851 restraints weight = 113558.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.068250 restraints weight = 74216.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.067832 restraints weight = 52658.267| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20917 Z= 0.258 Angle : 0.722 11.601 28402 Z= 0.376 Chirality : 0.043 0.244 3312 Planarity : 0.005 0.057 3719 Dihedral : 4.558 21.215 2912 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.05 % Allowed : 1.70 % Favored : 98.25 % 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: -0.31 (0.16), residues: 2661 helix: 0.38 (0.12), residues: 1800 sheet: None (None), residues: 0 loop : -1.32 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 209 HIS 0.015 0.002 HIS A 241 PHE 0.041 0.002 PHE P 388 TYR 0.029 0.002 TYR P 354 ARG 0.005 0.001 ARG J 210 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 1139) hydrogen bonds : angle 4.78323 ( 3393) covalent geometry : bond 0.00549 (20917) covalent geometry : angle 0.72182 (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 206 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 2.567 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: J 326 MET cc_start: 0.9167 (mmt) cc_final: 0.8899 (mmm) REVERT: J 438 ASP cc_start: 0.8798 (m-30) cc_final: 0.8548 (m-30) REVERT: A 213 ILE cc_start: 0.8818 (tt) cc_final: 0.8612 (mt) REVERT: A 280 MET cc_start: 0.9326 (mmp) cc_final: 0.8932 (tpp) REVERT: A 413 CYS cc_start: 0.8913 (m) cc_final: 0.8646 (m) REVERT: A 441 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8107 (mt-10) REVERT: A 503 THR cc_start: 0.9218 (p) cc_final: 0.8899 (p) REVERT: A 561 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7770 (tm-30) REVERT: O 14 GLU cc_start: 0.8474 (pt0) cc_final: 0.8036 (tm-30) REVERT: O 56 ASN cc_start: 0.8785 (m-40) cc_final: 0.8558 (m110) REVERT: O 133 ARG cc_start: 0.8297 (tpm170) cc_final: 0.8078 (tpp-160) REVERT: O 265 GLU cc_start: 0.6345 (mp0) cc_final: 0.5656 (tt0) REVERT: O 395 MET cc_start: 0.7660 (ptp) cc_final: 0.7278 (ptp) REVERT: O 422 MET cc_start: 0.7259 (mmt) cc_final: 0.6926 (mmm) REVERT: O 472 TYR cc_start: 0.8217 (t80) cc_final: 0.7950 (m-80) REVERT: O 476 HIS cc_start: 0.8541 (m90) cc_final: 0.8088 (m90) REVERT: P 144 ASN cc_start: 0.7834 (m-40) cc_final: 0.7578 (m-40) REVERT: P 254 GLU cc_start: 0.9103 (pt0) cc_final: 0.8790 (mm-30) REVERT: P 360 PHE cc_start: 0.8203 (p90) cc_final: 0.7951 (p90) REVERT: P 445 TYR cc_start: 0.8363 (m-80) cc_final: 0.7999 (m-10) REVERT: Q 121 MET cc_start: 0.8944 (ttp) cc_final: 0.8682 (ptm) outliers start: 1 outliers final: 1 residues processed: 206 average time/residue: 0.3030 time to fit residues: 100.6741 Evaluate side-chains 148 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 2.448 ------------------------------------------------------------------------------- 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: 0.2980 chunk 80 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 240 optimal weight: 4.9990 chunk 187 optimal weight: 0.2980 chunk 193 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 464 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 58 HIS ** 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 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 105 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 = 0.4171 r_free = 0.4171 target = 0.098674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.069542 restraints weight = 113382.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.070845 restraints weight = 73977.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.070907 restraints weight = 46395.976| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3889 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= 0.139 Angle : 0.618 15.359 28402 Z= 0.321 Chirality : 0.040 0.185 3312 Planarity : 0.004 0.055 3719 Dihedral : 4.421 20.867 2912 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 0.61 (0.12), residues: 1817 sheet: None (None), residues: 0 loop : -1.24 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 367 HIS 0.013 0.001 HIS A 241 PHE 0.021 0.002 PHE J 623 TYR 0.026 0.001 TYR P 354 ARG 0.009 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 1139) hydrogen bonds : angle 4.50573 ( 3393) covalent geometry : bond 0.00303 (20917) covalent geometry : angle 0.61813 (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 206 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.472 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 280 MET cc_start: 0.8967 (tmm) cc_final: 0.8592 (tpp) REVERT: J 326 MET cc_start: 0.9144 (mmt) cc_final: 0.8778 (mmt) REVERT: J 438 ASP cc_start: 0.8728 (m-30) cc_final: 0.8492 (m-30) REVERT: A 255 LEU cc_start: 0.9442 (tp) cc_final: 0.9186 (tt) REVERT: A 280 MET cc_start: 0.9187 (mmp) cc_final: 0.8927 (tpp) REVERT: A 437 MET cc_start: 0.8527 (tmm) cc_final: 0.7977 (tmm) REVERT: A 503 THR cc_start: 0.9006 (p) cc_final: 0.8735 (p) REVERT: A 561 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 590 LYS cc_start: 0.8897 (mttp) cc_final: 0.8656 (mtpt) REVERT: O 14 GLU cc_start: 0.8453 (pt0) cc_final: 0.7983 (tm-30) REVERT: O 56 ASN cc_start: 0.8763 (m-40) cc_final: 0.8529 (m110) REVERT: O 265 GLU cc_start: 0.6380 (mp0) cc_final: 0.5669 (tt0) REVERT: O 395 MET cc_start: 0.7637 (ptp) cc_final: 0.7324 (ptp) REVERT: O 422 MET cc_start: 0.7284 (mmt) cc_final: 0.6950 (mmm) REVERT: O 472 TYR cc_start: 0.8164 (t80) cc_final: 0.7909 (m-80) REVERT: O 476 HIS cc_start: 0.8585 (m90) cc_final: 0.8195 (m90) REVERT: P 144 ASN cc_start: 0.7752 (m-40) cc_final: 0.7496 (m-40) REVERT: P 312 GLN cc_start: 0.8481 (mp10) cc_final: 0.8174 (pm20) REVERT: P 360 PHE cc_start: 0.8177 (p90) cc_final: 0.7929 (p90) REVERT: P 445 TYR cc_start: 0.8372 (m-80) cc_final: 0.7986 (m-10) REVERT: Q 121 MET cc_start: 0.9006 (ttp) cc_final: 0.8703 (ttp) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.3089 time to fit residues: 103.3163 Evaluate side-chains 153 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 2.463 ------------------------------------------------------------------------------- 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: 0.9980 chunk 128 optimal weight: 5.9990 chunk 255 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 219 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 131 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 464 GLN ** O 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 58 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 105 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 = 0.4174 r_free = 0.4174 target = 0.098697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.069550 restraints weight = 112411.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.071203 restraints weight = 67946.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.071354 restraints weight = 39781.002| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20917 Z= 0.131 Angle : 0.609 11.319 28402 Z= 0.317 Chirality : 0.040 0.176 3312 Planarity : 0.004 0.056 3719 Dihedral : 4.333 20.695 2912 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.08 (0.16), residues: 2661 helix: 0.70 (0.12), residues: 1813 sheet: None (None), residues: 0 loop : -1.25 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 209 HIS 0.012 0.001 HIS A 241 PHE 0.019 0.002 PHE B 70 TYR 0.031 0.001 TYR P 354 ARG 0.003 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 1139) hydrogen bonds : angle 4.43418 ( 3393) covalent geometry : bond 0.00288 (20917) covalent geometry : angle 0.60854 (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 201 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 2.551 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 326 MET cc_start: 0.9165 (mmt) cc_final: 0.8812 (mmt) REVERT: J 342 ASP cc_start: 0.8170 (t70) cc_final: 0.7772 (t0) REVERT: J 438 ASP cc_start: 0.8770 (m-30) cc_final: 0.8522 (m-30) REVERT: A 255 LEU cc_start: 0.9423 (tp) cc_final: 0.9175 (tt) REVERT: A 280 MET cc_start: 0.9231 (mmp) cc_final: 0.8941 (tpp) REVERT: A 329 LEU cc_start: 0.9321 (mt) cc_final: 0.9093 (mt) REVERT: A 503 THR cc_start: 0.9058 (p) cc_final: 0.8783 (p) REVERT: A 561 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7565 (tm-30) REVERT: O 14 GLU cc_start: 0.8407 (pt0) cc_final: 0.7963 (tm-30) REVERT: O 56 ASN cc_start: 0.8751 (m-40) cc_final: 0.8524 (m110) REVERT: O 265 GLU cc_start: 0.6233 (mp0) cc_final: 0.5511 (tt0) REVERT: O 395 MET cc_start: 0.7676 (ptp) cc_final: 0.7358 (ptp) REVERT: O 422 MET cc_start: 0.7347 (mmt) cc_final: 0.7038 (mmm) REVERT: O 472 TYR cc_start: 0.8138 (t80) cc_final: 0.7586 (m-80) REVERT: P 144 ASN cc_start: 0.7741 (m-40) cc_final: 0.7527 (m-40) REVERT: P 210 ARG cc_start: 0.8915 (mmm-85) cc_final: 0.8298 (ttp80) REVERT: P 312 GLN cc_start: 0.8577 (mp10) cc_final: 0.8257 (pm20) REVERT: P 326 MET cc_start: 0.8353 (ppp) cc_final: 0.8037 (ppp) REVERT: P 360 PHE cc_start: 0.8193 (p90) cc_final: 0.7930 (p90) REVERT: P 445 TYR cc_start: 0.8393 (m-80) cc_final: 0.8005 (m-10) REVERT: P 464 GLN cc_start: 0.4720 (mp10) cc_final: 0.4385 (mp10) REVERT: P 465 CYS cc_start: 0.8700 (t) cc_final: 0.8330 (m) REVERT: Q 121 MET cc_start: 0.9008 (ttp) cc_final: 0.8744 (ptm) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.3028 time to fit residues: 98.4578 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 : 2.614 ------------------------------------------------------------------------------- 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: 4.9990 chunk 14 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 111 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 204 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 211 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 58 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.099119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.070196 restraints weight = 113812.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.071912 restraints weight = 73083.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.071741 restraints weight = 43442.261| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20917 Z= 0.127 Angle : 0.605 10.840 28402 Z= 0.314 Chirality : 0.040 0.181 3312 Planarity : 0.004 0.056 3719 Dihedral : 4.312 21.242 2912 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 0.14 (0.16), residues: 2661 helix: 0.73 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.23 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 367 HIS 0.011 0.001 HIS A 241 PHE 0.019 0.002 PHE J 284 TYR 0.030 0.001 TYR P 449 ARG 0.004 0.000 ARG O 177 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 1139) hydrogen bonds : angle 4.37829 ( 3393) covalent geometry : bond 0.00276 (20917) covalent geometry : angle 0.60483 (28402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8521.12 seconds wall clock time: 150 minutes 34.62 seconds (9034.62 seconds total)