Starting phenix.real_space_refine on Thu Sep 18 22:22:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7b_61200/09_2025/9j7b_61200.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7b_61200/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9j7b_61200/09_2025/9j7b_61200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7b_61200/09_2025/9j7b_61200.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j7b_61200/09_2025/9j7b_61200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7b_61200/09_2025/9j7b_61200.map" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2} 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: {'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 2, 'HIS:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1} 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, 'PHE:plan': 3, 'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 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, 'PHE:plan': 3, 'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 100 Time building chain proxies: 5.32, per 1000 atoms: 0.26 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: 1.91 Conformation dependent library (CDL) restraints added in 958.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.66 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: 3.93 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7101 1.34 - 1.46: 3997 1.46 - 1.58: 9663 1.58 - 1.70: 0 1.70 - 1.81: 156 Bond restraints: 20917 Sorted by residual: bond pdb=" N SER P 259 " pdb=" CA SER P 259 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.33e-02 5.65e+03 5.57e+00 bond pdb=" CA SER P 259 " pdb=" CB SER P 259 " ideal model delta sigma weight residual 1.530 1.507 0.023 1.68e-02 3.54e+03 1.92e+00 bond pdb=" CB PHE J 388 " pdb=" CG PHE J 388 " ideal model delta sigma weight residual 1.502 1.471 0.031 2.30e-02 1.89e+03 1.77e+00 bond pdb=" C THR P 48 " pdb=" N PRO P 49 " ideal model delta sigma weight residual 1.334 1.354 -0.020 1.51e-02 4.39e+03 1.70e+00 bond pdb=" CB PHE J 392 " pdb=" CG PHE J 392 " ideal model delta sigma weight residual 1.502 1.476 0.026 2.30e-02 1.89e+03 1.25e+00 ... (remaining 20912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 27658 1.62 - 3.24: 592 3.24 - 4.86: 101 4.86 - 6.48: 44 6.48 - 8.11: 7 Bond angle restraints: 28402 Sorted by residual: angle pdb=" N PRO G 11 " pdb=" CA PRO G 11 " pdb=" CB PRO G 11 " ideal model delta sigma weight residual 103.00 110.30 -7.30 1.10e+00 8.26e-01 4.40e+01 angle pdb=" N ILE A 616 " pdb=" CA ILE A 616 " pdb=" C ILE A 616 " ideal model delta sigma weight residual 109.19 104.77 4.42 8.20e-01 1.49e+00 2.90e+01 angle pdb=" C ILE A 616 " pdb=" CA ILE A 616 " pdb=" CB ILE A 616 " ideal model delta sigma weight residual 109.33 114.17 -4.84 9.80e-01 1.04e+00 2.44e+01 angle pdb=" N VAL A 39 " pdb=" CA VAL A 39 " pdb=" C VAL A 39 " ideal model delta sigma weight residual 112.29 108.57 3.72 9.40e-01 1.13e+00 1.57e+01 angle pdb=" CA ILE A 616 " pdb=" C ILE A 616 " pdb=" N PRO A 617 " ideal model delta sigma weight residual 116.57 120.20 -3.63 9.80e-01 1.04e+00 1.37e+01 ... (remaining 28397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11330 17.98 - 35.96: 1043 35.96 - 53.94: 181 53.94 - 71.92: 53 71.92 - 89.90: 20 Dihedral angle restraints: 12627 sinusoidal: 4729 harmonic: 7898 Sorted by residual: dihedral pdb=" CA LYS A 598 " pdb=" C LYS A 598 " pdb=" N CYS A 599 " pdb=" CA CYS A 599 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA MET A 595 " pdb=" C MET A 595 " pdb=" N SER A 596 " pdb=" CA SER A 596 " ideal model delta harmonic sigma weight residual 180.00 -159.88 -20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA THR B 113 " pdb=" C THR B 113 " pdb=" N LEU B 114 " pdb=" CA LEU B 114 " ideal model delta harmonic sigma weight residual 180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 12624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2784 0.057 - 0.114: 489 0.114 - 0.171: 32 0.171 - 0.228: 4 0.228 - 0.285: 3 Chirality restraints: 3312 Sorted by residual: chirality pdb=" CB VAL P 39 " pdb=" CA VAL P 39 " pdb=" CG1 VAL P 39 " pdb=" CG2 VAL P 39 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CG LEU A 35 " pdb=" CB LEU A 35 " pdb=" CD1 LEU A 35 " pdb=" CD2 LEU A 35 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA PRO G 11 " pdb=" N PRO G 11 " pdb=" C PRO G 11 " pdb=" CB PRO G 11 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3309 not shown) Planarity restraints: 3719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR P 48 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.13e+00 pdb=" N PRO P 49 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO P 49 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO P 49 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 616 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 617 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 617 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 617 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 392 " 0.024 2.00e-02 2.50e+03 1.90e-02 6.31e+00 pdb=" CG PHE J 392 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE J 392 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE J 392 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE J 392 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE J 392 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE J 392 " 0.011 2.00e-02 2.50e+03 ... (remaining 3716 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1076 2.73 - 3.27: 22979 3.27 - 3.82: 36942 3.82 - 4.36: 43297 4.36 - 4.90: 68559 Nonbonded interactions: 172853 Sorted by model distance: nonbonded pdb=" O ILE J 546 " pdb=" OH TYR A 275 " model vdw 2.190 3.040 nonbonded pdb=" O THR O 73 " pdb=" OG1 THR O 90 " model vdw 2.195 3.040 nonbonded pdb=" O ALA J 227 " pdb=" OG SER J 259 " model vdw 2.232 3.040 nonbonded pdb=" OG SER A 580 " pdb=" OG SER A 585 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR A 449 " pdb=" O PRO A 497 " model vdw 2.250 3.040 ... (remaining 172848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 523 or (resid 524 through 531 and ( \ name N or name CA or name C or name O or name CB )) or resid 532 or (resid 533 t \ hrough 562 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 523 or (resid 524 through 531 and ( \ name N or name CA or name C or name O or name CB )) or resid 532 or (resid 533 t \ hrough 562 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'O' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 523 or (resid 524 through 531 and ( \ name N or name CA or name C or name O or name CB )) or resid 532 or (resid 533 t \ hrough 562 and (name N or name CA or name C or name O or name CB )))) selection = chain 'P' } ncs_group { reference = (chain 'B' and resid 62 through 128) selection = chain 'Q' } ncs_group { reference = (chain 'C' and resid 66 through 125) selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 24.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.540 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.130 ------------------------------------------------------------------------------- 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 : 10.64 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG A 249 TYR 0.012 0.001 TYR J 542 PHE 0.040 0.002 PHE J 392 TRP 0.008 0.001 TRP P 93 HIS 0.009 0.001 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00275 (20917) covalent geometry : angle 0.61289 (28402) hydrogen bonds : bond 0.21457 ( 1139) hydrogen bonds : angle 6.85342 ( 3393) *********************** 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 : 0.891 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 177 ARG cc_start: 0.9024 (mmt180) cc_final: 0.8606 (ptt-90) REVERT: J 220 MET cc_start: 0.7714 (ptp) cc_final: 0.7513 (ptp) REVERT: J 326 MET cc_start: 0.9022 (mmt) cc_final: 0.8641 (mmt) REVERT: J 342 ASP cc_start: 0.7934 (t70) cc_final: 0.7572 (t0) REVERT: A 16 LYS cc_start: 0.8076 (mmpt) cc_final: 0.7519 (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: 0.8533 (tpp) REVERT: A 333 GLU cc_start: 0.8703 (tp30) cc_final: 0.8467 (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: 0.7920 (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: 0.8368 (mtpt) REVERT: O 326 MET cc_start: 0.5412 (tmm) cc_final: 0.4307 (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: 0.7227 (tm-30) REVERT: Q 119 PHE cc_start: 0.8393 (t80) cc_final: 0.7614 (t80) REVERT: Q 121 MET cc_start: 0.9015 (tmm) cc_final: 0.7934 (tmm) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.1582 time to fit residues: 89.7493 Evaluate side-chains 188 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.0030 chunk 111 optimal weight: 0.1980 overall best weight: 1.4594 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 541 GLN O 553 HIS P 56 ASN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 369 HIS ** 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** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.100829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.073325 restraints weight = 120617.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.074393 restraints weight = 85541.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.074727 restraints weight = 53659.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.074750 restraints weight = 50717.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.074796 restraints weight = 49661.963| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 20917 Z= 0.195 Angle : 0.620 11.067 28402 Z= 0.334 Chirality : 0.040 0.191 3312 Planarity : 0.005 0.066 3719 Dihedral : 4.459 20.141 2912 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.14 % Allowed : 5.68 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.16), residues: 2661 helix: 0.09 (0.12), residues: 1776 sheet: None (None), residues: 0 loop : -1.38 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 133 TYR 0.016 0.001 TYR P 273 PHE 0.036 0.002 PHE O 549 TRP 0.025 0.002 TRP P 367 HIS 0.009 0.001 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00413 (20917) covalent geometry : angle 0.61960 (28402) hydrogen bonds : bond 0.05217 ( 1139) hydrogen bonds : angle 5.01237 ( 3393) *********************** 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 239 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 236 time to evaluate : 0.907 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 159 MET cc_start: 0.8325 (mmt) cc_final: 0.7883 (mmm) REVERT: J 220 MET cc_start: 0.7772 (ptp) cc_final: 0.7300 (ptp) REVERT: J 280 MET cc_start: 0.8851 (ttt) cc_final: 0.8461 (tmm) REVERT: J 326 MET cc_start: 0.9214 (mmt) cc_final: 0.8713 (mmt) REVERT: J 438 ASP cc_start: 0.8849 (m-30) cc_final: 0.8570 (m-30) REVERT: A 16 LYS cc_start: 0.8390 (mmpt) cc_final: 0.7645 (pttm) REVERT: A 251 GLU cc_start: 0.8669 (pt0) cc_final: 0.8457 (pt0) REVERT: A 280 MET cc_start: 0.9086 (mmp) cc_final: 0.8761 (tpp) REVERT: A 358 MET cc_start: 0.9200 (mmt) cc_final: 0.8782 (mmm) REVERT: A 424 ARG cc_start: 0.8415 (mtm180) cc_final: 0.7778 (ptp-170) REVERT: A 587 ILE cc_start: 0.9015 (mt) cc_final: 0.8779 (mm) REVERT: A 590 LYS cc_start: 0.8831 (mttp) cc_final: 0.8517 (mtpt) REVERT: B 92 HIS cc_start: 0.8929 (m90) cc_final: 0.8720 (m90) REVERT: O 14 GLU cc_start: 0.8581 (pt0) cc_final: 0.8045 (tm-30) REVERT: O 56 ASN cc_start: 0.8899 (m-40) cc_final: 0.8666 (m-40) REVERT: O 133 ARG cc_start: 0.8394 (tpm170) cc_final: 0.8172 (tpm170) REVERT: O 422 MET cc_start: 0.6885 (mmt) cc_final: 0.6671 (mmm) REVERT: O 550 LEU cc_start: 0.8097 (mt) cc_final: 0.7762 (mm) REVERT: P 210 ARG cc_start: 0.9079 (tpp80) cc_final: 0.8507 (ttp80) REVERT: P 235 VAL cc_start: 0.8834 (m) cc_final: 0.8587 (m) REVERT: P 354 TYR cc_start: 0.7054 (m-10) cc_final: 0.6797 (m-10) REVERT: P 360 PHE cc_start: 0.7431 (m-80) cc_final: 0.7032 (m-80) REVERT: P 443 ASN cc_start: 0.7117 (m110) cc_final: 0.6886 (m-40) outliers start: 3 outliers final: 0 residues processed: 238 average time/residue: 0.1524 time to fit residues: 56.4388 Evaluate side-chains 162 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 152 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 257 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 189 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 310 ASN A 289 ASN ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN A 504 ASN A 573 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 120 GLN ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 476 HIS O 489 HIS ** O 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 476 HIS ** P 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 511 ASN ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.096710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.068937 restraints weight = 112529.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.068686 restraints weight = 64610.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.068532 restraints weight = 48589.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.068826 restraints weight = 45524.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.068921 restraints weight = 40554.089| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 20917 Z= 0.264 Angle : 0.694 11.994 28402 Z= 0.364 Chirality : 0.042 0.213 3312 Planarity : 0.005 0.058 3719 Dihedral : 4.640 21.079 2912 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.24 % Allowed : 5.54 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.16), residues: 2661 helix: 0.07 (0.12), residues: 1772 sheet: None (None), residues: 0 loop : -1.45 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 46 TYR 0.036 0.002 TYR P 445 PHE 0.025 0.002 PHE O 549 TRP 0.026 0.002 TRP P 209 HIS 0.013 0.002 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00556 (20917) covalent geometry : angle 0.69354 (28402) hydrogen bonds : bond 0.04579 ( 1139) hydrogen bonds : angle 5.00627 ( 3393) *********************** 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 213 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 208 time to evaluate : 0.762 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: 0.8476 (mmt) cc_final: 0.7882 (mmm) REVERT: J 177 ARG cc_start: 0.8881 (mmt180) cc_final: 0.8506 (ptt-90) REVERT: J 220 MET cc_start: 0.7988 (ptp) cc_final: 0.7611 (ptp) REVERT: J 326 MET cc_start: 0.9108 (mmt) cc_final: 0.8873 (mmm) REVERT: J 438 ASP cc_start: 0.8829 (m-30) cc_final: 0.8589 (m-30) REVERT: A 16 LYS cc_start: 0.8401 (mmpt) cc_final: 0.7666 (pttm) REVERT: A 251 GLU cc_start: 0.8654 (pt0) cc_final: 0.8412 (pt0) REVERT: A 280 MET cc_start: 0.9298 (mmp) cc_final: 0.9075 (tpp) REVERT: A 384 ASP cc_start: 0.8639 (m-30) cc_final: 0.8375 (m-30) REVERT: A 441 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8220 (mt-10) REVERT: A 503 THR cc_start: 0.9371 (p) cc_final: 0.9158 (p) REVERT: A 587 ILE cc_start: 0.8994 (mt) cc_final: 0.8759 (mm) REVERT: A 590 LYS cc_start: 0.8924 (mttp) cc_final: 0.8661 (mtpt) REVERT: O 14 GLU cc_start: 0.8624 (pt0) cc_final: 0.8011 (tm-30) REVERT: O 56 ASN cc_start: 0.8881 (m-40) cc_final: 0.8652 (m-40) REVERT: O 133 ARG cc_start: 0.8549 (tpm170) cc_final: 0.8244 (tpm170) REVERT: O 422 MET cc_start: 0.7030 (mmt) cc_final: 0.6692 (mmm) REVERT: O 502 HIS cc_start: 0.6882 (m170) cc_final: 0.6676 (m170) REVERT: P 210 ARG cc_start: 0.9011 (tpp80) cc_final: 0.8473 (ttp80) REVERT: P 360 PHE cc_start: 0.7466 (m-80) cc_final: 0.6964 (m-80) REVERT: P 441 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8274 (mp0) REVERT: P 445 TYR cc_start: 0.8118 (m-80) cc_final: 0.7716 (m-80) REVERT: P 447 PHE cc_start: 0.8502 (t80) cc_final: 0.8155 (t80) REVERT: Q 119 PHE cc_start: 0.7887 (t80) cc_final: 0.7632 (t80) REVERT: Q 121 MET cc_start: 0.9003 (ptp) cc_final: 0.8749 (ptm) outliers start: 5 outliers final: 0 residues processed: 211 average time/residue: 0.1490 time to fit residues: 49.2718 Evaluate side-chains 146 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 139 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 235 optimal weight: 0.9980 chunk 265 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN A 592 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 476 HIS P 511 ASN Q 102 GLN Q 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.094388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.064795 restraints weight = 115775.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.065611 restraints weight = 76888.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.065725 restraints weight = 48241.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.065889 restraints weight = 44940.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.066034 restraints weight = 39751.015| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 20917 Z= 0.363 Angle : 0.841 13.189 28402 Z= 0.437 Chirality : 0.046 0.215 3312 Planarity : 0.006 0.065 3719 Dihedral : 5.107 21.949 2912 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.16), residues: 2661 helix: -0.34 (0.12), residues: 1770 sheet: None (None), residues: 0 loop : -1.61 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 374 TYR 0.030 0.003 TYR O 440 PHE 0.045 0.003 PHE O 549 TRP 0.043 0.002 TRP P 209 HIS 0.029 0.002 HIS O 476 Details of bonding type rmsd covalent geometry : bond 0.00753 (20917) covalent geometry : angle 0.84096 (28402) hydrogen bonds : bond 0.04821 ( 1139) hydrogen bonds : angle 5.36331 ( 3393) *********************** 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 192 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.810 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 1 MET cc_start: 0.6200 (tpt) cc_final: 0.5936 (tpp) REVERT: J 7 TYR cc_start: 0.7195 (m-10) cc_final: 0.6976 (m-10) REVERT: J 220 MET cc_start: 0.8459 (ptp) cc_final: 0.8089 (ptp) REVERT: J 438 ASP cc_start: 0.8762 (m-30) cc_final: 0.8533 (m-30) REVERT: A 16 LYS cc_start: 0.8399 (mmpt) cc_final: 0.7536 (pttm) REVERT: A 51 ILE cc_start: 0.9482 (mm) cc_final: 0.9161 (pt) REVERT: A 251 GLU cc_start: 0.8690 (pt0) cc_final: 0.8427 (pt0) REVERT: A 280 MET cc_start: 0.9291 (mmp) cc_final: 0.8895 (tpp) REVERT: A 420 GLN cc_start: 0.9235 (mp10) cc_final: 0.8944 (mp10) REVERT: A 443 ASN cc_start: 0.8857 (m110) cc_final: 0.8619 (m-40) REVERT: A 503 THR cc_start: 0.9300 (p) cc_final: 0.8979 (p) REVERT: A 561 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7663 (tm-30) REVERT: A 587 ILE cc_start: 0.9065 (mt) cc_final: 0.8853 (mm) REVERT: O 14 GLU cc_start: 0.8645 (pt0) cc_final: 0.8115 (tm-30) REVERT: O 56 ASN cc_start: 0.8790 (m-40) cc_final: 0.8567 (m-40) REVERT: O 133 ARG cc_start: 0.8520 (tpm170) cc_final: 0.8267 (tpm170) REVERT: O 472 TYR cc_start: 0.7746 (t80) cc_final: 0.7539 (m-80) REVERT: O 476 HIS cc_start: 0.8511 (m-70) cc_final: 0.7982 (m90) REVERT: P 280 MET cc_start: 0.6535 (tpp) cc_final: 0.6318 (tpp) REVERT: P 360 PHE cc_start: 0.7375 (m-80) cc_final: 0.6963 (m-80) REVERT: P 367 TRP cc_start: 0.8089 (m100) cc_final: 0.7756 (m100) REVERT: P 445 TYR cc_start: 0.8234 (m-80) cc_final: 0.7792 (m-80) REVERT: P 447 PHE cc_start: 0.8662 (t80) cc_final: 0.8356 (t80) REVERT: P 464 GLN cc_start: 0.5684 (mm110) cc_final: 0.5308 (mm110) REVERT: P 468 ASN cc_start: 0.8891 (p0) cc_final: 0.8178 (t0) REVERT: Q 119 PHE cc_start: 0.8004 (t80) cc_final: 0.7686 (t80) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1383 time to fit residues: 41.8187 Evaluate side-chains 143 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 228 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 18 optimal weight: 0.3980 chunk 44 optimal weight: 0.5980 chunk 190 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 237 optimal weight: 0.5980 chunk 231 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 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 218 HIS ** 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 553 HIS ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 155 ASN O 380 ASN O 397 HIS O 443 ASN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 HIS ** P 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 120 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.099620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.079592 restraints weight = 121912.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.076657 restraints weight = 92446.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.077359 restraints weight = 82375.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.077277 restraints weight = 65881.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.077379 restraints weight = 66196.234| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20917 Z= 0.137 Angle : 0.605 11.901 28402 Z= 0.319 Chirality : 0.040 0.209 3312 Planarity : 0.004 0.055 3719 Dihedral : 4.747 21.530 2912 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.16), residues: 2661 helix: 0.18 (0.12), residues: 1790 sheet: None (None), residues: 0 loop : -1.50 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 350 TYR 0.022 0.001 TYR P 445 PHE 0.042 0.002 PHE A 284 TRP 0.013 0.001 TRP P 209 HIS 0.010 0.001 HIS J 325 Details of bonding type rmsd covalent geometry : bond 0.00294 (20917) covalent geometry : angle 0.60526 (28402) hydrogen bonds : bond 0.03954 ( 1139) hydrogen bonds : angle 4.68217 ( 3393) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.896 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 438 ASP cc_start: 0.8676 (m-30) cc_final: 0.8463 (m-30) REVERT: A 251 GLU cc_start: 0.8597 (pt0) cc_final: 0.8365 (pt0) REVERT: A 561 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7152 (tm-30) REVERT: O 14 GLU cc_start: 0.8620 (pt0) cc_final: 0.7858 (tm-30) REVERT: O 56 ASN cc_start: 0.8843 (m-40) cc_final: 0.8619 (m-40) REVERT: O 133 ARG cc_start: 0.8655 (tpm170) cc_final: 0.8396 (tpm170) REVERT: P 360 PHE cc_start: 0.7210 (m-80) cc_final: 0.6622 (m-80) REVERT: P 367 TRP cc_start: 0.7768 (m100) cc_final: 0.7382 (m100) REVERT: P 445 TYR cc_start: 0.8039 (m-80) cc_final: 0.7629 (m-80) REVERT: P 468 ASN cc_start: 0.9093 (p0) cc_final: 0.8339 (t0) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1446 time to fit residues: 50.7602 Evaluate side-chains 148 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 15 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 141 optimal weight: 0.0170 chunk 107 optimal weight: 0.6980 chunk 194 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 204 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 439 ASN ** O 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 553 HIS ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.098095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.067683 restraints weight = 112754.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.069490 restraints weight = 61906.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.070588 restraints weight = 40804.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.071298 restraints weight = 30555.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.071798 restraints weight = 25092.423| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20917 Z= 0.133 Angle : 0.598 10.145 28402 Z= 0.314 Chirality : 0.040 0.174 3312 Planarity : 0.004 0.055 3719 Dihedral : 4.586 23.323 2912 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.16), residues: 2661 helix: 0.40 (0.12), residues: 1790 sheet: None (None), residues: 0 loop : -1.44 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 210 TYR 0.042 0.001 TYR O 472 PHE 0.025 0.002 PHE O 549 TRP 0.008 0.001 TRP O 209 HIS 0.009 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00286 (20917) covalent geometry : angle 0.59793 (28402) hydrogen bonds : bond 0.03701 ( 1139) hydrogen bonds : angle 4.57690 ( 3393) *********************** 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 204 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.776 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: A 251 GLU cc_start: 0.8643 (pt0) cc_final: 0.8361 (pt0) REVERT: A 280 MET cc_start: 0.8793 (tpp) cc_final: 0.8449 (tpp) REVERT: A 326 MET cc_start: 0.8652 (mmm) cc_final: 0.8328 (mmm) REVERT: A 384 ASP cc_start: 0.8348 (m-30) cc_final: 0.8146 (m-30) REVERT: A 395 MET cc_start: 0.8011 (ppp) cc_final: 0.7606 (ppp) REVERT: A 420 GLN cc_start: 0.9133 (mp10) cc_final: 0.8825 (mp10) REVERT: A 443 ASN cc_start: 0.8718 (m-40) cc_final: 0.8502 (m110) REVERT: A 470 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8691 (tp-100) REVERT: A 503 THR cc_start: 0.9053 (p) cc_final: 0.8689 (p) REVERT: A 561 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7414 (tm-30) REVERT: O 14 GLU cc_start: 0.8447 (pt0) cc_final: 0.8077 (tm-30) REVERT: O 56 ASN cc_start: 0.8755 (m-40) cc_final: 0.8535 (m110) REVERT: P 326 MET cc_start: 0.8911 (ptt) cc_final: 0.8672 (ppp) REVERT: P 367 TRP cc_start: 0.7860 (m100) cc_final: 0.7425 (m100) REVERT: P 445 TYR cc_start: 0.8360 (m-80) cc_final: 0.7938 (m-10) REVERT: Q 80 LEU cc_start: 0.7171 (tp) cc_final: 0.6902 (tp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1389 time to fit residues: 45.5580 Evaluate side-chains 152 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 11 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 74 optimal weight: 0.0670 chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 175 optimal weight: 10.0000 chunk 256 optimal weight: 20.0000 chunk 257 optimal weight: 40.0000 overall best weight: 1.4122 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.096848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.065872 restraints weight = 111982.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.067795 restraints weight = 59400.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.068960 restraints weight = 38040.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.069659 restraints weight = 28392.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.070015 restraints weight = 23457.514| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20917 Z= 0.175 Angle : 0.634 9.463 28402 Z= 0.333 Chirality : 0.041 0.175 3312 Planarity : 0.004 0.056 3719 Dihedral : 4.566 22.429 2912 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.16), residues: 2661 helix: 0.40 (0.12), residues: 1794 sheet: None (None), residues: 0 loop : -1.44 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 133 TYR 0.042 0.002 TYR P 354 PHE 0.026 0.002 PHE J 284 TRP 0.008 0.001 TRP J 367 HIS 0.007 0.001 HIS J 369 Details of bonding type rmsd covalent geometry : bond 0.00378 (20917) covalent geometry : angle 0.63441 (28402) hydrogen bonds : bond 0.03736 ( 1139) hydrogen bonds : angle 4.66618 ( 3393) *********************** 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 209 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.774 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 280 MET cc_start: 0.8872 (tmm) cc_final: 0.8656 (tpp) REVERT: J 438 ASP cc_start: 0.8665 (m-30) cc_final: 0.8459 (m-30) REVERT: A 213 ILE cc_start: 0.8721 (tt) cc_final: 0.8515 (mt) REVERT: A 251 GLU cc_start: 0.8714 (pt0) cc_final: 0.8410 (pt0) REVERT: A 280 MET cc_start: 0.8840 (tpp) cc_final: 0.8337 (tpt) REVERT: A 326 MET cc_start: 0.8666 (mmm) cc_final: 0.8372 (mmm) REVERT: A 420 GLN cc_start: 0.9115 (mp10) cc_final: 0.8883 (mp10) REVERT: A 443 ASN cc_start: 0.8787 (m-40) cc_final: 0.8570 (m110) REVERT: A 503 THR cc_start: 0.9313 (p) cc_final: 0.8979 (p) REVERT: A 561 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7518 (tm-30) REVERT: O 14 GLU cc_start: 0.8424 (pt0) cc_final: 0.8076 (tm-30) REVERT: O 56 ASN cc_start: 0.8731 (m-40) cc_final: 0.8510 (m110) REVERT: O 196 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7563 (pt0) REVERT: O 218 HIS cc_start: 0.8304 (m-70) cc_final: 0.8070 (t70) REVERT: O 472 TYR cc_start: 0.7764 (t80) cc_final: 0.7381 (m-80) REVERT: P 220 MET cc_start: 0.5203 (mmt) cc_final: 0.4561 (mmt) REVERT: P 274 HIS cc_start: 0.9023 (m90) cc_final: 0.8705 (m90) REVERT: P 367 TRP cc_start: 0.7681 (m100) cc_final: 0.7311 (m100) REVERT: P 384 ASP cc_start: 0.8014 (m-30) cc_final: 0.7418 (m-30) REVERT: P 445 TYR cc_start: 0.8419 (m-80) cc_final: 0.7987 (m-10) REVERT: Q 80 LEU cc_start: 0.7265 (tp) cc_final: 0.6950 (tp) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1373 time to fit residues: 46.5277 Evaluate side-chains 155 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 210 optimal weight: 0.0870 chunk 216 optimal weight: 0.8980 chunk 115 optimal weight: 0.4980 chunk 258 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN A 502 HIS ** A 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 553 HIS ** P 56 ASN ** 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 143 ASN ** P 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 102 GLN ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.098401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.067523 restraints weight = 113260.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.069459 restraints weight = 60102.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.070667 restraints weight = 38985.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.071392 restraints weight = 28877.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.071888 restraints weight = 23752.543| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4160 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= 0.130 Angle : 0.601 8.160 28402 Z= 0.315 Chirality : 0.040 0.228 3312 Planarity : 0.004 0.054 3719 Dihedral : 4.507 22.452 2912 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 2661 helix: 0.54 (0.12), residues: 1801 sheet: None (None), residues: 0 loop : -1.39 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 305 TYR 0.033 0.001 TYR O 472 PHE 0.050 0.002 PHE O 549 TRP 0.014 0.001 TRP A 367 HIS 0.014 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00283 (20917) covalent geometry : angle 0.60062 (28402) hydrogen bonds : bond 0.03575 ( 1139) hydrogen bonds : angle 4.48508 ( 3393) *********************** 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 218 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.812 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 438 ASP cc_start: 0.8638 (m-30) cc_final: 0.8435 (m-30) REVERT: A 251 GLU cc_start: 0.8660 (pt0) cc_final: 0.8415 (pt0) REVERT: A 280 MET cc_start: 0.8762 (tpp) cc_final: 0.8396 (tpp) REVERT: A 420 GLN cc_start: 0.9129 (mp10) cc_final: 0.8885 (mp10) REVERT: A 443 ASN cc_start: 0.8765 (m-40) cc_final: 0.8554 (m110) REVERT: A 503 THR cc_start: 0.9192 (p) cc_final: 0.8918 (p) REVERT: A 561 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7458 (tm-30) REVERT: O 14 GLU cc_start: 0.8282 (pt0) cc_final: 0.7998 (tm-30) REVERT: O 56 ASN cc_start: 0.8675 (m-40) cc_final: 0.8462 (m110) REVERT: O 196 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7586 (pt0) REVERT: O 422 MET cc_start: 0.7197 (mmt) cc_final: 0.6945 (mmm) REVERT: O 472 TYR cc_start: 0.7710 (t80) cc_final: 0.7336 (m-80) REVERT: P 220 MET cc_start: 0.5157 (mmt) cc_final: 0.4574 (mmt) REVERT: P 367 TRP cc_start: 0.7636 (m100) cc_final: 0.7354 (m100) REVERT: P 437 MET cc_start: 0.7702 (tpt) cc_final: 0.6320 (mtm) REVERT: P 445 TYR cc_start: 0.8426 (m-80) cc_final: 0.8039 (m-10) REVERT: P 465 CYS cc_start: 0.8494 (t) cc_final: 0.8223 (m) REVERT: Q 80 LEU cc_start: 0.7202 (tp) cc_final: 0.6972 (tp) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1378 time to fit residues: 48.9977 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 : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 40 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 222 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 139 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 439 ASN ** O 476 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** ** P 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.097912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.069068 restraints weight = 113227.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.070486 restraints weight = 69390.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.070331 restraints weight = 45259.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.070575 restraints weight = 44115.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.070625 restraints weight = 40440.677| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4295 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= 0.150 Angle : 0.636 10.885 28402 Z= 0.332 Chirality : 0.041 0.203 3312 Planarity : 0.004 0.055 3719 Dihedral : 4.528 22.138 2912 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 2661 helix: 0.55 (0.12), residues: 1800 sheet: None (None), residues: 0 loop : -1.41 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 46 TYR 0.036 0.002 TYR P 354 PHE 0.055 0.002 PHE O 549 TRP 0.067 0.002 TRP P 209 HIS 0.013 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00330 (20917) covalent geometry : angle 0.63609 (28402) hydrogen bonds : bond 0.03560 ( 1139) hydrogen bonds : angle 4.56130 ( 3393) *********************** 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 209 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 438 ASP cc_start: 0.8670 (m-30) cc_final: 0.8436 (m-30) REVERT: A 251 GLU cc_start: 0.8684 (pt0) cc_final: 0.8381 (pt0) REVERT: A 384 ASP cc_start: 0.8239 (m-30) cc_final: 0.8033 (m-30) REVERT: A 422 MET cc_start: 0.8771 (ppp) cc_final: 0.8569 (ppp) REVERT: A 503 THR cc_start: 0.9201 (p) cc_final: 0.8894 (p) REVERT: A 561 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7362 (tm-30) REVERT: O 14 GLU cc_start: 0.8390 (pt0) cc_final: 0.7920 (tm-30) REVERT: O 56 ASN cc_start: 0.8724 (m-40) cc_final: 0.8489 (m110) REVERT: O 196 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7612 (pt0) REVERT: O 218 HIS cc_start: 0.8162 (m-70) cc_final: 0.7868 (t-90) REVERT: O 422 MET cc_start: 0.7326 (mmt) cc_final: 0.7044 (mmm) REVERT: O 472 TYR cc_start: 0.7820 (t80) cc_final: 0.7475 (m-80) REVERT: P 210 ARG cc_start: 0.8888 (mmm-85) cc_final: 0.8585 (mmm160) REVERT: P 220 MET cc_start: 0.5466 (mmt) cc_final: 0.5183 (mmt) REVERT: P 274 HIS cc_start: 0.9118 (m90) cc_final: 0.8750 (m90) REVERT: P 280 MET cc_start: 0.6743 (tpt) cc_final: 0.6491 (tpp) REVERT: P 367 TRP cc_start: 0.7686 (m100) cc_final: 0.7402 (m100) REVERT: P 437 MET cc_start: 0.7641 (tpt) cc_final: 0.6505 (mtm) REVERT: P 445 TYR cc_start: 0.8523 (m-80) cc_final: 0.8162 (m-10) REVERT: P 465 CYS cc_start: 0.8691 (t) cc_final: 0.8349 (m) REVERT: Q 80 LEU cc_start: 0.7287 (tp) cc_final: 0.7061 (tp) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1395 time to fit residues: 47.5383 Evaluate side-chains 149 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 199 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 190 optimal weight: 20.0000 chunk 229 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 476 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 ** P 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 397 HIS ** P 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.097007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.066051 restraints weight = 110743.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.067908 restraints weight = 59619.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.069048 restraints weight = 38725.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.069766 restraints weight = 29015.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.070112 restraints weight = 23931.334| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20917 Z= 0.164 Angle : 0.645 15.743 28402 Z= 0.335 Chirality : 0.041 0.199 3312 Planarity : 0.004 0.056 3719 Dihedral : 4.546 21.999 2912 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.16), residues: 2661 helix: 0.54 (0.12), residues: 1806 sheet: None (None), residues: 0 loop : -1.44 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 171 TYR 0.032 0.001 TYR O 472 PHE 0.049 0.002 PHE O 549 TRP 0.046 0.002 TRP P 209 HIS 0.013 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00361 (20917) covalent geometry : angle 0.64513 (28402) hydrogen bonds : bond 0.03570 ( 1139) hydrogen bonds : angle 4.56955 ( 3393) ********************** 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 198 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.827 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: J 438 ASP cc_start: 0.8659 (m-30) cc_final: 0.8447 (m-30) REVERT: A 251 GLU cc_start: 0.8713 (pt0) cc_final: 0.8430 (pt0) REVERT: A 503 THR cc_start: 0.9261 (p) cc_final: 0.8962 (p) REVERT: A 561 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7534 (tm-30) REVERT: O 14 GLU cc_start: 0.8292 (pt0) cc_final: 0.7981 (tm-30) REVERT: O 56 ASN cc_start: 0.8668 (m-40) cc_final: 0.8432 (m110) REVERT: O 196 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7607 (pt0) REVERT: O 218 HIS cc_start: 0.8291 (m-70) cc_final: 0.8016 (t-90) REVERT: O 422 MET cc_start: 0.7334 (mmt) cc_final: 0.7057 (mmm) REVERT: O 472 TYR cc_start: 0.7858 (t80) cc_final: 0.7595 (m-80) REVERT: P 210 ARG cc_start: 0.8726 (mmm-85) cc_final: 0.8423 (mmm160) REVERT: P 220 MET cc_start: 0.5270 (mmt) cc_final: 0.4940 (mmt) REVERT: P 274 HIS cc_start: 0.9053 (m90) cc_final: 0.8689 (m90) REVERT: P 280 MET cc_start: 0.6771 (tpt) cc_final: 0.6532 (tpt) REVERT: P 326 MET cc_start: 0.8388 (ppp) cc_final: 0.8144 (ppp) REVERT: P 367 TRP cc_start: 0.7491 (m100) cc_final: 0.7273 (m100) REVERT: P 437 MET cc_start: 0.7705 (tpt) cc_final: 0.6407 (mtm) REVERT: P 445 TYR cc_start: 0.8565 (m-80) cc_final: 0.8198 (m-10) REVERT: P 465 CYS cc_start: 0.8521 (t) cc_final: 0.8257 (m) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1365 time to fit residues: 44.2028 Evaluate side-chains 145 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 191 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 237 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN B 92 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 553 HIS ** P 58 HIS ** 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 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.097728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.067284 restraints weight = 112308.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.068808 restraints weight = 62213.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.069892 restraints weight = 40976.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.070648 restraints weight = 30647.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.070966 restraints weight = 25211.032| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4522 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= 0.140 Angle : 0.634 12.774 28402 Z= 0.328 Chirality : 0.041 0.238 3312 Planarity : 0.004 0.055 3719 Dihedral : 4.530 22.239 2912 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 2661 helix: 0.54 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.41 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG J 332 TYR 0.032 0.001 TYR O 472 PHE 0.050 0.002 PHE O 549 TRP 0.039 0.001 TRP P 209 HIS 0.012 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00308 (20917) covalent geometry : angle 0.63402 (28402) hydrogen bonds : bond 0.03516 ( 1139) hydrogen bonds : angle 4.53077 ( 3393) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4932.24 seconds wall clock time: 86 minutes 5.09 seconds (5165.09 seconds total)