Starting phenix.real_space_refine on Mon Aug 25 21:45:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yl9_33215/08_2025/7yl9_33215.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yl9_33215/08_2025/7yl9_33215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yl9_33215/08_2025/7yl9_33215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yl9_33215/08_2025/7yl9_33215.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yl9_33215/08_2025/7yl9_33215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yl9_33215/08_2025/7yl9_33215.map" } resolution = 4.7 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= 0.003 sd= 0.037 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 56 5.16 5 C 19442 2.51 5 N 5424 2.21 5 O 6193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31115 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 4466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4466 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 15, 'TRANS': 565} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 42 Chain: "I" Number of atoms: 4480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4480 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 15, 'TRANS': 565} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 24 Chain: "J" Number of atoms: 4487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4487 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 15, 'TRANS': 565} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 3, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "K" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4403 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 15, 'TRANS': 565} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 7, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "L" Number of atoms: 4454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4454 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 565} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 4, 'ASP:plan': 1, 'ARG:plan': 2, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "M" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4426 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 15, 'TRANS': 565} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 5, 'TYR:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 83 Chain: "N" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4399 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 15, 'TRANS': 565} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 7, 'TYR:plan': 3, 'ASP:plan': 1, 'ARG:plan': 6, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 92 Time building chain proxies: 6.74, per 1000 atoms: 0.22 Number of scatterers: 31115 At special positions: 0 Unit cell: (152.72, 152.72, 153.64, 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 56 16.00 O 6193 8.00 N 5424 7.00 C 19442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 175 " distance=2.02 Simple disulfide: pdb=" SG CYS H 472 " - pdb=" SG CYS H 486 " distance=2.03 Simple disulfide: pdb=" SG CYS H 512 " - pdb=" SG CYS H 524 " distance=2.03 Simple disulfide: pdb=" SG CYS I 157 " - pdb=" SG CYS I 175 " distance=2.03 Simple disulfide: pdb=" SG CYS I 472 " - pdb=" SG CYS I 486 " distance=2.03 Simple disulfide: pdb=" SG CYS I 512 " - pdb=" SG CYS I 524 " distance=2.03 Simple disulfide: pdb=" SG CYS J 157 " - pdb=" SG CYS J 175 " distance=2.03 Simple disulfide: pdb=" SG CYS J 472 " - pdb=" SG CYS J 486 " distance=2.03 Simple disulfide: pdb=" SG CYS J 512 " - pdb=" SG CYS J 524 " distance=2.03 Simple disulfide: pdb=" SG CYS K 157 " - pdb=" SG CYS K 175 " distance=2.03 Simple disulfide: pdb=" SG CYS K 472 " - pdb=" SG CYS K 486 " distance=2.03 Simple disulfide: pdb=" SG CYS K 512 " - pdb=" SG CYS K 524 " distance=2.03 Simple disulfide: pdb=" SG CYS L 157 " - pdb=" SG CYS L 175 " distance=2.03 Simple disulfide: pdb=" SG CYS L 472 " - pdb=" SG CYS L 486 " distance=2.03 Simple disulfide: pdb=" SG CYS L 512 " - pdb=" SG CYS L 524 " distance=2.03 Simple disulfide: pdb=" SG CYS M 157 " - pdb=" SG CYS M 175 " distance=2.03 Simple disulfide: pdb=" SG CYS M 472 " - pdb=" SG CYS M 486 " distance=2.03 Simple disulfide: pdb=" SG CYS M 512 " - pdb=" SG CYS M 524 " distance=2.03 Simple disulfide: pdb=" SG CYS N 157 " - pdb=" SG CYS N 175 " distance=2.03 Simple disulfide: pdb=" SG CYS N 472 " - pdb=" SG CYS N 486 " distance=2.03 Simple disulfide: pdb=" SG CYS N 512 " - pdb=" SG CYS N 524 " distance=2.01 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: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7532 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 98 sheets defined 5.3% alpha, 46.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'H' and resid 153 through 157 removed outlier: 3.847A pdb=" N CYS H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 153 through 157' Processing helix chain 'H' and resid 349 through 354 Processing helix chain 'H' and resid 374 through 379 removed outlier: 3.687A pdb=" N TYR H 378 " --> pdb=" O SER H 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 457 removed outlier: 3.501A pdb=" N GLY H 457 " --> pdb=" O VAL H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 490 through 493 Processing helix chain 'H' and resid 527 through 530 Processing helix chain 'I' and resid 153 through 156 Processing helix chain 'I' and resid 350 through 354 Processing helix chain 'I' and resid 374 through 378 Processing helix chain 'I' and resid 452 through 457 removed outlier: 4.012A pdb=" N GLY I 457 " --> pdb=" O VAL I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 490 through 493 Processing helix chain 'I' and resid 527 through 531 Processing helix chain 'I' and resid 622 through 626 removed outlier: 4.017A pdb=" N LEU I 626 " --> pdb=" O SER I 623 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 156 Processing helix chain 'J' and resid 349 through 354 removed outlier: 3.721A pdb=" N LEU J 354 " --> pdb=" O GLU J 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 379 removed outlier: 3.814A pdb=" N TYR J 378 " --> pdb=" O SER J 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 457 removed outlier: 3.749A pdb=" N GLY J 457 " --> pdb=" O VAL J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 490 through 493 Processing helix chain 'J' and resid 527 through 530 Processing helix chain 'K' and resid 349 through 354 Processing helix chain 'K' and resid 374 through 379 removed outlier: 3.921A pdb=" N TYR K 378 " --> pdb=" O SER K 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 452 through 457 removed outlier: 3.790A pdb=" N GLY K 457 " --> pdb=" O VAL K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 490 through 493 Processing helix chain 'K' and resid 527 through 531 Processing helix chain 'K' and resid 622 through 626 removed outlier: 3.662A pdb=" N LEU K 626 " --> pdb=" O SER K 623 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 156 Processing helix chain 'L' and resid 350 through 354 Processing helix chain 'L' and resid 374 through 379 removed outlier: 3.827A pdb=" N TYR L 378 " --> pdb=" O SER L 374 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 457 removed outlier: 3.518A pdb=" N GLY L 457 " --> pdb=" O VAL L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 490 through 493 Processing helix chain 'L' and resid 527 through 530 Processing helix chain 'M' and resid 153 through 157 Processing helix chain 'M' and resid 349 through 354 removed outlier: 3.588A pdb=" N LEU M 354 " --> pdb=" O GLU M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 379 removed outlier: 3.832A pdb=" N TYR M 378 " --> pdb=" O SER M 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 452 through 456 Processing helix chain 'M' and resid 490 through 493 Processing helix chain 'M' and resid 527 through 531 Processing helix chain 'N' and resid 154 through 156 No H-bonds generated for 'chain 'N' and resid 154 through 156' Processing helix chain 'N' and resid 349 through 354 removed outlier: 3.584A pdb=" N LEU N 354 " --> pdb=" O GLU N 351 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 379 removed outlier: 3.918A pdb=" N TYR N 378 " --> pdb=" O SER N 374 " (cutoff:3.500A) Processing helix chain 'N' and resid 452 through 456 Processing helix chain 'N' and resid 490 through 494 Processing helix chain 'N' and resid 527 through 530 Processing sheet with id=AA1, first strand: chain 'H' and resid 142 through 151 removed outlier: 6.623A pdb=" N ASP H 386 " --> pdb=" O THR H 270 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR H 270 " --> pdb=" O ASP H 386 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE H 388 " --> pdb=" O LEU H 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 142 through 151 Processing sheet with id=AA3, first strand: chain 'H' and resid 158 through 160 Processing sheet with id=AA4, first strand: chain 'H' and resid 228 through 231 removed outlier: 6.947A pdb=" N ALA H 416 " --> pdb=" O PHE H 242 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLU H 244 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASN H 414 " --> pdb=" O GLU H 244 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY H 415 " --> pdb=" O HIS H 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 326 through 332 removed outlier: 8.428A pdb=" N GLN H 252 " --> pdb=" O ARG H 344 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA H 251 " --> pdb=" O ARG H 410 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG H 410 " --> pdb=" O ALA H 251 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP H 253 " --> pdb=" O ASN H 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 279 through 298 removed outlier: 6.797A pdb=" N LYS H 279 " --> pdb=" O ASN H 322 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN H 322 " --> pdb=" O LYS H 279 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN H 315 " --> pdb=" O PHE N 288 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE N 288 " --> pdb=" O GLN H 315 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG H 317 " --> pdb=" O SER N 286 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER N 286 " --> pdb=" O ARG H 317 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU N 284 " --> pdb=" O LEU H 319 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR H 321 " --> pdb=" O ARG N 282 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LYS N 279 " --> pdb=" O ASN N 322 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ASN N 322 " --> pdb=" O LYS N 279 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA N 309 " --> pdb=" O GLY M 294 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS L 279 " --> pdb=" O ASN L 322 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN L 322 " --> pdb=" O LYS L 279 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN L 315 " --> pdb=" O PHE K 288 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE K 288 " --> pdb=" O GLN L 315 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG L 317 " --> pdb=" O SER K 286 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER K 286 " --> pdb=" O ARG L 317 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS K 279 " --> pdb=" O ASN K 322 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN K 322 " --> pdb=" O LYS K 279 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR K 321 " --> pdb=" O ARG J 282 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG J 282 " --> pdb=" O TYR K 321 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR J 323 " --> pdb=" O PHE I 280 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS I 279 " --> pdb=" O ASN I 322 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ASN I 322 " --> pdb=" O LYS I 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 464 through 465 removed outlier: 3.595A pdb=" N ILE H 574 " --> pdb=" O GLN H 464 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 472 through 475 Processing sheet with id=AA9, first strand: chain 'H' and resid 495 through 497 Processing sheet with id=AB1, first strand: chain 'H' and resid 511 through 512 Processing sheet with id=AB2, first strand: chain 'H' and resid 532 through 534 Processing sheet with id=AB3, first strand: chain 'H' and resid 560 through 562 Processing sheet with id=AB4, first strand: chain 'H' and resid 590 through 591 Processing sheet with id=AB5, first strand: chain 'H' and resid 616 through 620 Processing sheet with id=AB6, first strand: chain 'H' and resid 671 through 675 removed outlier: 5.418A pdb=" N GLN H 657 " --> pdb=" O PHE H 652 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE H 652 " --> pdb=" O GLN H 657 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU H 659 " --> pdb=" O GLY H 650 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY H 650 " --> pdb=" O LEU H 659 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP H 651 " --> pdb=" O ASN H 682 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASN H 682 " --> pdb=" O ASP H 651 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 142 through 151 removed outlier: 6.623A pdb=" N ASP I 386 " --> pdb=" O THR I 270 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR I 270 " --> pdb=" O ASP I 386 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE I 388 " --> pdb=" O LEU I 268 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 142 through 151 Processing sheet with id=AB9, first strand: chain 'I' and resid 158 through 160 Processing sheet with id=AC1, first strand: chain 'I' and resid 228 through 232 removed outlier: 6.738A pdb=" N TYR I 241 " --> pdb=" O LYS I 418 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS I 418 " --> pdb=" O TYR I 241 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG I 243 " --> pdb=" O ALA I 416 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE I 412 " --> pdb=" O THR I 247 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA I 249 " --> pdb=" O ARG I 410 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG I 410 " --> pdb=" O ALA I 249 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA I 251 " --> pdb=" O ASN I 408 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASN I 408 " --> pdb=" O ALA I 251 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASP I 253 " --> pdb=" O SER I 406 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N SER I 406 " --> pdb=" O ASP I 253 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG I 255 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP I 404 " --> pdb=" O ARG I 255 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL I 257 " --> pdb=" O ILE I 402 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE I 402 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN I 259 " --> pdb=" O ASP I 400 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASP I 400 " --> pdb=" O ASN I 259 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 326 through 334 removed outlier: 3.557A pdb=" N ARG I 327 " --> pdb=" O ASN I 343 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN I 343 " --> pdb=" O ARG I 327 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA I 337 " --> pdb=" O LYS I 333 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N GLN I 252 " --> pdb=" O ARG I 344 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR I 241 " --> pdb=" O LYS I 418 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS I 418 " --> pdb=" O TYR I 241 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG I 243 " --> pdb=" O ALA I 416 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE I 412 " --> pdb=" O THR I 247 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA I 249 " --> pdb=" O ARG I 410 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG I 410 " --> pdb=" O ALA I 249 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA I 251 " --> pdb=" O ASN I 408 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASN I 408 " --> pdb=" O ALA I 251 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASP I 253 " --> pdb=" O SER I 406 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N SER I 406 " --> pdb=" O ASP I 253 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG I 255 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP I 404 " --> pdb=" O ARG I 255 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL I 257 " --> pdb=" O ILE I 402 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE I 402 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN I 259 " --> pdb=" O ASP I 400 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASP I 400 " --> pdb=" O ASN I 259 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 464 through 465 Processing sheet with id=AC4, first strand: chain 'I' and resid 472 through 475 Processing sheet with id=AC5, first strand: chain 'I' and resid 495 through 497 Processing sheet with id=AC6, first strand: chain 'I' and resid 511 through 512 removed outlier: 3.551A pdb=" N CYS I 512 " --> pdb=" O GLN I 522 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN I 522 " --> pdb=" O CYS I 512 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 533 through 534 Processing sheet with id=AC8, first strand: chain 'I' and resid 559 through 562 Processing sheet with id=AC9, first strand: chain 'I' and resid 590 through 591 Processing sheet with id=AD1, first strand: chain 'I' and resid 627 through 628 removed outlier: 6.546A pdb=" N ARG I 611 " --> pdb=" O ASP I 617 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU I 619 " --> pdb=" O TYR I 609 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR I 609 " --> pdb=" O LEU I 619 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 671 through 675 removed outlier: 5.629A pdb=" N GLN I 657 " --> pdb=" O PHE I 652 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE I 652 " --> pdb=" O GLN I 657 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU I 659 " --> pdb=" O GLY I 650 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY I 650 " --> pdb=" O LEU I 659 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP I 651 " --> pdb=" O ASN I 682 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN I 682 " --> pdb=" O ASP I 651 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 142 through 151 removed outlier: 6.721A pdb=" N ASP J 386 " --> pdb=" O THR J 270 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR J 270 " --> pdb=" O ASP J 386 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE J 388 " --> pdb=" O LEU J 268 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 142 through 151 Processing sheet with id=AD5, first strand: chain 'J' and resid 158 through 160 Processing sheet with id=AD6, first strand: chain 'J' and resid 228 through 231 removed outlier: 6.726A pdb=" N ALA J 416 " --> pdb=" O PHE J 242 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLU J 244 " --> pdb=" O ASN J 414 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASN J 414 " --> pdb=" O GLU J 244 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 326 through 334 removed outlier: 6.482A pdb=" N ALA J 337 " --> pdb=" O LYS J 333 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLN J 252 " --> pdb=" O ARG J 344 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG J 410 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASN J 408 " --> pdb=" O GLN J 252 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TYR J 254 " --> pdb=" O SER J 406 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER J 406 " --> pdb=" O TYR J 254 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE J 256 " --> pdb=" O ASP J 404 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP J 404 " --> pdb=" O PHE J 256 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE J 258 " --> pdb=" O ILE J 402 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE J 402 " --> pdb=" O PHE J 258 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA J 260 " --> pdb=" O ASP J 400 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP J 400 " --> pdb=" O ALA J 260 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 464 through 465 Processing sheet with id=AD9, first strand: chain 'J' and resid 472 through 475 Processing sheet with id=AE1, first strand: chain 'J' and resid 495 through 497 Processing sheet with id=AE2, first strand: chain 'J' and resid 511 through 512 Processing sheet with id=AE3, first strand: chain 'J' and resid 532 through 534 Processing sheet with id=AE4, first strand: chain 'J' and resid 560 through 562 Processing sheet with id=AE5, first strand: chain 'J' and resid 590 through 591 removed outlier: 3.942A pdb=" N LEU J 590 " --> pdb=" O VAL J 711 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 627 through 628 Processing sheet with id=AE7, first strand: chain 'J' and resid 672 through 675 removed outlier: 5.453A pdb=" N GLN J 657 " --> pdb=" O PHE J 652 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE J 652 " --> pdb=" O GLN J 657 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU J 659 " --> pdb=" O GLY J 650 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY J 650 " --> pdb=" O LEU J 659 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP J 651 " --> pdb=" O ASN J 682 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN J 682 " --> pdb=" O ASP J 651 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 142 through 151 removed outlier: 6.514A pdb=" N ASP K 386 " --> pdb=" O THR K 270 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR K 270 " --> pdb=" O ASP K 386 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE K 388 " --> pdb=" O LEU K 268 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 142 through 151 Processing sheet with id=AF1, first strand: chain 'K' and resid 158 through 160 Processing sheet with id=AF2, first strand: chain 'K' and resid 228 through 232 removed outlier: 6.634A pdb=" N ALA K 416 " --> pdb=" O PHE K 242 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLU K 244 " --> pdb=" O ASN K 414 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASN K 414 " --> pdb=" O GLU K 244 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS K 426 " --> pdb=" O HIS K 419 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 328 through 334 removed outlier: 6.319A pdb=" N ALA K 337 " --> pdb=" O LYS K 333 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ALA K 251 " --> pdb=" O ARG K 410 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG K 410 " --> pdb=" O ALA K 251 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP K 253 " --> pdb=" O ASN K 408 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 464 through 465 Processing sheet with id=AF5, first strand: chain 'K' and resid 472 through 475 Processing sheet with id=AF6, first strand: chain 'K' and resid 495 through 497 removed outlier: 5.907A pdb=" N LEU K 511 " --> pdb=" O SER K 505 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 533 through 534 Processing sheet with id=AF8, first strand: chain 'K' and resid 559 through 562 Processing sheet with id=AF9, first strand: chain 'K' and resid 596 through 601 Processing sheet with id=AG1, first strand: chain 'K' and resid 627 through 628 Processing sheet with id=AG2, first strand: chain 'K' and resid 671 through 675 removed outlier: 5.125A pdb=" N LEU K 659 " --> pdb=" O GLY K 650 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY K 650 " --> pdb=" O LEU K 659 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP K 651 " --> pdb=" O ASN K 682 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN K 682 " --> pdb=" O ASP K 651 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 142 through 151 removed outlier: 6.900A pdb=" N ASP L 386 " --> pdb=" O THR L 270 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR L 270 " --> pdb=" O ASP L 386 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE L 388 " --> pdb=" O LEU L 268 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 142 through 151 Processing sheet with id=AG5, first strand: chain 'L' and resid 158 through 160 Processing sheet with id=AG6, first strand: chain 'L' and resid 228 through 231 removed outlier: 6.626A pdb=" N TYR L 241 " --> pdb=" O LYS L 418 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LYS L 418 " --> pdb=" O TYR L 241 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG L 243 " --> pdb=" O ALA L 416 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN L 414 " --> pdb=" O TRP L 245 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR L 247 " --> pdb=" O ILE L 412 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE L 412 " --> pdb=" O THR L 247 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA L 249 " --> pdb=" O ARG L 410 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ARG L 410 " --> pdb=" O ALA L 249 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA L 251 " --> pdb=" O ASN L 408 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN L 408 " --> pdb=" O ALA L 251 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASP L 253 " --> pdb=" O SER L 406 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER L 406 " --> pdb=" O ASP L 253 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG L 255 " --> pdb=" O ASP L 404 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP L 404 " --> pdb=" O ARG L 255 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL L 257 " --> pdb=" O ILE L 402 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE L 402 " --> pdb=" O VAL L 257 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN L 259 " --> pdb=" O ASP L 400 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP L 400 " --> pdb=" O ASN L 259 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 326 through 334 removed outlier: 6.276A pdb=" N ALA L 337 " --> pdb=" O LYS L 333 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLN L 252 " --> pdb=" O ARG L 344 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR L 241 " --> pdb=" O LYS L 418 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LYS L 418 " --> pdb=" O TYR L 241 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG L 243 " --> pdb=" O ALA L 416 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN L 414 " --> pdb=" O TRP L 245 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR L 247 " --> pdb=" O ILE L 412 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE L 412 " --> pdb=" O THR L 247 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA L 249 " --> pdb=" O ARG L 410 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ARG L 410 " --> pdb=" O ALA L 249 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA L 251 " --> pdb=" O ASN L 408 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN L 408 " --> pdb=" O ALA L 251 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASP L 253 " --> pdb=" O SER L 406 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER L 406 " --> pdb=" O ASP L 253 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG L 255 " --> pdb=" O ASP L 404 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP L 404 " --> pdb=" O ARG L 255 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL L 257 " --> pdb=" O ILE L 402 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE L 402 " --> pdb=" O VAL L 257 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN L 259 " --> pdb=" O ASP L 400 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP L 400 " --> pdb=" O ASN L 259 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 464 through 465 Processing sheet with id=AG9, first strand: chain 'L' and resid 472 through 475 Processing sheet with id=AH1, first strand: chain 'L' and resid 495 through 496 Processing sheet with id=AH2, first strand: chain 'L' and resid 511 through 512 removed outlier: 3.547A pdb=" N GLN L 522 " --> pdb=" O CYS L 512 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 532 through 534 Processing sheet with id=AH4, first strand: chain 'L' and resid 559 through 562 Processing sheet with id=AH5, first strand: chain 'L' and resid 589 through 590 Processing sheet with id=AH6, first strand: chain 'L' and resid 616 through 620 Processing sheet with id=AH7, first strand: chain 'L' and resid 671 through 675 removed outlier: 5.912A pdb=" N GLN L 657 " --> pdb=" O PHE L 652 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE L 652 " --> pdb=" O GLN L 657 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU L 659 " --> pdb=" O GLY L 650 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY L 650 " --> pdb=" O LEU L 659 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N LYS L 643 " --> pdb=" O ASP L 689 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP L 689 " --> pdb=" O LYS L 643 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE L 645 " --> pdb=" O ARG L 687 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG L 687 " --> pdb=" O ILE L 645 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ALA L 647 " --> pdb=" O GLU L 685 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU L 685 " --> pdb=" O ALA L 647 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N SER L 649 " --> pdb=" O ALA L 683 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA L 683 " --> pdb=" O SER L 649 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 142 through 151 removed outlier: 6.601A pdb=" N ASP M 386 " --> pdb=" O THR M 270 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR M 270 " --> pdb=" O ASP M 386 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE M 388 " --> pdb=" O LEU M 268 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'M' and resid 142 through 151 Processing sheet with id=AI1, first strand: chain 'M' and resid 158 through 160 Processing sheet with id=AI2, first strand: chain 'M' and resid 228 through 232 removed outlier: 6.230A pdb=" N ASP M 248 " --> pdb=" O ILE M 412 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE M 412 " --> pdb=" O ASP M 248 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG M 410 " --> pdb=" O ILE M 250 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 398 through 412 current: chain 'M' and resid 425 through 431 Processing sheet with id=AI3, first strand: chain 'M' and resid 326 through 334 removed outlier: 6.376A pdb=" N ALA M 337 " --> pdb=" O LYS M 333 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP M 253 " --> pdb=" O ASN M 408 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG M 410 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE M 412 " --> pdb=" O ASP M 248 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP M 248 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 464 through 465 removed outlier: 3.576A pdb=" N ILE M 574 " --> pdb=" O GLN M 464 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 472 through 475 Processing sheet with id=AI6, first strand: chain 'M' and resid 495 through 497 Processing sheet with id=AI7, first strand: chain 'M' and resid 511 through 512 removed outlier: 3.631A pdb=" N CYS M 512 " --> pdb=" O GLN M 522 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN M 522 " --> pdb=" O CYS M 512 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'M' and resid 533 through 534 Processing sheet with id=AI9, first strand: chain 'M' and resid 559 through 562 Processing sheet with id=AJ1, first strand: chain 'M' and resid 590 through 591 Processing sheet with id=AJ2, first strand: chain 'M' and resid 627 through 628 Processing sheet with id=AJ3, first strand: chain 'M' and resid 671 through 675 removed outlier: 5.154A pdb=" N LEU M 659 " --> pdb=" O GLY M 650 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLY M 650 " --> pdb=" O LEU M 659 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N LYS M 643 " --> pdb=" O ASP M 689 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASP M 689 " --> pdb=" O LYS M 643 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE M 645 " --> pdb=" O ARG M 687 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG M 687 " --> pdb=" O ILE M 645 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA M 647 " --> pdb=" O GLU M 685 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU M 685 " --> pdb=" O ALA M 647 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER M 649 " --> pdb=" O ALA M 683 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA M 683 " --> pdb=" O SER M 649 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'N' and resid 142 through 151 removed outlier: 6.638A pdb=" N ASP N 386 " --> pdb=" O THR N 270 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR N 270 " --> pdb=" O ASP N 386 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE N 388 " --> pdb=" O LEU N 268 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'N' and resid 142 through 151 Processing sheet with id=AJ6, first strand: chain 'N' and resid 158 through 160 Processing sheet with id=AJ7, first strand: chain 'N' and resid 228 through 231 removed outlier: 6.752A pdb=" N ALA N 416 " --> pdb=" O PHE N 242 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU N 244 " --> pdb=" O ASN N 414 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN N 414 " --> pdb=" O GLU N 244 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER N 246 " --> pdb=" O ILE N 412 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE N 412 " --> pdb=" O SER N 246 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'N' and resid 328 through 334 removed outlier: 6.468A pdb=" N ALA N 337 " --> pdb=" O LYS N 333 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP N 253 " --> pdb=" O ASN N 408 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'N' and resid 464 through 465 removed outlier: 3.702A pdb=" N ILE N 574 " --> pdb=" O GLN N 464 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'N' and resid 472 through 475 Processing sheet with id=AK2, first strand: chain 'N' and resid 496 through 497 Processing sheet with id=AK3, first strand: chain 'N' and resid 511 through 512 Processing sheet with id=AK4, first strand: chain 'N' and resid 532 through 534 Processing sheet with id=AK5, first strand: chain 'N' and resid 559 through 562 Processing sheet with id=AK6, first strand: chain 'N' and resid 590 through 591 removed outlier: 6.100A pdb=" N TRP N 702 " --> pdb=" O LYS N 709 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL N 711 " --> pdb=" O LYS N 700 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS N 700 " --> pdb=" O VAL N 711 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N PHE N 713 " --> pdb=" O GLN N 698 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLN N 698 " --> pdb=" O PHE N 713 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'N' and resid 627 through 628 Processing sheet with id=AK8, first strand: chain 'N' and resid 671 through 674 removed outlier: 4.198A pdb=" N ASP N 651 " --> pdb=" O ASN N 682 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN N 682 " --> pdb=" O ASP N 651 " (cutoff:3.500A) 1267 hydrogen bonds defined for protein. 3282 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: 8.09 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10114 1.33 - 1.45: 5633 1.45 - 1.57: 15966 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 31783 Sorted by residual: bond pdb=" N PHE L 271 " pdb=" CA PHE L 271 " ideal model delta sigma weight residual 1.462 1.492 -0.030 8.50e-03 1.38e+04 1.28e+01 bond pdb=" N ASP J 704 " pdb=" CA ASP J 704 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.09e-02 8.42e+03 9.82e+00 bond pdb=" N VAL K 273 " pdb=" CA VAL K 273 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.32e+00 bond pdb=" N PHE I 271 " pdb=" CA PHE I 271 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.01e+00 bond pdb=" N ILE H 701 " pdb=" CA ILE H 701 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.70e+00 ... (remaining 31778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 43097 3.40 - 6.79: 218 6.79 - 10.19: 7 10.19 - 13.59: 2 13.59 - 16.98: 2 Bond angle restraints: 43326 Sorted by residual: angle pdb=" N PRO L 272 " pdb=" CA PRO L 272 " pdb=" C PRO L 272 " ideal model delta sigma weight residual 112.47 95.49 16.98 2.06e+00 2.36e-01 6.80e+01 angle pdb=" N PRO M 272 " pdb=" CA PRO M 272 " pdb=" C PRO M 272 " ideal model delta sigma weight residual 112.47 95.53 16.94 2.06e+00 2.36e-01 6.77e+01 angle pdb=" N PRO N 272 " pdb=" CA PRO N 272 " pdb=" C PRO N 272 " ideal model delta sigma weight residual 112.47 100.78 11.69 2.06e+00 2.36e-01 3.22e+01 angle pdb=" N PRO H 272 " pdb=" CA PRO H 272 " pdb=" C PRO H 272 " ideal model delta sigma weight residual 112.47 101.21 11.26 2.06e+00 2.36e-01 2.99e+01 angle pdb=" C ASP J 704 " pdb=" N ASP J 705 " pdb=" CA ASP J 705 " ideal model delta sigma weight residual 122.56 114.25 8.31 1.72e+00 3.38e-01 2.33e+01 ... (remaining 43321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 17046 17.97 - 35.94: 1291 35.94 - 53.91: 165 53.91 - 71.88: 60 71.88 - 89.85: 35 Dihedral angle restraints: 18597 sinusoidal: 6811 harmonic: 11786 Sorted by residual: dihedral pdb=" CB CYS H 512 " pdb=" SG CYS H 512 " pdb=" SG CYS H 524 " pdb=" CB CYS H 524 " ideal model delta sinusoidal sigma weight residual -86.00 -3.15 -82.85 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS M 157 " pdb=" SG CYS M 157 " pdb=" SG CYS M 175 " pdb=" CB CYS M 175 " ideal model delta sinusoidal sigma weight residual 93.00 170.44 -77.44 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS K 512 " pdb=" SG CYS K 512 " pdb=" SG CYS K 524 " pdb=" CB CYS K 524 " ideal model delta sinusoidal sigma weight residual -86.00 -160.75 74.75 1 1.00e+01 1.00e-02 7.07e+01 ... (remaining 18594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3458 0.048 - 0.095: 1024 0.095 - 0.143: 247 0.143 - 0.191: 50 0.191 - 0.238: 9 Chirality restraints: 4788 Sorted by residual: chirality pdb=" CA LYS N 166 " pdb=" N LYS N 166 " pdb=" C LYS N 166 " pdb=" CB LYS N 166 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA PRO M 272 " pdb=" N PRO M 272 " pdb=" C PRO M 272 " pdb=" CB PRO M 272 " both_signs ideal model delta sigma weight residual False 2.72 2.95 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO L 272 " pdb=" N PRO L 272 " pdb=" C PRO L 272 " pdb=" CB PRO L 272 " both_signs ideal model delta sigma weight residual False 2.72 2.94 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 4785 not shown) Planarity restraints: 5747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR L 270 " 0.022 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C THR L 270 " -0.074 2.00e-02 2.50e+03 pdb=" O THR L 270 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE L 271 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL N 382 " -0.046 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO N 383 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO N 383 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO N 383 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP M 702 " -0.013 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C TRP M 702 " 0.047 2.00e-02 2.50e+03 pdb=" O TRP M 702 " -0.018 2.00e-02 2.50e+03 pdb=" N SER M 703 " -0.016 2.00e-02 2.50e+03 ... (remaining 5744 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 6 2.10 - 2.80: 9632 2.80 - 3.50: 47233 3.50 - 4.20: 78048 4.20 - 4.90: 126384 Nonbonded interactions: 261303 Sorted by model distance: nonbonded pdb=" CD1 LEU H 268 " pdb=" CE LYS H 390 " model vdw 1.401 3.860 nonbonded pdb=" OD1 ASP I 704 " pdb=" N LEU I 707 " model vdw 1.947 3.120 nonbonded pdb=" O GLY K 655 " pdb=" NE2 GLN K 658 " model vdw 2.060 3.120 nonbonded pdb=" OD1 ASP I 704 " pdb=" O LEU I 707 " model vdw 2.062 3.040 nonbonded pdb=" O THR J 349 " pdb=" OG SER J 352 " model vdw 2.073 3.040 ... (remaining 261298 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 'H' and (resid 136 through 166 or (resid 167 through 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 212 or (resid 213 \ and (name N or name CA or name C or name O or name CB )) or resid 214 through 22 \ 4 or (resid 225 and (name N or name CA or name C or name O or name CB )) or resi \ d 226 through 234 or (resid 235 and (name N or name CA or name C or name O or na \ me CB )) or resid 236 or (resid 237 through 238 and (name N or name CA or name C \ or name O or name CB )) or resid 239 through 272 or (resid 273 through 274 and \ (name N or name CA or name C or name O or name CB )) or resid 275 through 296 or \ (resid 297 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 8 through 309 or (resid 310 through 311 and (name N or name CA or name C or name \ O or name CB )) or resid 312 through 313 or (resid 314 and (name N or name CA o \ r name C or name O or name CB )) or resid 315 through 326 or (resid 327 and (nam \ e N or name CA or name C or name O or name CB )) or resid 328 through 332 or (re \ sid 333 and (name N or name CA or name C or name O or name CB )) or resid 334 th \ rough 391 or (resid 392 through 393 and (name N or name CA or name C or name O o \ r name CB )) or resid 394 through 419 or (resid 420 and (name N or name CA or na \ me C or name O or name CB )) or resid 421 through 422 or (resid 423 and (name N \ or name CA or name C or name O or name CB )) or resid 424 through 427 or (resid \ 428 and (name N or name CA or name C or name O or name CB )) or resid 429 throug \ h 477 or (resid 478 and (name N or name CA or name C or name O or name CB )) or \ resid 479 through 509 or (resid 510 and (name N or name CA or name C or name O o \ r name CB )) or resid 511 through 554 or (resid 555 and (name N or name CA or na \ me C or name O or name CB )) or resid 556 through 584 or (resid 585 and (name N \ or name CA or name C or name O or name CB )) or resid 586 through 593 or (resid \ 594 and (name N or name CA or name C or name O or name CB )) or resid 595 throug \ h 597 or (resid 598 and (name N or name CA or name C or name O or name CB )) or \ resid 599 through 606 or (resid 607 and (name N or name CA or name C or name O o \ r name CB )) or resid 608 through 610 or (resid 611 through 612 and (name N or n \ ame CA or name C or name O or name CB )) or resid 613 through 633 or (resid 634 \ and (name N or name CA or name C or name O or name CB )) or resid 635 through 65 \ 2 or (resid 653 through 654 and (name N or name CA or name C or name O or name C \ B )) or resid 655 through 670 or (resid 671 through 672 and (name N or name CA o \ r name C or name O or name CB )) or resid 673 through 676 or (resid 677 through \ 679 and (name N or name CA or name C or name O or name CB )) or resid 680 throug \ h 701 or (resid 702 through 703 and (name N or name CA or name C or name O or na \ me CB )) or resid 704 or (resid 705 through 706 and (name N or name CA or name C \ or name O or name CB )) or resid 707 through 708 or (resid 709 and (name N or n \ ame CA or name C or name O or name CB )) or resid 710 through 716)) selection = (chain 'I' and (resid 136 through 165 or (resid 166 through 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 212 or (resid 213 \ and (name N or name CA or name C or name O or name CB )) or resid 214 through 22 \ 4 or (resid 225 and (name N or name CA or name C or name O or name CB )) or resi \ d 226 through 234 or (resid 235 and (name N or name CA or name C or name O or na \ me CB )) or resid 236 or (resid 237 through 238 and (name N or name CA or name C \ or name O or name CB )) or resid 239 through 273 or (resid 274 and (name N or n \ ame CA or name C or name O or name CB )) or resid 275 through 296 or (resid 297 \ and (name N or name CA or name C or name O or name CB )) or resid 298 through 30 \ 9 or (resid 310 through 311 and (name N or name CA or name C or name O or name C \ B )) or resid 312 through 326 or (resid 327 and (name N or name CA or name C or \ name O or name CB )) or resid 328 through 391 or (resid 392 through 393 and (nam \ e N or name CA or name C or name O or name CB )) or resid 394 through 419 or (re \ sid 420 and (name N or name CA or name C or name O or name CB )) or resid 421 or \ (resid 422 through 423 and (name N or name CA or name C or name O or name CB )) \ or resid 424 through 426 or (resid 427 through 428 and (name N or name CA or na \ me C or name O or name CB )) or resid 429 through 477 or (resid 478 and (name N \ or name CA or name C or name O or name CB )) or resid 479 through 584 or (resid \ 585 and (name N or name CA or name C or name O or name CB )) or resid 586 throug \ h 593 or (resid 594 and (name N or name CA or name C or name O or name CB )) or \ resid 595 through 597 or (resid 598 and (name N or name CA or name C or name O o \ r name CB )) or resid 599 through 600 or (resid 601 and (name N or name CA or na \ me C or name O or name CB )) or resid 602 through 603 or (resid 604 and (name N \ or name CA or name C or name O or name CB )) or resid 605 through 606 or (resid \ 607 and (name N or name CA or name C or name O or name CB )) or resid 608 throug \ h 610 or (resid 611 through 612 and (name N or name CA or name C or name O or na \ me CB )) or resid 613 through 633 or (resid 634 and (name N or name CA or name C \ or name O or name CB )) or resid 635 through 652 or (resid 653 through 654 and \ (name N or name CA or name C or name O or name CB )) or resid 655 through 666 or \ (resid 667 and (name N or name CA or name C or name O or name CB )) or resid 66 \ 8 through 670 or (resid 671 through 672 and (name N or name CA or name C or name \ O or name CB )) or resid 673 through 676 or (resid 677 through 679 and (name N \ or name CA or name C or name O or name CB )) or resid 680 through 686 or (resid \ 687 and (name N or name CA or name C or name O or name CB )) or resid 688 throug \ h 701 or (resid 702 through 703 and (name N or name CA or name C or name O or na \ me CB )) or resid 704 or (resid 705 through 706 and (name N or name CA or name C \ or name O or name CB )) or resid 707 through 708 or (resid 709 and (name N or n \ ame CA or name C or name O or name CB )) or resid 710 through 716)) selection = (chain 'J' and (resid 136 through 165 or (resid 166 through 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 175 or (resid 176 \ and (name N or name CA or name C or name O or name CB )) or resid 177 through 21 \ 2 or (resid 213 and (name N or name CA or name C or name O or name CB )) or resi \ d 214 through 234 or (resid 235 and (name N or name CA or name C or name O or na \ me CB )) or resid 236 or (resid 237 through 238 and (name N or name CA or name C \ or name O or name CB )) or resid 239 through 273 or (resid 274 and (name N or n \ ame CA or name C or name O or name CB )) or resid 275 through 296 or (resid 297 \ and (name N or name CA or name C or name O or name CB )) or resid 298 through 30 \ 9 or (resid 310 through 311 and (name N or name CA or name C or name O or name C \ B )) or resid 312 through 326 or (resid 327 and (name N or name CA or name C or \ name O or name CB )) or resid 328 through 332 or (resid 333 and (name N or name \ CA or name C or name O or name CB )) or resid 334 through 391 or (resid 392 thro \ ugh 393 and (name N or name CA or name C or name O or name CB )) or resid 394 th \ rough 419 or (resid 420 and (name N or name CA or name C or name O or name CB )) \ or resid 421 or (resid 422 through 423 and (name N or name CA or name C or name \ O or name CB )) or resid 424 through 426 or (resid 427 through 428 and (name N \ or name CA or name C or name O or name CB )) or resid 429 through 477 or (resid \ 478 and (name N or name CA or name C or name O or name CB )) or resid 479 throug \ h 509 or (resid 510 and (name N or name CA or name C or name O or name CB )) or \ resid 511 through 554 or (resid 555 and (name N or name CA or name C or name O o \ r name CB )) or resid 556 through 584 or (resid 585 and (name N or name CA or na \ me C or name O or name CB )) or resid 586 through 593 or (resid 594 and (name N \ or name CA or name C or name O or name CB )) or resid 595 through 597 or (resid \ 598 and (name N or name CA or name C or name O or name CB )) or resid 599 throug \ h 600 or (resid 601 and (name N or name CA or name C or name O or name CB )) or \ resid 602 through 606 or (resid 607 and (name N or name CA or name C or name O o \ r name CB )) or resid 608 through 610 or (resid 611 through 612 and (name N or n \ ame CA or name C or name O or name CB )) or resid 613 through 633 or (resid 634 \ and (name N or name CA or name C or name O or name CB )) or resid 635 through 65 \ 2 or (resid 653 through 654 and (name N or name CA or name C or name O or name C \ B )) or resid 655 through 666 or (resid 667 and (name N or name CA or name C or \ name O or name CB )) or resid 668 through 670 or (resid 671 through 672 and (nam \ e N or name CA or name C or name O or name CB )) or resid 673 through 676 or (re \ sid 677 through 679 and (name N or name CA or name C or name O or name CB )) or \ resid 680 through 686 or (resid 687 and (name N or name CA or name C or name O o \ r name CB )) or resid 688 through 701 or (resid 702 through 703 and (name N or n \ ame CA or name C or name O or name CB )) or resid 704 or (resid 705 through 706 \ and (name N or name CA or name C or name O or name CB )) or resid 707 through 70 \ 8 or (resid 709 and (name N or name CA or name C or name O or name CB )) or resi \ d 710 through 716)) selection = (chain 'K' and (resid 136 through 166 or (resid 167 through 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 212 or (resid 213 \ and (name N or name CA or name C or name O or name CB )) or resid 214 through 22 \ 4 or (resid 225 and (name N or name CA or name C or name O or name CB )) or resi \ d 226 through 234 or (resid 235 and (name N or name CA or name C or name O or na \ me CB )) or resid 236 or (resid 237 through 238 and (name N or name CA or name C \ or name O or name CB )) or resid 239 through 272 or (resid 273 through 274 and \ (name N or name CA or name C or name O or name CB )) or resid 275 through 309 or \ (resid 310 through 311 and (name N or name CA or name C or name O or name CB )) \ or resid 312 through 326 or (resid 327 and (name N or name CA or name C or name \ O or name CB )) or resid 328 through 332 or (resid 333 and (name N or name CA o \ r name C or name O or name CB )) or resid 334 through 391 or (resid 392 through \ 393 and (name N or name CA or name C or name O or name CB )) or resid 394 throug \ h 422 or (resid 423 and (name N or name CA or name C or name O or name CB )) or \ resid 424 through 426 or (resid 427 through 428 and (name N or name CA or name C \ or name O or name CB )) or resid 429 through 479 or (resid 480 and (name N or n \ ame CA or name C or name O or name CB )) or resid 481 through 509 or (resid 510 \ and (name N or name CA or name C or name O or name CB )) or resid 511 through 59 \ 7 or (resid 598 and (name N or name CA or name C or name O or name CB )) or resi \ d 599 through 606 or (resid 607 and (name N or name CA or name C or name O or na \ me CB )) or resid 608 through 653 or (resid 654 and (name N or name CA or name C \ or name O or name CB )) or resid 655 through 670 or (resid 671 through 672 and \ (name N or name CA or name C or name O or name CB )) or resid 673 through 676 or \ (resid 677 through 679 and (name N or name CA or name C or name O or name CB )) \ or resid 680 through 686 or (resid 687 and (name N or name CA or name C or name \ O or name CB )) or resid 688 through 701 or (resid 702 through 703 and (name N \ or name CA or name C or name O or name CB )) or resid 704 or (resid 705 through \ 706 and (name N or name CA or name C or name O or name CB )) or resid 707 throug \ h 716)) selection = (chain 'L' and (resid 136 through 165 or (resid 166 through 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 212 or (resid 213 \ and (name N or name CA or name C or name O or name CB )) or resid 214 through 23 \ 4 or (resid 235 and (name N or name CA or name C or name O or name CB )) or resi \ d 236 through 272 or (resid 273 through 274 and (name N or name CA or name C or \ name O or name CB )) or resid 275 through 296 or (resid 297 and (name N or name \ CA or name C or name O or name CB )) or resid 298 through 309 or (resid 310 thro \ ugh 311 and (name N or name CA or name C or name O or name CB )) or resid 312 th \ rough 313 or (resid 314 and (name N or name CA or name C or name O or name CB )) \ or resid 315 through 326 or (resid 327 and (name N or name CA or name C or name \ O or name CB )) or resid 328 through 332 or (resid 333 and (name N or name CA o \ r name C or name O or name CB )) or resid 334 through 391 or (resid 392 through \ 393 and (name N or name CA or name C or name O or name CB )) or resid 394 throug \ h 422 or (resid 423 and (name N or name CA or name C or name O or name CB )) or \ resid 424 through 426 or (resid 427 through 428 and (name N or name CA or name C \ or name O or name CB )) or resid 429 through 477 or (resid 478 and (name N or n \ ame CA or name C or name O or name CB )) or resid 479 through 509 or (resid 510 \ and (name N or name CA or name C or name O or name CB )) or resid 511 through 55 \ 4 or (resid 555 and (name N or name CA or name C or name O or name CB )) or resi \ d 556 through 584 or (resid 585 and (name N or name CA or name C or name O or na \ me CB )) or resid 586 through 593 or (resid 594 and (name N or name CA or name C \ or name O or name CB )) or resid 595 through 597 or (resid 598 and (name N or n \ ame CA or name C or name O or name CB )) or resid 599 through 600 or (resid 601 \ and (name N or name CA or name C or name O or name CB )) or resid 602 through 60 \ 6 or (resid 607 and (name N or name CA or name C or name O or name CB )) or resi \ d 608 through 610 or (resid 611 through 612 and (name N or name CA or name C or \ name O or name CB )) or resid 613 through 666 or (resid 667 and (name N or name \ CA or name C or name O or name CB )) or resid 668 through 670 or (resid 671 thro \ ugh 672 and (name N or name CA or name C or name O or name CB )) or resid 673 th \ rough 676 or (resid 677 through 679 and (name N or name CA or name C or name O o \ r name CB )) or resid 680 through 686 or (resid 687 and (name N or name CA or na \ me C or name O or name CB )) or resid 688 through 701 or (resid 702 through 703 \ and (name N or name CA or name C or name O or name CB )) or resid 704 or (resid \ 705 through 706 and (name N or name CA or name C or name O or name CB )) or resi \ d 707 through 708 or (resid 709 and (name N or name CA or name C or name O or na \ me CB )) or resid 710 through 716)) selection = (chain 'M' and (resid 136 through 165 or (resid 166 through 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 175 or (resid 176 \ and (name N or name CA or name C or name O or name CB )) or resid 177 through 22 \ 4 or (resid 225 and (name N or name CA or name C or name O or name CB )) or resi \ d 226 through 234 or (resid 235 and (name N or name CA or name C or name O or na \ me CB )) or resid 236 or (resid 237 through 238 and (name N or name CA or name C \ or name O or name CB )) or resid 239 through 272 or (resid 273 through 274 and \ (name N or name CA or name C or name O or name CB )) or resid 275 through 296 or \ (resid 297 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 8 through 326 or (resid 327 and (name N or name CA or name C or name O or name C \ B )) or resid 328 through 391 or (resid 392 through 393 and (name N or name CA o \ r name C or name O or name CB )) or resid 394 through 419 or (resid 420 and (nam \ e N or name CA or name C or name O or name CB )) or resid 421 or (resid 422 thro \ ugh 423 and (name N or name CA or name C or name O or name CB )) or resid 424 th \ rough 426 or (resid 427 through 428 and (name N or name CA or name C or name O o \ r name CB )) or resid 429 through 477 or (resid 478 and (name N or name CA or na \ me C or name O or name CB )) or resid 479 through 509 or (resid 510 and (name N \ or name CA or name C or name O or name CB )) or resid 511 through 584 or (resid \ 585 and (name N or name CA or name C or name O or name CB )) or resid 586 throug \ h 593 or (resid 594 and (name N or name CA or name C or name O or name CB )) or \ resid 595 through 597 or (resid 598 and (name N or name CA or name C or name O o \ r name CB )) or resid 599 through 600 or (resid 601 and (name N or name CA or na \ me C or name O or name CB )) or resid 602 through 606 or (resid 607 and (name N \ or name CA or name C or name O or name CB )) or resid 608 through 610 or (resid \ 611 through 612 and (name N or name CA or name C or name O or name CB )) or resi \ d 613 through 633 or (resid 634 and (name N or name CA or name C or name O or na \ me CB )) or resid 635 through 670 or (resid 671 through 672 and (name N or name \ CA or name C or name O or name CB )) or resid 673 through 676 or (resid 677 thro \ ugh 679 and (name N or name CA or name C or name O or name CB )) or resid 680 th \ rough 686 or (resid 687 and (name N or name CA or name C or name O or name CB )) \ or resid 688 through 702 or (resid 703 and (name N or name CA or name C or name \ O or name CB )) or resid 704 through 708 or (resid 709 and (name N or name CA o \ r name C or name O or name CB )) or resid 710 through 716)) selection = (chain 'N' and (resid 136 or (resid 137 and (name N or name CA or name C or name \ O or name CB )) or resid 138 through 167 or (resid 168 through 169 and (name N \ or name CA or name C or name O or name CB )) or resid 170 through 175 or (resid \ 176 and (name N or name CA or name C or name O or name CB )) or resid 177 throug \ h 212 or (resid 213 and (name N or name CA or name C or name O or name CB )) or \ resid 214 through 236 or (resid 237 through 238 and (name N or name CA or name C \ or name O or name CB )) or resid 239 through 272 or (resid 273 through 274 and \ (name N or name CA or name C or name O or name CB )) or resid 275 through 296 or \ (resid 297 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 8 through 309 or (resid 310 through 311 and (name N or name CA or name C or name \ O or name CB )) or resid 312 through 313 or (resid 314 and (name N or name CA o \ r name C or name O or name CB )) or resid 315 through 419 or (resid 420 and (nam \ e N or name CA or name C or name O or name CB )) or resid 421 through 426 or (re \ sid 427 through 428 and (name N or name CA or name C or name O or name CB )) or \ resid 429 through 554 or (resid 555 and (name N or name CA or name C or name O o \ r name CB )) or resid 556 through 593 or (resid 594 and (name N or name CA or na \ me C or name O or name CB )) or resid 595 through 603 or (resid 604 and (name N \ or name CA or name C or name O or name CB )) or resid 605 through 633 or (resid \ 634 and (name N or name CA or name C or name O or name CB )) or resid 635 throug \ h 686 or (resid 687 and (name N or name CA or name C or name O or name CB )) or \ resid 688 through 701 or (resid 702 through 703 and (name N or name CA or name C \ or name O or name CB )) or resid 704 or (resid 705 through 706 and (name N or n \ ame CA or name C or name O or name CB )) or resid 707 through 708 or (resid 709 \ and (name N or name CA or name C or name O or name CB )) or resid 710 through 71 \ 6)) } 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: 0.850 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: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 29.210 Find NCS groups from input model: 0.800 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: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 : 0.005 0.058 31804 Z= 0.268 Angle : 0.777 16.985 43368 Z= 0.465 Chirality : 0.049 0.238 4788 Planarity : 0.004 0.070 5747 Dihedral : 13.472 89.845 11002 Min Nonbonded Distance : 1.401 Molprobity Statistics. All-atom Clashscore : 29.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.79 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.95 (0.13), residues: 4053 helix: -2.85 (0.48), residues: 84 sheet: -0.80 (0.13), residues: 1484 loop : -1.58 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 243 TYR 0.025 0.002 TYR H 184 PHE 0.027 0.002 PHE H 652 TRP 0.042 0.002 TRP K 163 HIS 0.008 0.001 HIS L 221 Details of bonding type rmsd covalent geometry : bond 0.00486 (31783) covalent geometry : angle 0.77613 (43326) SS BOND : bond 0.00575 ( 21) SS BOND : angle 1.35331 ( 42) hydrogen bonds : bond 0.17667 ( 1190) hydrogen bonds : angle 9.05718 ( 3282) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 1.070 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: H 347 TYR cc_start: 0.9458 (m-80) cc_final: 0.8927 (m-80) REVERT: H 449 ASP cc_start: 0.7907 (t0) cc_final: 0.7516 (t0) REVERT: H 541 LEU cc_start: 0.9347 (tp) cc_final: 0.9145 (tp) REVERT: H 688 PHE cc_start: 0.7664 (t80) cc_final: 0.7301 (t80) REVERT: H 699 LEU cc_start: 0.8850 (tp) cc_final: 0.8528 (pp) REVERT: I 243 ARG cc_start: 0.9404 (mmp80) cc_final: 0.9128 (mmm160) REVERT: I 257 VAL cc_start: 0.9475 (t) cc_final: 0.9270 (t) REVERT: I 385 MET cc_start: 0.8261 (pmm) cc_final: 0.7998 (pmm) REVERT: I 594 GLN cc_start: 0.9383 (mp10) cc_final: 0.8888 (mp10) REVERT: J 253 ASP cc_start: 0.8796 (p0) cc_final: 0.8562 (p0) REVERT: J 312 SER cc_start: 0.9310 (t) cc_final: 0.8921 (p) REVERT: J 388 ILE cc_start: 0.9823 (mp) cc_final: 0.9615 (mp) REVERT: J 449 ASP cc_start: 0.8312 (t0) cc_final: 0.8039 (t0) REVERT: K 385 MET cc_start: 0.8037 (pmm) cc_final: 0.7707 (pmm) REVERT: K 597 MET cc_start: 0.8610 (tmm) cc_final: 0.8384 (tpt) REVERT: M 139 LEU cc_start: 0.9576 (tp) cc_final: 0.9249 (tt) REVERT: M 225 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8498 (tm-30) REVERT: M 253 ASP cc_start: 0.8903 (p0) cc_final: 0.8671 (p0) REVERT: N 371 ASN cc_start: 0.9445 (m110) cc_final: 0.9156 (m110) REVERT: N 385 MET cc_start: 0.8405 (pmm) cc_final: 0.8054 (pmm) outliers start: 0 outliers final: 0 residues processed: 556 average time/residue: 0.1514 time to fit residues: 141.7685 Evaluate side-chains 416 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 0.0170 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 overall best weight: 1.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 149 ASN H 266 GLN H 336 GLN H 430 HIS ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 657 GLN ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 252 GLN ** I 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 430 HIS J 470 ASN ** J 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 252 GLN K 322 ASN K 371 ASN L 230 GLN ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 530 GLN M 594 GLN N 331 ASN N 414 ASN ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 606 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.087880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.064363 restraints weight = 117035.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.066622 restraints weight = 68723.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.068144 restraints weight = 47282.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.069159 restraints weight = 36343.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.069817 restraints weight = 30359.171| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31804 Z= 0.130 Angle : 0.606 8.865 43368 Z= 0.333 Chirality : 0.046 0.203 4788 Planarity : 0.004 0.049 5747 Dihedral : 5.929 49.899 4463 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.12 % Allowed : 4.94 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.13), residues: 4053 helix: -3.19 (0.44), residues: 84 sheet: -0.15 (0.14), residues: 1323 loop : -1.40 (0.12), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 535 TYR 0.025 0.001 TYR L 254 PHE 0.025 0.002 PHE J 688 TRP 0.026 0.001 TRP I 163 HIS 0.009 0.001 HIS J 221 Details of bonding type rmsd covalent geometry : bond 0.00281 (31783) covalent geometry : angle 0.60609 (43326) SS BOND : bond 0.00216 ( 21) SS BOND : angle 0.86596 ( 42) hydrogen bonds : bond 0.04126 ( 1190) hydrogen bonds : angle 7.31559 ( 3282) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 578 time to evaluate : 0.894 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: H 280 PHE cc_start: 0.9279 (m-80) cc_final: 0.8721 (m-10) REVERT: H 319 LEU cc_start: 0.9324 (tt) cc_final: 0.9102 (tt) REVERT: H 328 ILE cc_start: 0.8994 (mt) cc_final: 0.8784 (mt) REVERT: H 347 TYR cc_start: 0.9343 (m-80) cc_final: 0.9134 (m-80) REVERT: H 449 ASP cc_start: 0.8137 (t0) cc_final: 0.7757 (t0) REVERT: H 532 TRP cc_start: 0.9047 (m100) cc_final: 0.8627 (m100) REVERT: H 541 LEU cc_start: 0.9320 (tp) cc_final: 0.9095 (tp) REVERT: H 688 PHE cc_start: 0.7599 (t80) cc_final: 0.7115 (t80) REVERT: H 699 LEU cc_start: 0.8871 (tp) cc_final: 0.8526 (pp) REVERT: I 385 MET cc_start: 0.8420 (pmm) cc_final: 0.8049 (pmm) REVERT: I 388 ILE cc_start: 0.9784 (mp) cc_final: 0.9257 (tp) REVERT: I 390 LYS cc_start: 0.9277 (tmtt) cc_final: 0.8924 (tptp) REVERT: I 399 THR cc_start: 0.9102 (m) cc_final: 0.8501 (m) REVERT: I 532 TRP cc_start: 0.9334 (m100) cc_final: 0.7998 (m100) REVERT: I 541 LEU cc_start: 0.9416 (tp) cc_final: 0.9087 (tp) REVERT: I 590 LEU cc_start: 0.8081 (pp) cc_final: 0.7784 (pp) REVERT: I 594 GLN cc_start: 0.9286 (mp10) cc_final: 0.8833 (mp10) REVERT: J 154 ASP cc_start: 0.9478 (m-30) cc_final: 0.8826 (t0) REVERT: J 163 TRP cc_start: 0.8362 (t-100) cc_final: 0.7652 (t-100) REVERT: J 230 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7760 (tp-100) REVERT: J 325 ASP cc_start: 0.8650 (t70) cc_final: 0.8446 (t70) REVERT: J 328 ILE cc_start: 0.9307 (mt) cc_final: 0.9086 (mt) REVERT: J 385 MET cc_start: 0.8633 (pmm) cc_final: 0.8381 (pmm) REVERT: J 449 ASP cc_start: 0.8427 (t0) cc_final: 0.8161 (t0) REVERT: J 658 GLN cc_start: 0.7977 (pm20) cc_final: 0.7220 (pm20) REVERT: K 183 ILE cc_start: 0.9493 (mm) cc_final: 0.9170 (tp) REVERT: K 188 LEU cc_start: 0.9557 (mm) cc_final: 0.9341 (mm) REVERT: K 319 LEU cc_start: 0.9476 (tt) cc_final: 0.9185 (tt) REVERT: K 334 ASN cc_start: 0.9301 (p0) cc_final: 0.8917 (p0) REVERT: K 347 TYR cc_start: 0.8926 (m-80) cc_final: 0.8497 (m-80) REVERT: K 376 LEU cc_start: 0.9791 (tp) cc_final: 0.9250 (tp) REVERT: K 385 MET cc_start: 0.8460 (pmm) cc_final: 0.8062 (pmm) REVERT: K 463 LEU cc_start: 0.9173 (mt) cc_final: 0.8931 (mt) REVERT: L 139 LEU cc_start: 0.9491 (tp) cc_final: 0.9263 (tp) REVERT: L 167 ASN cc_start: 0.9449 (p0) cc_final: 0.8830 (p0) REVERT: L 541 LEU cc_start: 0.9146 (tp) cc_final: 0.8874 (tp) REVERT: M 166 LYS cc_start: 0.8685 (mmtm) cc_final: 0.8484 (mmtm) REVERT: M 253 ASP cc_start: 0.9078 (p0) cc_final: 0.8714 (p0) REVERT: M 280 PHE cc_start: 0.9202 (m-80) cc_final: 0.8825 (m-10) REVERT: M 281 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8788 (tm-30) REVERT: M 331 ASN cc_start: 0.9186 (t0) cc_final: 0.8912 (t0) REVERT: M 599 GLN cc_start: 0.8936 (tt0) cc_final: 0.8628 (tt0) REVERT: N 340 PHE cc_start: 0.9252 (m-10) cc_final: 0.8893 (m-10) REVERT: N 347 TYR cc_start: 0.9239 (m-80) cc_final: 0.8965 (m-80) REVERT: N 371 ASN cc_start: 0.9458 (m110) cc_final: 0.9168 (m110) REVERT: N 385 MET cc_start: 0.8638 (pmm) cc_final: 0.8229 (pmm) REVERT: N 390 LYS cc_start: 0.9266 (tmtt) cc_final: 0.9010 (tmtt) REVERT: N 417 TYR cc_start: 0.6920 (t80) cc_final: 0.6694 (t80) REVERT: N 657 GLN cc_start: 0.9238 (pm20) cc_final: 0.8731 (pm20) outliers start: 4 outliers final: 0 residues processed: 581 average time/residue: 0.1554 time to fit residues: 151.4579 Evaluate side-chains 456 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 192 optimal weight: 8.9990 chunk 269 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 281 optimal weight: 30.0000 chunk 234 optimal weight: 10.0000 chunk 202 optimal weight: 40.0000 chunk 301 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 203 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 108 optimal weight: 40.0000 overall best weight: 7.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 430 HIS ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 427 GLN J 430 HIS ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 ASN K 657 GLN L 141 HIS ** L 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 427 GLN L 543 ASN ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 657 GLN ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.084150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.060768 restraints weight = 121501.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.062861 restraints weight = 71606.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.064297 restraints weight = 49686.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.065243 restraints weight = 38474.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.065791 restraints weight = 32401.720| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 31804 Z= 0.234 Angle : 0.638 7.940 43368 Z= 0.350 Chirality : 0.044 0.191 4788 Planarity : 0.004 0.051 5747 Dihedral : 6.020 48.656 4463 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.19 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.61 (0.13), residues: 4053 helix: -3.02 (0.47), residues: 84 sheet: -0.57 (0.13), residues: 1428 loop : -1.32 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 437 TYR 0.020 0.002 TYR M 592 PHE 0.020 0.002 PHE I 231 TRP 0.020 0.002 TRP I 163 HIS 0.009 0.002 HIS J 221 Details of bonding type rmsd covalent geometry : bond 0.00498 (31783) covalent geometry : angle 0.63659 (43326) SS BOND : bond 0.00270 ( 21) SS BOND : angle 1.40958 ( 42) hydrogen bonds : bond 0.04141 ( 1190) hydrogen bonds : angle 7.16516 ( 3282) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 319 LEU cc_start: 0.9428 (tt) cc_final: 0.9188 (tt) REVERT: H 328 ILE cc_start: 0.9116 (mt) cc_final: 0.8865 (mt) REVERT: H 449 ASP cc_start: 0.8125 (t0) cc_final: 0.7723 (t0) REVERT: H 688 PHE cc_start: 0.7767 (t80) cc_final: 0.7296 (t80) REVERT: H 699 LEU cc_start: 0.8982 (tp) cc_final: 0.8515 (pp) REVERT: H 713 PHE cc_start: 0.9447 (m-10) cc_final: 0.9175 (m-10) REVERT: I 188 LEU cc_start: 0.9552 (mm) cc_final: 0.9220 (mt) REVERT: I 340 PHE cc_start: 0.9280 (m-10) cc_final: 0.9057 (m-10) REVERT: I 385 MET cc_start: 0.8621 (pmm) cc_final: 0.8323 (pmm) REVERT: I 388 ILE cc_start: 0.9820 (mp) cc_final: 0.9344 (tp) REVERT: I 532 TRP cc_start: 0.9317 (m100) cc_final: 0.8508 (m100) REVERT: I 541 LEU cc_start: 0.9441 (tp) cc_final: 0.9096 (tp) REVERT: I 590 LEU cc_start: 0.7908 (pp) cc_final: 0.7681 (pp) REVERT: I 594 GLN cc_start: 0.9344 (mp10) cc_final: 0.9051 (mp10) REVERT: J 154 ASP cc_start: 0.9524 (m-30) cc_final: 0.8934 (t0) REVERT: J 163 TRP cc_start: 0.8382 (t-100) cc_final: 0.7812 (t-100) REVERT: J 211 LEU cc_start: 0.9403 (tp) cc_final: 0.9173 (tp) REVERT: J 253 ASP cc_start: 0.8930 (p0) cc_final: 0.8682 (p0) REVERT: J 326 TYR cc_start: 0.9116 (m-10) cc_final: 0.8814 (m-10) REVERT: J 328 ILE cc_start: 0.9307 (mt) cc_final: 0.9069 (mt) REVERT: J 347 TYR cc_start: 0.9685 (m-10) cc_final: 0.9471 (m-10) REVERT: J 385 MET cc_start: 0.8514 (pmm) cc_final: 0.8211 (pmm) REVERT: J 434 ASP cc_start: 0.7947 (p0) cc_final: 0.7632 (p0) REVERT: J 449 ASP cc_start: 0.8359 (t0) cc_final: 0.8126 (t0) REVERT: J 658 GLN cc_start: 0.7977 (pm20) cc_final: 0.7296 (pm20) REVERT: K 188 LEU cc_start: 0.9535 (mm) cc_final: 0.9273 (mm) REVERT: K 334 ASN cc_start: 0.9390 (p0) cc_final: 0.8912 (p0) REVERT: K 347 TYR cc_start: 0.9024 (m-80) cc_final: 0.8669 (m-80) REVERT: K 713 PHE cc_start: 0.9453 (m-80) cc_final: 0.9240 (m-80) REVERT: L 139 LEU cc_start: 0.9534 (tp) cc_final: 0.9312 (tp) REVERT: L 167 ASN cc_start: 0.9264 (p0) cc_final: 0.8778 (p0) REVERT: L 168 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9127 (mp0) REVERT: L 541 LEU cc_start: 0.9188 (tp) cc_final: 0.8960 (tp) REVERT: M 166 LYS cc_start: 0.8725 (mmtm) cc_final: 0.8490 (mmtm) REVERT: M 184 TYR cc_start: 0.9130 (m-10) cc_final: 0.8643 (m-10) REVERT: M 194 TYR cc_start: 0.9110 (t80) cc_final: 0.8790 (t80) REVERT: M 225 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8248 (tm-30) REVERT: M 253 ASP cc_start: 0.9096 (p0) cc_final: 0.8855 (p0) REVERT: M 599 GLN cc_start: 0.8999 (tt0) cc_final: 0.8797 (tt0) REVERT: M 714 ASP cc_start: 0.8610 (t70) cc_final: 0.8392 (t70) REVERT: N 371 ASN cc_start: 0.9486 (m110) cc_final: 0.9216 (m110) REVERT: N 417 TYR cc_start: 0.7282 (t80) cc_final: 0.7020 (t80) REVERT: N 657 GLN cc_start: 0.9248 (pm20) cc_final: 0.8655 (pm20) outliers start: 0 outliers final: 0 residues processed: 531 average time/residue: 0.1488 time to fit residues: 133.8755 Evaluate side-chains 414 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 2 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 chunk 326 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 290 optimal weight: 8.9990 chunk 381 optimal weight: 20.0000 chunk 221 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 657 GLN ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 275 ASN ** I 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 ASN ** K 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 252 GLN ** L 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 582 ASN M 682 ASN ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.082673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.059559 restraints weight = 122015.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.061606 restraints weight = 72108.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.062992 restraints weight = 50161.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.063828 restraints weight = 39019.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.064415 restraints weight = 33189.065| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 31804 Z= 0.271 Angle : 0.675 8.680 43368 Z= 0.368 Chirality : 0.045 0.194 4788 Planarity : 0.004 0.052 5747 Dihedral : 6.199 51.495 4463 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.88 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.13), residues: 4053 helix: -2.94 (0.49), residues: 84 sheet: -0.70 (0.14), residues: 1365 loop : -1.33 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 611 TYR 0.020 0.002 TYR M 592 PHE 0.024 0.002 PHE H 652 TRP 0.025 0.002 TRP M 342 HIS 0.010 0.002 HIS J 221 Details of bonding type rmsd covalent geometry : bond 0.00570 (31783) covalent geometry : angle 0.67362 (43326) SS BOND : bond 0.00280 ( 21) SS BOND : angle 1.35821 ( 42) hydrogen bonds : bond 0.04178 ( 1190) hydrogen bonds : angle 7.21920 ( 3282) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 1.082 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: H 328 ILE cc_start: 0.9200 (mt) cc_final: 0.8992 (mt) REVERT: H 417 TYR cc_start: 0.8874 (t80) cc_final: 0.8587 (t80) REVERT: H 449 ASP cc_start: 0.8134 (t0) cc_final: 0.7703 (t0) REVERT: H 465 LEU cc_start: 0.9513 (mp) cc_final: 0.9141 (mt) REVERT: H 543 ASN cc_start: 0.9017 (t0) cc_final: 0.8623 (p0) REVERT: H 688 PHE cc_start: 0.7836 (t80) cc_final: 0.7425 (t80) REVERT: H 699 LEU cc_start: 0.8983 (tp) cc_final: 0.8493 (pp) REVERT: H 713 PHE cc_start: 0.9435 (m-10) cc_final: 0.9172 (m-10) REVERT: I 188 LEU cc_start: 0.9468 (mm) cc_final: 0.9153 (mt) REVERT: I 284 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8133 (mm-30) REVERT: I 347 TYR cc_start: 0.9233 (m-80) cc_final: 0.8893 (m-80) REVERT: I 385 MET cc_start: 0.8615 (pmm) cc_final: 0.8337 (pmm) REVERT: I 388 ILE cc_start: 0.9840 (mp) cc_final: 0.9408 (tp) REVERT: I 532 TRP cc_start: 0.9374 (m100) cc_final: 0.8643 (m100) REVERT: I 541 LEU cc_start: 0.9504 (tp) cc_final: 0.9187 (tp) REVERT: I 594 GLN cc_start: 0.9342 (mp10) cc_final: 0.9068 (mp10) REVERT: J 154 ASP cc_start: 0.9545 (m-30) cc_final: 0.8952 (t0) REVERT: J 211 LEU cc_start: 0.9326 (tp) cc_final: 0.9115 (tp) REVERT: J 253 ASP cc_start: 0.8881 (p0) cc_final: 0.8647 (p0) REVERT: J 328 ILE cc_start: 0.9381 (mt) cc_final: 0.9114 (mt) REVERT: J 385 MET cc_start: 0.8572 (pmm) cc_final: 0.8311 (pmm) REVERT: J 658 GLN cc_start: 0.8045 (pm20) cc_final: 0.7384 (pm20) REVERT: K 334 ASN cc_start: 0.9395 (p0) cc_final: 0.8966 (p0) REVERT: K 347 TYR cc_start: 0.9005 (m-80) cc_final: 0.8702 (m-80) REVERT: L 139 LEU cc_start: 0.9556 (tp) cc_final: 0.9346 (tp) REVERT: L 168 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9122 (mp0) REVERT: L 185 ARG cc_start: 0.8712 (ttt180) cc_final: 0.8471 (ttt90) REVERT: M 166 LYS cc_start: 0.8741 (mmtm) cc_final: 0.8485 (mmtm) REVERT: M 184 TYR cc_start: 0.9184 (m-10) cc_final: 0.8698 (m-10) REVERT: M 225 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8242 (tm-30) REVERT: M 253 ASP cc_start: 0.9120 (p0) cc_final: 0.8760 (p0) REVERT: N 356 ARG cc_start: 0.9148 (ttm110) cc_final: 0.8779 (ttm110) REVERT: N 371 ASN cc_start: 0.9511 (m110) cc_final: 0.9204 (m110) REVERT: N 385 MET cc_start: 0.8553 (pmm) cc_final: 0.8228 (pmm) REVERT: N 417 TYR cc_start: 0.7412 (t80) cc_final: 0.7085 (t80) REVERT: N 657 GLN cc_start: 0.9324 (pm20) cc_final: 0.8884 (pm20) outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 0.1520 time to fit residues: 131.1271 Evaluate side-chains 401 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 108 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 365 optimal weight: 7.9990 chunk 50 optimal weight: 50.0000 chunk 188 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 295 optimal weight: 7.9990 chunk 265 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 371 ASN ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 275 ASN ** I 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 419 HIS J 230 GLN ** J 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 ASN ** K 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 712 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 = 0.3342 r_free = 0.3342 target = 0.083718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.060537 restraints weight = 121671.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.062658 restraints weight = 71470.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.064085 restraints weight = 49435.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.064945 restraints weight = 38269.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.065621 restraints weight = 32409.725| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 31804 Z= 0.225 Angle : 0.638 10.329 43368 Z= 0.347 Chirality : 0.045 0.258 4788 Planarity : 0.004 0.074 5747 Dihedral : 6.068 50.834 4463 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.22 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.68 (0.13), residues: 4053 helix: -2.95 (0.49), residues: 84 sheet: -0.67 (0.13), residues: 1400 loop : -1.33 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 172 TYR 0.023 0.002 TYR K 184 PHE 0.024 0.002 PHE H 652 TRP 0.022 0.002 TRP N 318 HIS 0.010 0.001 HIS M 221 Details of bonding type rmsd covalent geometry : bond 0.00479 (31783) covalent geometry : angle 0.63545 (43326) SS BOND : bond 0.00283 ( 21) SS BOND : angle 1.98423 ( 42) hydrogen bonds : bond 0.03918 ( 1190) hydrogen bonds : angle 7.07637 ( 3282) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 517 time to evaluate : 0.886 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: H 328 ILE cc_start: 0.8974 (mt) cc_final: 0.8740 (mt) REVERT: H 334 ASN cc_start: 0.9391 (p0) cc_final: 0.9109 (p0) REVERT: H 417 TYR cc_start: 0.8818 (t80) cc_final: 0.8525 (t80) REVERT: H 449 ASP cc_start: 0.8097 (t0) cc_final: 0.7646 (t0) REVERT: H 465 LEU cc_start: 0.9489 (mp) cc_final: 0.9090 (mt) REVERT: H 688 PHE cc_start: 0.7849 (t80) cc_final: 0.7412 (t80) REVERT: H 699 LEU cc_start: 0.8954 (tp) cc_final: 0.8445 (pp) REVERT: H 713 PHE cc_start: 0.9436 (m-10) cc_final: 0.9168 (m-10) REVERT: I 188 LEU cc_start: 0.9487 (mm) cc_final: 0.9163 (mt) REVERT: I 243 ARG cc_start: 0.9269 (mmp-170) cc_final: 0.9050 (mmm160) REVERT: I 259 ASN cc_start: 0.9281 (t0) cc_final: 0.8726 (t0) REVERT: I 347 TYR cc_start: 0.9237 (m-80) cc_final: 0.8853 (m-80) REVERT: I 385 MET cc_start: 0.8584 (pmm) cc_final: 0.8268 (pmm) REVERT: I 388 ILE cc_start: 0.9846 (mp) cc_final: 0.9366 (tp) REVERT: I 532 TRP cc_start: 0.9358 (m100) cc_final: 0.8686 (m100) REVERT: I 594 GLN cc_start: 0.9310 (mp10) cc_final: 0.9033 (mp10) REVERT: J 154 ASP cc_start: 0.9537 (m-30) cc_final: 0.8925 (t0) REVERT: J 163 TRP cc_start: 0.8650 (t-100) cc_final: 0.7921 (t-100) REVERT: J 253 ASP cc_start: 0.8833 (p0) cc_final: 0.8623 (p0) REVERT: J 328 ILE cc_start: 0.9334 (mt) cc_final: 0.9052 (mt) REVERT: J 385 MET cc_start: 0.8498 (pmm) cc_final: 0.8265 (pmm) REVERT: J 449 ASP cc_start: 0.8368 (t0) cc_final: 0.8115 (t0) REVERT: J 657 GLN cc_start: 0.7843 (tt0) cc_final: 0.7617 (tt0) REVERT: J 658 GLN cc_start: 0.7994 (pm20) cc_final: 0.7415 (pm20) REVERT: K 257 VAL cc_start: 0.9522 (t) cc_final: 0.9251 (t) REVERT: K 278 GLU cc_start: 0.8943 (mp0) cc_final: 0.8706 (mp0) REVERT: K 334 ASN cc_start: 0.9426 (p0) cc_final: 0.8977 (p0) REVERT: K 385 MET cc_start: 0.8275 (pmm) cc_final: 0.8035 (pmm) REVERT: K 713 PHE cc_start: 0.9602 (m-10) cc_final: 0.9252 (m-80) REVERT: L 139 LEU cc_start: 0.9557 (tp) cc_final: 0.9337 (tp) REVERT: L 167 ASN cc_start: 0.9244 (p0) cc_final: 0.8807 (p0) REVERT: L 168 GLU cc_start: 0.9454 (mt-10) cc_final: 0.9105 (mp0) REVERT: L 185 ARG cc_start: 0.8656 (ttt180) cc_final: 0.8409 (ttt90) REVERT: M 166 LYS cc_start: 0.8745 (mmtm) cc_final: 0.8447 (mmtm) REVERT: M 184 TYR cc_start: 0.9187 (m-80) cc_final: 0.8762 (m-10) REVERT: M 225 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8200 (tm-30) REVERT: M 253 ASP cc_start: 0.9106 (p0) cc_final: 0.8760 (p0) REVERT: M 599 GLN cc_start: 0.8982 (tt0) cc_final: 0.8754 (tt0) REVERT: M 714 ASP cc_start: 0.8638 (t70) cc_final: 0.8415 (t70) REVERT: N 356 ARG cc_start: 0.9137 (ttm110) cc_final: 0.8817 (ttm110) REVERT: N 371 ASN cc_start: 0.9495 (m110) cc_final: 0.9208 (m110) REVERT: N 385 MET cc_start: 0.8548 (pmm) cc_final: 0.8283 (pmm) REVERT: N 390 LYS cc_start: 0.9337 (tmtt) cc_final: 0.9037 (tmtt) REVERT: N 401 PHE cc_start: 0.8982 (m-80) cc_final: 0.8497 (m-80) REVERT: N 417 TYR cc_start: 0.7306 (t80) cc_final: 0.6973 (t80) REVERT: N 657 GLN cc_start: 0.9351 (pm20) cc_final: 0.8940 (pm20) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.1496 time to fit residues: 131.3016 Evaluate side-chains 410 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 274 optimal weight: 20.0000 chunk 153 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 221 optimal weight: 50.0000 chunk 98 optimal weight: 7.9990 chunk 110 optimal weight: 40.0000 chunk 293 optimal weight: 0.8980 chunk 314 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 341 optimal weight: 40.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 275 ASN ** I 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 ASN ** K 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 667 GLN ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 522 GLN ** N 712 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 = 0.3349 r_free = 0.3349 target = 0.084021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.061072 restraints weight = 122960.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.063174 restraints weight = 72723.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.064590 restraints weight = 50465.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.065513 restraints weight = 39155.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.066132 restraints weight = 33031.259| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31804 Z= 0.219 Angle : 0.634 7.515 43368 Z= 0.345 Chirality : 0.045 0.198 4788 Planarity : 0.004 0.073 5747 Dihedral : 6.037 49.286 4463 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.12 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.13), residues: 4053 helix: -3.00 (0.48), residues: 84 sheet: -0.70 (0.13), residues: 1414 loop : -1.34 (0.12), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 356 TYR 0.029 0.002 TYR H 184 PHE 0.025 0.002 PHE H 652 TRP 0.033 0.002 TRP I 706 HIS 0.007 0.001 HIS J 221 Details of bonding type rmsd covalent geometry : bond 0.00465 (31783) covalent geometry : angle 0.63300 (43326) SS BOND : bond 0.00240 ( 21) SS BOND : angle 1.50705 ( 42) hydrogen bonds : bond 0.03857 ( 1190) hydrogen bonds : angle 7.01024 ( 3282) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 525 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 280 PHE cc_start: 0.9217 (m-80) cc_final: 0.8689 (m-10) REVERT: H 328 ILE cc_start: 0.8931 (mt) cc_final: 0.8669 (mt) REVERT: H 334 ASN cc_start: 0.9393 (p0) cc_final: 0.9082 (p0) REVERT: H 417 TYR cc_start: 0.8744 (t80) cc_final: 0.8461 (t80) REVERT: H 449 ASP cc_start: 0.8076 (t0) cc_final: 0.7621 (t0) REVERT: H 463 LEU cc_start: 0.9561 (mt) cc_final: 0.9231 (mt) REVERT: H 465 LEU cc_start: 0.9479 (mp) cc_final: 0.9072 (mt) REVERT: H 543 ASN cc_start: 0.9027 (t0) cc_final: 0.8648 (p0) REVERT: H 688 PHE cc_start: 0.7865 (t80) cc_final: 0.7480 (t80) REVERT: H 699 LEU cc_start: 0.8952 (tp) cc_final: 0.8438 (pp) REVERT: H 713 PHE cc_start: 0.9449 (m-10) cc_final: 0.9197 (m-10) REVERT: I 188 LEU cc_start: 0.9481 (mm) cc_final: 0.9131 (mt) REVERT: I 259 ASN cc_start: 0.9281 (t0) cc_final: 0.8774 (t0) REVERT: I 347 TYR cc_start: 0.9244 (m-80) cc_final: 0.8767 (m-80) REVERT: I 385 MET cc_start: 0.8698 (pmm) cc_final: 0.8417 (pmm) REVERT: I 390 LYS cc_start: 0.9222 (tmtt) cc_final: 0.8967 (tmtt) REVERT: I 532 TRP cc_start: 0.9349 (m100) cc_final: 0.8675 (m100) REVERT: I 594 GLN cc_start: 0.9317 (mp10) cc_final: 0.9036 (mp10) REVERT: J 154 ASP cc_start: 0.9549 (m-30) cc_final: 0.8924 (t0) REVERT: J 163 TRP cc_start: 0.8410 (t-100) cc_final: 0.7893 (t-100) REVERT: J 211 LEU cc_start: 0.9422 (tp) cc_final: 0.9196 (tp) REVERT: J 328 ILE cc_start: 0.9292 (mt) cc_final: 0.9018 (mt) REVERT: J 385 MET cc_start: 0.8557 (pmm) cc_final: 0.8303 (pmm) REVERT: J 434 ASP cc_start: 0.7884 (p0) cc_final: 0.7595 (p0) REVERT: J 449 ASP cc_start: 0.8361 (t0) cc_final: 0.8108 (t0) REVERT: J 657 GLN cc_start: 0.7821 (tt0) cc_final: 0.7569 (tt0) REVERT: J 658 GLN cc_start: 0.7978 (pm20) cc_final: 0.7413 (pm20) REVERT: K 139 LEU cc_start: 0.9489 (tp) cc_final: 0.9270 (tp) REVERT: K 257 VAL cc_start: 0.9553 (t) cc_final: 0.9258 (t) REVERT: K 278 GLU cc_start: 0.8984 (mp0) cc_final: 0.8730 (mp0) REVERT: K 334 ASN cc_start: 0.9428 (p0) cc_final: 0.8988 (p0) REVERT: K 713 PHE cc_start: 0.9595 (m-10) cc_final: 0.9248 (m-80) REVERT: L 167 ASN cc_start: 0.9240 (p0) cc_final: 0.8830 (p0) REVERT: L 168 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9101 (mp0) REVERT: L 185 ARG cc_start: 0.8586 (ttt180) cc_final: 0.8296 (ttt90) REVERT: L 254 TYR cc_start: 0.8838 (m-10) cc_final: 0.8624 (m-10) REVERT: L 268 LEU cc_start: 0.9724 (tp) cc_final: 0.9524 (tp) REVERT: M 166 LYS cc_start: 0.8743 (mmtm) cc_final: 0.8460 (mmtm) REVERT: M 184 TYR cc_start: 0.9204 (m-80) cc_final: 0.8931 (m-10) REVERT: M 225 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8241 (tm-30) REVERT: M 253 ASP cc_start: 0.9126 (p0) cc_final: 0.8792 (p0) REVERT: M 351 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8874 (mm-30) REVERT: M 417 TYR cc_start: 0.8316 (t80) cc_final: 0.8005 (t80) REVERT: N 356 ARG cc_start: 0.9139 (ttm110) cc_final: 0.8801 (ttm110) REVERT: N 371 ASN cc_start: 0.9475 (m110) cc_final: 0.9203 (m110) REVERT: N 385 MET cc_start: 0.8564 (pmm) cc_final: 0.8353 (pmm) REVERT: N 401 PHE cc_start: 0.9067 (m-80) cc_final: 0.8530 (m-80) REVERT: N 417 TYR cc_start: 0.7334 (t80) cc_final: 0.7025 (t80) REVERT: N 657 GLN cc_start: 0.9394 (pm20) cc_final: 0.8945 (pm20) outliers start: 0 outliers final: 0 residues processed: 525 average time/residue: 0.1447 time to fit residues: 127.8306 Evaluate side-chains 411 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 63 optimal weight: 8.9990 chunk 333 optimal weight: 30.0000 chunk 226 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 351 optimal weight: 8.9990 chunk 202 optimal weight: 40.0000 chunk 316 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 362 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 ASN ** K 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 606 HIS ** K 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 427 GLN ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.061852 restraints weight = 119456.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.064039 restraints weight = 69860.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.065520 restraints weight = 48019.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.066408 restraints weight = 36956.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.067105 restraints weight = 31169.519| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31804 Z= 0.188 Angle : 0.610 8.276 43368 Z= 0.332 Chirality : 0.045 0.222 4788 Planarity : 0.004 0.074 5747 Dihedral : 5.901 47.769 4463 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.13), residues: 4053 helix: -2.99 (0.48), residues: 84 sheet: -0.56 (0.13), residues: 1400 loop : -1.30 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 607 TYR 0.032 0.002 TYR M 577 PHE 0.024 0.002 PHE H 652 TRP 0.038 0.002 TRP I 163 HIS 0.007 0.001 HIS L 221 Details of bonding type rmsd covalent geometry : bond 0.00407 (31783) covalent geometry : angle 0.60937 (43326) SS BOND : bond 0.00524 ( 21) SS BOND : angle 1.17464 ( 42) hydrogen bonds : bond 0.03677 ( 1190) hydrogen bonds : angle 6.86065 ( 3282) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 328 ILE cc_start: 0.8919 (mt) cc_final: 0.8689 (mt) REVERT: H 334 ASN cc_start: 0.9392 (p0) cc_final: 0.9055 (p0) REVERT: H 417 TYR cc_start: 0.8713 (t80) cc_final: 0.8435 (t80) REVERT: H 449 ASP cc_start: 0.8107 (t0) cc_final: 0.7652 (t0) REVERT: H 465 LEU cc_start: 0.9384 (mp) cc_final: 0.8839 (mt) REVERT: H 543 ASN cc_start: 0.9032 (t0) cc_final: 0.8647 (p0) REVERT: H 688 PHE cc_start: 0.7850 (t80) cc_final: 0.7426 (t80) REVERT: H 699 LEU cc_start: 0.8928 (tp) cc_final: 0.8407 (pp) REVERT: H 703 SER cc_start: 0.8908 (p) cc_final: 0.8656 (m) REVERT: H 713 PHE cc_start: 0.9439 (m-10) cc_final: 0.9172 (m-10) REVERT: I 188 LEU cc_start: 0.9525 (mm) cc_final: 0.9212 (mt) REVERT: I 247 THR cc_start: 0.9344 (m) cc_final: 0.9107 (p) REVERT: I 259 ASN cc_start: 0.9245 (t0) cc_final: 0.8971 (t0) REVERT: I 347 TYR cc_start: 0.9220 (m-80) cc_final: 0.8699 (m-80) REVERT: I 385 MET cc_start: 0.8528 (pmm) cc_final: 0.8174 (pmm) REVERT: I 532 TRP cc_start: 0.9348 (m100) cc_final: 0.8775 (m100) REVERT: I 594 GLN cc_start: 0.9310 (mp10) cc_final: 0.8985 (mp10) REVERT: J 154 ASP cc_start: 0.9527 (m-30) cc_final: 0.8911 (t0) REVERT: J 163 TRP cc_start: 0.8396 (t-100) cc_final: 0.7866 (t-100) REVERT: J 211 LEU cc_start: 0.9405 (tp) cc_final: 0.9158 (tp) REVERT: J 253 ASP cc_start: 0.8858 (p0) cc_final: 0.8620 (p0) REVERT: J 274 ASP cc_start: 0.8948 (t0) cc_final: 0.8661 (t70) REVERT: J 328 ILE cc_start: 0.9260 (mt) cc_final: 0.9009 (mt) REVERT: J 385 MET cc_start: 0.8558 (pmm) cc_final: 0.8285 (pmm) REVERT: J 434 ASP cc_start: 0.7913 (p0) cc_final: 0.7594 (p0) REVERT: J 657 GLN cc_start: 0.7826 (tt0) cc_final: 0.7506 (tt0) REVERT: J 658 GLN cc_start: 0.8042 (pm20) cc_final: 0.7440 (pm20) REVERT: J 688 PHE cc_start: 0.7797 (t80) cc_final: 0.7440 (t80) REVERT: K 139 LEU cc_start: 0.9485 (tp) cc_final: 0.9284 (tp) REVERT: K 211 LEU cc_start: 0.9080 (mm) cc_final: 0.8686 (tp) REVERT: K 253 ASP cc_start: 0.9152 (p0) cc_final: 0.8918 (p0) REVERT: K 257 VAL cc_start: 0.9560 (t) cc_final: 0.9273 (t) REVERT: K 278 GLU cc_start: 0.8948 (mp0) cc_final: 0.8738 (mp0) REVERT: K 334 ASN cc_start: 0.9416 (p0) cc_final: 0.8972 (p0) REVERT: K 376 LEU cc_start: 0.9732 (tp) cc_final: 0.9231 (tp) REVERT: K 713 PHE cc_start: 0.9601 (m-10) cc_final: 0.9241 (m-80) REVERT: L 139 LEU cc_start: 0.9542 (tp) cc_final: 0.9337 (tp) REVERT: L 167 ASN cc_start: 0.9193 (p0) cc_final: 0.8789 (p0) REVERT: L 168 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9086 (mp0) REVERT: L 185 ARG cc_start: 0.8586 (ttt180) cc_final: 0.8316 (ttt90) REVERT: L 254 TYR cc_start: 0.8834 (m-10) cc_final: 0.8597 (m-10) REVERT: L 658 GLN cc_start: 0.7556 (pm20) cc_final: 0.6747 (pm20) REVERT: M 166 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8474 (mmtm) REVERT: M 225 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8247 (tm-30) REVERT: M 253 ASP cc_start: 0.9117 (p0) cc_final: 0.8790 (p0) REVERT: M 281 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8689 (tm-30) REVERT: M 417 TYR cc_start: 0.8299 (t80) cc_final: 0.7992 (t80) REVERT: N 371 ASN cc_start: 0.9451 (m110) cc_final: 0.9171 (m110) REVERT: N 385 MET cc_start: 0.8612 (pmm) cc_final: 0.8364 (pmm) REVERT: N 401 PHE cc_start: 0.9059 (m-80) cc_final: 0.8536 (m-80) REVERT: N 417 TYR cc_start: 0.7316 (t80) cc_final: 0.6963 (t80) REVERT: N 657 GLN cc_start: 0.9324 (pm20) cc_final: 0.8988 (pm20) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.1555 time to fit residues: 138.8851 Evaluate side-chains 418 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 379 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 204 optimal weight: 9.9990 chunk 230 optimal weight: 5.9990 chunk 337 optimal weight: 6.9990 chunk 114 optimal weight: 50.0000 chunk 319 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 chunk 339 optimal weight: 8.9990 chunk 255 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 464 GLN ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 179 ASN K 371 ASN ** K 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 658 GLN ** L 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 712 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 = 0.3371 r_free = 0.3371 target = 0.085103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.061433 restraints weight = 118000.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.063665 restraints weight = 68714.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.065178 restraints weight = 47210.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.066097 restraints weight = 36329.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.066813 restraints weight = 30587.525| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31804 Z= 0.184 Angle : 0.603 8.022 43368 Z= 0.328 Chirality : 0.045 0.203 4788 Planarity : 0.004 0.087 5747 Dihedral : 5.795 45.856 4463 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.58 % Favored : 94.40 % Rotamer: Outliers : 0.03 % Allowed : 1.59 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.60 (0.13), residues: 4053 helix: -3.05 (0.47), residues: 84 sheet: -0.61 (0.13), residues: 1456 loop : -1.28 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 330 TYR 0.022 0.002 TYR M 184 PHE 0.024 0.002 PHE H 652 TRP 0.030 0.002 TRP I 163 HIS 0.008 0.001 HIS J 221 Details of bonding type rmsd covalent geometry : bond 0.00397 (31783) covalent geometry : angle 0.60245 (43326) SS BOND : bond 0.00277 ( 21) SS BOND : angle 1.05120 ( 42) hydrogen bonds : bond 0.03636 ( 1190) hydrogen bonds : angle 6.74047 ( 3282) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 521 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 188 LEU cc_start: 0.9565 (mm) cc_final: 0.8387 (pp) REVERT: H 254 TYR cc_start: 0.8801 (m-10) cc_final: 0.8594 (m-10) REVERT: H 328 ILE cc_start: 0.8881 (mt) cc_final: 0.8635 (mt) REVERT: H 334 ASN cc_start: 0.9453 (p0) cc_final: 0.9194 (p0) REVERT: H 417 TYR cc_start: 0.8690 (t80) cc_final: 0.7803 (t80) REVERT: H 465 LEU cc_start: 0.9433 (mp) cc_final: 0.8991 (mt) REVERT: H 543 ASN cc_start: 0.9086 (t0) cc_final: 0.8638 (p0) REVERT: H 688 PHE cc_start: 0.7935 (t80) cc_final: 0.7556 (t80) REVERT: H 699 LEU cc_start: 0.8924 (tp) cc_final: 0.8388 (pp) REVERT: H 703 SER cc_start: 0.8931 (p) cc_final: 0.8663 (m) REVERT: H 713 PHE cc_start: 0.9436 (m-10) cc_final: 0.9156 (m-10) REVERT: I 188 LEU cc_start: 0.9537 (mm) cc_final: 0.9250 (mt) REVERT: I 247 THR cc_start: 0.9338 (m) cc_final: 0.9067 (p) REVERT: I 253 ASP cc_start: 0.9096 (p0) cc_final: 0.8885 (p0) REVERT: I 259 ASN cc_start: 0.9218 (t0) cc_final: 0.8777 (t0) REVERT: I 347 TYR cc_start: 0.9232 (m-80) cc_final: 0.8672 (m-80) REVERT: I 385 MET cc_start: 0.8448 (pmm) cc_final: 0.8164 (pmm) REVERT: I 390 LYS cc_start: 0.9187 (tmtt) cc_final: 0.8785 (tptp) REVERT: I 532 TRP cc_start: 0.9361 (m100) cc_final: 0.8770 (m100) REVERT: I 594 GLN cc_start: 0.9283 (mp10) cc_final: 0.8944 (mp10) REVERT: J 154 ASP cc_start: 0.9504 (m-30) cc_final: 0.8841 (t0) REVERT: J 163 TRP cc_start: 0.8317 (t-100) cc_final: 0.7746 (t-100) REVERT: J 211 LEU cc_start: 0.9426 (tp) cc_final: 0.9124 (tp) REVERT: J 253 ASP cc_start: 0.8869 (p0) cc_final: 0.8650 (p0) REVERT: J 274 ASP cc_start: 0.8855 (t0) cc_final: 0.8628 (t70) REVERT: J 434 ASP cc_start: 0.7922 (p0) cc_final: 0.7625 (p0) REVERT: J 449 ASP cc_start: 0.8453 (t0) cc_final: 0.8166 (t0) REVERT: J 657 GLN cc_start: 0.7821 (tt0) cc_final: 0.7508 (tt0) REVERT: J 658 GLN cc_start: 0.7986 (pm20) cc_final: 0.7457 (pm20) REVERT: J 688 PHE cc_start: 0.7851 (t80) cc_final: 0.7430 (t80) REVERT: K 211 LEU cc_start: 0.9050 (mm) cc_final: 0.8622 (tp) REVERT: K 253 ASP cc_start: 0.9163 (p0) cc_final: 0.8955 (p0) REVERT: K 278 GLU cc_start: 0.8924 (mp0) cc_final: 0.8710 (mp0) REVERT: K 334 ASN cc_start: 0.9410 (p0) cc_final: 0.9062 (p0) REVERT: K 347 TYR cc_start: 0.8878 (m-80) cc_final: 0.8258 (m-80) REVERT: K 376 LEU cc_start: 0.9728 (tp) cc_final: 0.9222 (tp) REVERT: K 385 MET cc_start: 0.8304 (pmm) cc_final: 0.7913 (pmm) REVERT: K 648 THR cc_start: 0.8518 (p) cc_final: 0.8253 (p) REVERT: K 649 SER cc_start: 0.8259 (p) cc_final: 0.7902 (t) REVERT: K 713 PHE cc_start: 0.9589 (m-10) cc_final: 0.9238 (m-80) REVERT: L 139 LEU cc_start: 0.9531 (tp) cc_final: 0.9303 (tp) REVERT: L 167 ASN cc_start: 0.9185 (p0) cc_final: 0.8758 (p0) REVERT: L 168 GLU cc_start: 0.9426 (mt-10) cc_final: 0.9082 (mp0) REVERT: L 254 TYR cc_start: 0.8838 (m-10) cc_final: 0.8587 (m-10) REVERT: L 319 LEU cc_start: 0.9307 (tp) cc_final: 0.9077 (tt) REVERT: L 658 GLN cc_start: 0.7584 (pm20) cc_final: 0.6779 (pm20) REVERT: M 166 LYS cc_start: 0.8717 (mmtm) cc_final: 0.8383 (mmtm) REVERT: M 184 TYR cc_start: 0.9060 (m-10) cc_final: 0.8707 (m-10) REVERT: M 225 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8297 (tm-30) REVERT: M 253 ASP cc_start: 0.9124 (p0) cc_final: 0.8781 (p0) REVERT: M 342 TRP cc_start: 0.8930 (m-90) cc_final: 0.8681 (m-90) REVERT: M 417 TYR cc_start: 0.8285 (t80) cc_final: 0.7981 (t80) REVERT: N 371 ASN cc_start: 0.9443 (m110) cc_final: 0.9160 (m110) REVERT: N 385 MET cc_start: 0.8617 (pmm) cc_final: 0.8396 (pmm) REVERT: N 390 LYS cc_start: 0.9311 (tmtt) cc_final: 0.8989 (tptp) REVERT: N 401 PHE cc_start: 0.9016 (m-80) cc_final: 0.8546 (m-80) REVERT: N 417 TYR cc_start: 0.7402 (t80) cc_final: 0.7050 (t80) REVERT: N 657 GLN cc_start: 0.9284 (pm20) cc_final: 0.9027 (pm20) outliers start: 1 outliers final: 0 residues processed: 522 average time/residue: 0.1658 time to fit residues: 147.3611 Evaluate side-chains 421 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 386 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 329 optimal weight: 6.9990 chunk 173 optimal weight: 30.0000 chunk 336 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 384 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 30.0000 chunk 319 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 464 GLN ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 ASN K 598 ASN K 682 ASN ** L 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 266 GLN N 599 GLN ** N 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.062309 restraints weight = 116849.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.064603 restraints weight = 68001.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.066139 restraints weight = 46583.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.067065 restraints weight = 35770.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.067800 restraints weight = 30102.231| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31804 Z= 0.158 Angle : 0.597 10.164 43368 Z= 0.323 Chirality : 0.045 0.305 4788 Planarity : 0.004 0.073 5747 Dihedral : 5.662 44.422 4463 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.16 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.13), residues: 4053 helix: -3.02 (0.47), residues: 84 sheet: -0.55 (0.13), residues: 1428 loop : -1.20 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 243 TYR 0.018 0.002 TYR N 254 PHE 0.024 0.002 PHE H 652 TRP 0.047 0.002 TRP L 163 HIS 0.006 0.001 HIS L 221 Details of bonding type rmsd covalent geometry : bond 0.00348 (31783) covalent geometry : angle 0.59520 (43326) SS BOND : bond 0.00211 ( 21) SS BOND : angle 1.64170 ( 42) hydrogen bonds : bond 0.03527 ( 1190) hydrogen bonds : angle 6.60967 ( 3282) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 280 PHE cc_start: 0.9029 (m-80) cc_final: 0.8660 (m-80) REVERT: H 328 ILE cc_start: 0.8874 (mt) cc_final: 0.8605 (mt) REVERT: H 334 ASN cc_start: 0.9440 (p0) cc_final: 0.9187 (p0) REVERT: H 417 TYR cc_start: 0.8684 (t80) cc_final: 0.7807 (t80) REVERT: H 449 ASP cc_start: 0.8159 (t0) cc_final: 0.7279 (t0) REVERT: H 465 LEU cc_start: 0.9386 (mp) cc_final: 0.8955 (mt) REVERT: H 543 ASN cc_start: 0.9088 (t0) cc_final: 0.8639 (p0) REVERT: H 688 PHE cc_start: 0.7861 (t80) cc_final: 0.7531 (t80) REVERT: H 699 LEU cc_start: 0.8909 (tp) cc_final: 0.8389 (pp) REVERT: H 703 SER cc_start: 0.8897 (p) cc_final: 0.8638 (m) REVERT: H 713 PHE cc_start: 0.9445 (m-10) cc_final: 0.9171 (m-10) REVERT: I 188 LEU cc_start: 0.9543 (mm) cc_final: 0.9256 (mt) REVERT: I 243 ARG cc_start: 0.9371 (mmp80) cc_final: 0.9066 (mmm160) REVERT: I 247 THR cc_start: 0.9382 (m) cc_final: 0.9084 (p) REVERT: I 253 ASP cc_start: 0.9095 (p0) cc_final: 0.8872 (p0) REVERT: I 259 ASN cc_start: 0.9198 (t0) cc_final: 0.8979 (t0) REVERT: I 347 TYR cc_start: 0.9237 (m-80) cc_final: 0.8617 (m-80) REVERT: I 385 MET cc_start: 0.8451 (pmm) cc_final: 0.8146 (pmm) REVERT: I 594 GLN cc_start: 0.9262 (mp10) cc_final: 0.8816 (mp10) REVERT: J 154 ASP cc_start: 0.9501 (m-30) cc_final: 0.8833 (t0) REVERT: J 163 TRP cc_start: 0.8241 (t-100) cc_final: 0.7665 (t-100) REVERT: J 211 LEU cc_start: 0.9398 (tp) cc_final: 0.9119 (tp) REVERT: J 253 ASP cc_start: 0.8872 (p0) cc_final: 0.8650 (p0) REVERT: J 385 MET cc_start: 0.8623 (pmm) cc_final: 0.8378 (pmm) REVERT: J 417 TYR cc_start: 0.8740 (t80) cc_final: 0.8473 (t80) REVERT: J 434 ASP cc_start: 0.7942 (p0) cc_final: 0.7636 (p0) REVERT: J 449 ASP cc_start: 0.8433 (t0) cc_final: 0.8129 (t0) REVERT: J 657 GLN cc_start: 0.7815 (tt0) cc_final: 0.7513 (tt0) REVERT: J 658 GLN cc_start: 0.7997 (pm20) cc_final: 0.7463 (pm20) REVERT: J 688 PHE cc_start: 0.7800 (t80) cc_final: 0.7347 (t80) REVERT: K 139 LEU cc_start: 0.9457 (tp) cc_final: 0.9193 (tp) REVERT: K 278 GLU cc_start: 0.8922 (mp0) cc_final: 0.8719 (mp0) REVERT: K 316 SER cc_start: 0.9338 (p) cc_final: 0.8903 (t) REVERT: K 319 LEU cc_start: 0.9410 (tp) cc_final: 0.9199 (tt) REVERT: K 334 ASN cc_start: 0.9385 (p0) cc_final: 0.9043 (p0) REVERT: K 347 TYR cc_start: 0.8832 (m-80) cc_final: 0.8213 (m-80) REVERT: K 372 ARG cc_start: 0.8376 (ptp90) cc_final: 0.8055 (ptp-170) REVERT: K 376 LEU cc_start: 0.9662 (tp) cc_final: 0.9142 (tp) REVERT: K 648 THR cc_start: 0.8518 (p) cc_final: 0.8264 (p) REVERT: K 649 SER cc_start: 0.8240 (p) cc_final: 0.7876 (t) REVERT: L 139 LEU cc_start: 0.9515 (tp) cc_final: 0.9281 (tp) REVERT: L 167 ASN cc_start: 0.9178 (p0) cc_final: 0.8752 (p0) REVERT: L 168 GLU cc_start: 0.9416 (mt-10) cc_final: 0.9069 (mp0) REVERT: L 254 TYR cc_start: 0.8825 (m-10) cc_final: 0.8545 (m-10) REVERT: L 319 LEU cc_start: 0.9325 (tp) cc_final: 0.9076 (tt) REVERT: M 184 TYR cc_start: 0.9025 (m-10) cc_final: 0.8725 (m-10) REVERT: M 194 TYR cc_start: 0.9069 (t80) cc_final: 0.8662 (t80) REVERT: M 225 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8292 (tm-30) REVERT: M 253 ASP cc_start: 0.9123 (p0) cc_final: 0.8804 (p0) REVERT: M 417 TYR cc_start: 0.8280 (t80) cc_final: 0.7973 (t80) REVERT: N 371 ASN cc_start: 0.9440 (m110) cc_final: 0.9146 (m110) REVERT: N 401 PHE cc_start: 0.8971 (m-80) cc_final: 0.8522 (m-80) REVERT: N 417 TYR cc_start: 0.7386 (t80) cc_final: 0.7024 (t80) REVERT: N 657 GLN cc_start: 0.9267 (pm20) cc_final: 0.9050 (pm20) outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.1676 time to fit residues: 150.5079 Evaluate side-chains 421 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 260 optimal weight: 30.0000 chunk 106 optimal weight: 20.0000 chunk 405 optimal weight: 5.9990 chunk 111 optimal weight: 40.0000 chunk 327 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 176 optimal weight: 20.0000 chunk 358 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 GLN K 371 ASN ** L 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 712 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 = 0.3359 r_free = 0.3359 target = 0.084392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.061252 restraints weight = 119965.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.063417 restraints weight = 70268.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.064881 restraints weight = 48351.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.065827 restraints weight = 37275.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.066388 restraints weight = 31293.509| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 31804 Z= 0.231 Angle : 0.649 10.613 43368 Z= 0.351 Chirality : 0.045 0.210 4788 Planarity : 0.005 0.099 5747 Dihedral : 5.860 45.796 4463 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.34 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.13), residues: 4053 helix: -2.88 (0.49), residues: 84 sheet: -0.57 (0.13), residues: 1435 loop : -1.30 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 356 TYR 0.021 0.002 TYR N 254 PHE 0.027 0.002 PHE H 652 TRP 0.035 0.002 TRP M 342 HIS 0.007 0.002 HIS L 221 Details of bonding type rmsd covalent geometry : bond 0.00494 (31783) covalent geometry : angle 0.64841 (43326) SS BOND : bond 0.00272 ( 21) SS BOND : angle 1.21972 ( 42) hydrogen bonds : bond 0.03861 ( 1190) hydrogen bonds : angle 6.73096 ( 3282) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 0.917 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: H 188 LEU cc_start: 0.9554 (mm) cc_final: 0.8448 (pp) REVERT: H 328 ILE cc_start: 0.8915 (mt) cc_final: 0.8675 (mt) REVERT: H 334 ASN cc_start: 0.9455 (p0) cc_final: 0.9218 (p0) REVERT: H 417 TYR cc_start: 0.8658 (t80) cc_final: 0.7729 (t80) REVERT: H 465 LEU cc_start: 0.9401 (mp) cc_final: 0.8808 (mt) REVERT: H 543 ASN cc_start: 0.9072 (t0) cc_final: 0.8653 (p0) REVERT: H 688 PHE cc_start: 0.7901 (t80) cc_final: 0.7550 (t80) REVERT: H 699 LEU cc_start: 0.8940 (tp) cc_final: 0.8373 (pp) REVERT: H 703 SER cc_start: 0.8918 (p) cc_final: 0.8661 (m) REVERT: H 713 PHE cc_start: 0.9436 (m-10) cc_final: 0.9146 (m-10) REVERT: I 188 LEU cc_start: 0.9546 (mm) cc_final: 0.9236 (mt) REVERT: I 247 THR cc_start: 0.9367 (m) cc_final: 0.9098 (p) REVERT: I 253 ASP cc_start: 0.9112 (p0) cc_final: 0.8901 (p0) REVERT: I 259 ASN cc_start: 0.9235 (t0) cc_final: 0.8991 (t0) REVERT: I 347 TYR cc_start: 0.9232 (m-80) cc_final: 0.8654 (m-80) REVERT: I 385 MET cc_start: 0.8432 (pmm) cc_final: 0.8203 (pmm) REVERT: I 390 LYS cc_start: 0.9127 (tmtt) cc_final: 0.8743 (tptp) REVERT: I 532 TRP cc_start: 0.9382 (m100) cc_final: 0.8858 (m100) REVERT: I 594 GLN cc_start: 0.9292 (mp10) cc_final: 0.8994 (mp10) REVERT: J 154 ASP cc_start: 0.9515 (m-30) cc_final: 0.8876 (t0) REVERT: J 163 TRP cc_start: 0.8394 (t-100) cc_final: 0.7740 (t-100) REVERT: J 253 ASP cc_start: 0.8845 (p0) cc_final: 0.8613 (p0) REVERT: J 274 ASP cc_start: 0.8774 (t0) cc_final: 0.8494 (t70) REVERT: J 417 TYR cc_start: 0.8784 (t80) cc_final: 0.8537 (t80) REVERT: J 434 ASP cc_start: 0.7967 (p0) cc_final: 0.7578 (p0) REVERT: J 449 ASP cc_start: 0.8366 (t0) cc_final: 0.8090 (t0) REVERT: J 657 GLN cc_start: 0.7817 (tt0) cc_final: 0.7514 (tt0) REVERT: J 658 GLN cc_start: 0.8006 (pm20) cc_final: 0.7476 (pm20) REVERT: K 139 LEU cc_start: 0.9493 (tp) cc_final: 0.9248 (tp) REVERT: K 253 ASP cc_start: 0.9180 (p0) cc_final: 0.8965 (p0) REVERT: K 278 GLU cc_start: 0.8936 (mp0) cc_final: 0.8712 (mp0) REVERT: K 316 SER cc_start: 0.9000 (p) cc_final: 0.8798 (t) REVERT: K 334 ASN cc_start: 0.9397 (p0) cc_final: 0.9090 (p0) REVERT: K 347 TYR cc_start: 0.8743 (m-80) cc_final: 0.8104 (m-80) REVERT: K 372 ARG cc_start: 0.8358 (ptp90) cc_final: 0.8048 (ptp-170) REVERT: K 376 LEU cc_start: 0.9651 (tp) cc_final: 0.9216 (tp) REVERT: K 713 PHE cc_start: 0.9456 (m-80) cc_final: 0.9203 (m-80) REVERT: L 139 LEU cc_start: 0.9537 (tp) cc_final: 0.9310 (tp) REVERT: L 167 ASN cc_start: 0.9203 (p0) cc_final: 0.8737 (p0) REVERT: L 168 GLU cc_start: 0.9439 (mt-10) cc_final: 0.9088 (mp0) REVERT: L 254 TYR cc_start: 0.8867 (m-10) cc_final: 0.8602 (m-10) REVERT: L 268 LEU cc_start: 0.9706 (tp) cc_final: 0.9499 (tp) REVERT: M 166 LYS cc_start: 0.8741 (mmtm) cc_final: 0.8516 (mmtm) REVERT: M 184 TYR cc_start: 0.9058 (m-10) cc_final: 0.8756 (m-10) REVERT: M 194 TYR cc_start: 0.9062 (t80) cc_final: 0.8658 (t80) REVERT: M 225 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8706 (tm-30) REVERT: M 253 ASP cc_start: 0.9036 (p0) cc_final: 0.8818 (p0) REVERT: M 417 TYR cc_start: 0.8283 (t80) cc_final: 0.7944 (t80) REVERT: N 356 ARG cc_start: 0.9176 (ttm110) cc_final: 0.8529 (mtm110) REVERT: N 371 ASN cc_start: 0.9454 (m110) cc_final: 0.9168 (m110) REVERT: N 385 MET cc_start: 0.8416 (pmm) cc_final: 0.8133 (pmm) REVERT: N 390 LYS cc_start: 0.9252 (tmtt) cc_final: 0.8945 (tptp) REVERT: N 401 PHE cc_start: 0.9083 (m-80) cc_final: 0.8648 (m-80) REVERT: N 417 TYR cc_start: 0.7418 (t80) cc_final: 0.7067 (t80) REVERT: N 664 PHE cc_start: 0.9094 (m-80) cc_final: 0.8869 (m-10) outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 0.1750 time to fit residues: 151.1270 Evaluate side-chains 407 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 188 optimal weight: 8.9990 chunk 206 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 53 optimal weight: 50.0000 chunk 299 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 325 optimal weight: 0.5980 chunk 398 optimal weight: 40.0000 chunk 330 optimal weight: 7.9990 chunk 208 optimal weight: 30.0000 chunk 306 optimal weight: 9.9990 overall best weight: 6.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 ASN ** L 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 682 ASN ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 712 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 = 0.3358 r_free = 0.3358 target = 0.084366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.061166 restraints weight = 120305.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.063336 restraints weight = 70448.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.064816 restraints weight = 48484.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.065774 restraints weight = 37318.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.066431 restraints weight = 31365.385| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 31804 Z= 0.222 Angle : 0.644 10.130 43368 Z= 0.348 Chirality : 0.045 0.306 4788 Planarity : 0.004 0.090 5747 Dihedral : 5.895 45.924 4463 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.12 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.62 (0.13), residues: 4053 helix: -2.89 (0.49), residues: 84 sheet: -0.60 (0.13), residues: 1435 loop : -1.32 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 687 TYR 0.022 0.002 TYR N 254 PHE 0.027 0.002 PHE H 652 TRP 0.032 0.002 TRP M 245 HIS 0.008 0.001 HIS L 221 Details of bonding type rmsd covalent geometry : bond 0.00477 (31783) covalent geometry : angle 0.64269 (43326) SS BOND : bond 0.00313 ( 21) SS BOND : angle 1.29181 ( 42) hydrogen bonds : bond 0.03853 ( 1190) hydrogen bonds : angle 6.75137 ( 3282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4422.25 seconds wall clock time: 78 minutes 10.80 seconds (4690.80 seconds total)