Starting phenix.real_space_refine on Wed May 28 17:48:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yl9_33215/05_2025/7yl9_33215.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yl9_33215/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yl9_33215/05_2025/7yl9_33215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yl9_33215/05_2025/7yl9_33215.map" model { file = "/net/cci-nas-00/data/ceres_data/7yl9_33215/05_2025/7yl9_33215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yl9_33215/05_2025/7yl9_33215.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.33s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 4, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} 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: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} 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: {'GLN:plan1': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} 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: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} 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: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2} 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: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} 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: {'GLN:plan1': 7, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 92 Time building chain proxies: 17.54, per 1000 atoms: 0.56 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: 7.58 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 5.20 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: 13.71 Time building geometry restraints manager: 8.84 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.400 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 69.710 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.320 ------------------------------------------------------------------------------- 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 : 29.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (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 TRP 0.042 0.002 TRP K 163 HIS 0.008 0.001 HIS L 221 PHE 0.027 0.002 PHE H 652 TYR 0.025 0.002 TYR H 184 ARG 0.013 0.001 ARG I 243 Details of bonding type rmsd hydrogen bonds : bond 0.17667 ( 1190) hydrogen bonds : angle 9.05718 ( 3282) SS BOND : bond 0.00575 ( 21) SS BOND : angle 1.35331 ( 42) covalent geometry : bond 0.00486 (31783) covalent geometry : angle 0.77613 (43326) *********************** 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 : 3.741 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: 0.8527 (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: 0.7999 (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: 0.7706 (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: 0.8670 (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: 0.3807 time to fit residues: 351.8096 Evaluate side-chains 417 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 342 optimal weight: 9.9990 chunk 307 optimal weight: 30.0000 chunk 170 optimal weight: 30.0000 chunk 105 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 164 optimal weight: 50.0000 chunk 318 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 236 optimal weight: 0.6980 chunk 368 optimal weight: 10.0000 overall best weight: 6.1388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 430 HIS J 470 ASN ** J 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 252 GLN K 322 ASN K 371 ASN K 657 GLN ** K 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 230 GLN ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 594 GLN ** N 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 606 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.060651 restraints weight = 120164.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.062773 restraints weight = 70786.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.064232 restraints weight = 49072.483| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31804 Z= 0.212 Angle : 0.642 8.123 43368 Z= 0.355 Chirality : 0.045 0.193 4788 Planarity : 0.005 0.050 5747 Dihedral : 6.268 53.312 4463 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.17 % Favored : 93.81 % Rotamer: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 4053 helix: -3.04 (0.48), residues: 84 sheet: -0.62 (0.13), residues: 1463 loop : -1.42 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 163 HIS 0.011 0.002 HIS J 221 PHE 0.027 0.002 PHE J 688 TYR 0.028 0.002 TYR L 254 ARG 0.005 0.001 ARG L 437 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 1190) hydrogen bonds : angle 7.60812 ( 3282) SS BOND : bond 0.00252 ( 21) SS BOND : angle 0.87743 ( 42) covalent geometry : bond 0.00449 (31783) covalent geometry : angle 0.64159 (43326) *********************** 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 531 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 528 time to evaluate : 3.390 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: 0.9158 (mt) cc_final: 0.8948 (mt) REVERT: H 449 ASP cc_start: 0.8151 (t0) cc_final: 0.7791 (t0) REVERT: H 465 LEU cc_start: 0.9563 (mt) cc_final: 0.9294 (mt) REVERT: H 688 PHE cc_start: 0.7717 (t80) cc_final: 0.7208 (t80) REVERT: H 699 LEU cc_start: 0.8999 (tp) cc_final: 0.8627 (pp) REVERT: I 188 LEU cc_start: 0.9554 (mm) cc_final: 0.9174 (mt) REVERT: I 243 ARG cc_start: 0.9297 (mmp80) cc_final: 0.9065 (mmm160) REVERT: I 257 VAL cc_start: 0.9552 (t) cc_final: 0.9345 (t) REVERT: I 377 SER cc_start: 0.9649 (m) cc_final: 0.9444 (p) REVERT: I 385 MET cc_start: 0.8609 (pmm) cc_final: 0.8292 (pmm) REVERT: I 388 ILE cc_start: 0.9794 (mp) cc_final: 0.9307 (tp) REVERT: I 590 LEU cc_start: 0.7883 (pp) cc_final: 0.7637 (pp) REVERT: I 594 GLN cc_start: 0.9372 (mp10) cc_final: 0.8926 (mp10) REVERT: J 163 TRP cc_start: 0.8555 (t-100) cc_final: 0.7751 (t-100) REVERT: J 328 ILE cc_start: 0.9365 (mt) cc_final: 0.9159 (mt) REVERT: J 385 MET cc_start: 0.8655 (pmm) cc_final: 0.8230 (pmm) REVERT: J 388 ILE cc_start: 0.9775 (mp) cc_final: 0.9149 (tp) REVERT: J 449 ASP cc_start: 0.8411 (t0) cc_final: 0.8160 (t0) REVERT: J 658 GLN cc_start: 0.7926 (pm20) cc_final: 0.7157 (pm20) REVERT: K 188 LEU cc_start: 0.9571 (mm) cc_final: 0.9253 (mm) REVERT: K 278 GLU cc_start: 0.8949 (mp0) cc_final: 0.8722 (mp0) REVERT: K 319 LEU cc_start: 0.9427 (tt) cc_final: 0.9195 (tt) REVERT: K 334 ASN cc_start: 0.9321 (p0) cc_final: 0.8905 (p0) REVERT: K 347 TYR cc_start: 0.9008 (m-80) cc_final: 0.8670 (m-80) REVERT: K 385 MET cc_start: 0.8526 (pmm) cc_final: 0.8116 (pmm) REVERT: K 463 LEU cc_start: 0.9223 (mt) cc_final: 0.9002 (mt) REVERT: L 139 LEU cc_start: 0.9519 (tp) cc_final: 0.9306 (tp) REVERT: L 167 ASN cc_start: 0.9489 (p0) cc_final: 0.9210 (p0) REVERT: L 347 TYR cc_start: 0.9490 (m-80) cc_final: 0.9248 (m-10) REVERT: M 166 LYS cc_start: 0.8722 (mmtm) cc_final: 0.8508 (mmtm) REVERT: M 225 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8461 (tm-30) REVERT: M 253 ASP cc_start: 0.9165 (p0) cc_final: 0.8859 (p0) REVERT: N 371 ASN cc_start: 0.9505 (m110) cc_final: 0.9244 (m110) REVERT: N 385 MET cc_start: 0.8733 (pmm) cc_final: 0.8326 (pmm) REVERT: N 417 TYR cc_start: 0.7058 (t80) cc_final: 0.6842 (t80) REVERT: N 657 GLN cc_start: 0.9263 (pm20) cc_final: 0.8739 (pm20) outliers start: 3 outliers final: 1 residues processed: 531 average time/residue: 0.3665 time to fit residues: 326.7181 Evaluate side-chains 415 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 374 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 225 optimal weight: 7.9990 chunk 394 optimal weight: 50.0000 chunk 22 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 64 optimal weight: 0.0370 chunk 75 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 352 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 overall best weight: 5.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 230 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 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** H 657 GLN ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 419 HIS J 427 GLN ** J 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 ASN 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 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 682 ASN ** N 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.084808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.061500 restraints weight = 120598.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.063607 restraints weight = 71399.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.065034 restraints weight = 49590.507| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31804 Z= 0.194 Angle : 0.615 7.789 43368 Z= 0.337 Chirality : 0.045 0.193 4788 Planarity : 0.004 0.058 5747 Dihedral : 6.043 51.694 4463 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.85 % Favored : 94.13 % Rotamer: Outliers : 0.03 % Allowed : 5.40 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.13), residues: 4053 helix: -3.16 (0.46), residues: 84 sheet: -0.62 (0.13), residues: 1428 loop : -1.38 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 163 HIS 0.008 0.001 HIS J 221 PHE 0.024 0.002 PHE H 652 TYR 0.021 0.002 TYR H 184 ARG 0.005 0.001 ARG J 185 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 1190) hydrogen bonds : angle 7.21086 ( 3282) SS BOND : bond 0.00237 ( 21) SS BOND : angle 1.52620 ( 42) covalent geometry : bond 0.00413 (31783) covalent geometry : angle 0.61312 (43326) *********************** 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 536 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 535 time to evaluate : 3.548 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 183 ILE cc_start: 0.9412 (mm) cc_final: 0.9183 (tp) REVERT: H 268 LEU cc_start: 0.9732 (tp) cc_final: 0.9480 (tp) REVERT: H 280 PHE cc_start: 0.9336 (m-80) cc_final: 0.8921 (m-80) REVERT: H 328 ILE cc_start: 0.9092 (mt) cc_final: 0.8848 (mt) REVERT: H 449 ASP cc_start: 0.8159 (t0) cc_final: 0.7759 (t0) REVERT: H 688 PHE cc_start: 0.7769 (t80) cc_final: 0.7320 (t80) REVERT: H 699 LEU cc_start: 0.8999 (tp) cc_final: 0.8533 (pp) REVERT: H 713 PHE cc_start: 0.9442 (m-10) cc_final: 0.9184 (m-10) REVERT: I 188 LEU cc_start: 0.9554 (mm) cc_final: 0.9190 (mt) REVERT: I 247 THR cc_start: 0.9281 (m) cc_final: 0.9002 (p) REVERT: I 347 TYR cc_start: 0.9215 (m-80) cc_final: 0.8846 (m-80) REVERT: I 385 MET cc_start: 0.8525 (pmm) cc_final: 0.8274 (pmm) REVERT: I 532 TRP cc_start: 0.9361 (m100) cc_final: 0.8630 (m100) REVERT: I 541 LEU cc_start: 0.9492 (tp) cc_final: 0.9175 (tp) REVERT: I 594 GLN cc_start: 0.9341 (mp10) cc_final: 0.8877 (mp10) REVERT: J 154 ASP cc_start: 0.9531 (m-30) cc_final: 0.8949 (t0) REVERT: J 163 TRP cc_start: 0.8371 (t-100) cc_final: 0.7773 (t-100) REVERT: J 211 LEU cc_start: 0.9412 (tp) cc_final: 0.9175 (tp) REVERT: J 253 ASP cc_start: 0.8951 (p0) cc_final: 0.8694 (p0) REVERT: J 325 ASP cc_start: 0.8906 (t70) cc_final: 0.8705 (t70) REVERT: J 326 TYR cc_start: 0.9161 (m-10) cc_final: 0.8739 (m-10) REVERT: J 328 ILE cc_start: 0.9299 (mt) cc_final: 0.9066 (mt) REVERT: J 385 MET cc_start: 0.8610 (pmm) cc_final: 0.8255 (pmm) REVERT: J 434 ASP cc_start: 0.7891 (p0) cc_final: 0.7580 (p0) REVERT: J 449 ASP cc_start: 0.8414 (t0) cc_final: 0.8167 (t0) REVERT: J 658 GLN cc_start: 0.7967 (pm20) cc_final: 0.7294 (pm20) REVERT: K 139 LEU cc_start: 0.9472 (tp) cc_final: 0.9272 (tp) REVERT: K 183 ILE cc_start: 0.9501 (mm) cc_final: 0.9198 (tp) REVERT: K 188 LEU cc_start: 0.9531 (mm) cc_final: 0.9315 (mm) REVERT: K 257 VAL cc_start: 0.9509 (t) cc_final: 0.9202 (t) REVERT: K 278 GLU cc_start: 0.8945 (mp0) cc_final: 0.8734 (mp0) REVERT: K 319 LEU cc_start: 0.9472 (tt) cc_final: 0.9268 (tp) REVERT: K 334 ASN cc_start: 0.9385 (p0) cc_final: 0.8972 (p0) REVERT: K 347 TYR cc_start: 0.9008 (m-80) cc_final: 0.8677 (m-80) REVERT: K 385 MET cc_start: 0.8533 (pmm) cc_final: 0.8283 (pmm) REVERT: L 139 LEU cc_start: 0.9527 (tp) cc_final: 0.9293 (tp) REVERT: L 167 ASN cc_start: 0.9289 (p0) cc_final: 0.8825 (p0) REVERT: L 254 TYR cc_start: 0.8952 (m-80) cc_final: 0.8685 (m-80) REVERT: M 166 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8493 (mmtm) REVERT: M 253 ASP cc_start: 0.9158 (p0) cc_final: 0.8945 (p0) REVERT: N 371 ASN cc_start: 0.9516 (m110) cc_final: 0.9241 (m110) REVERT: N 385 MET cc_start: 0.8801 (pmm) cc_final: 0.8408 (pmm) REVERT: N 417 TYR cc_start: 0.7325 (t80) cc_final: 0.7057 (t80) REVERT: N 657 GLN cc_start: 0.9243 (pm20) cc_final: 0.8762 (pm20) outliers start: 1 outliers final: 1 residues processed: 536 average time/residue: 0.3781 time to fit residues: 337.4385 Evaluate side-chains 417 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 416 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 342 optimal weight: 6.9990 chunk 234 optimal weight: 20.0000 chunk 48 optimal weight: 50.0000 chunk 15 optimal weight: 40.0000 chunk 46 optimal weight: 0.3980 chunk 202 optimal weight: 40.0000 chunk 337 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 302 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 overall best weight: 6.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 230 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 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** H 657 GLN ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 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** ** K 658 GLN ** 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 543 ASN ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 582 ASN ** N 331 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.060822 restraints weight = 121530.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.062926 restraints weight = 71931.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.064332 restraints weight = 49903.018| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31804 Z= 0.221 Angle : 0.639 11.651 43368 Z= 0.347 Chirality : 0.045 0.196 4788 Planarity : 0.004 0.063 5747 Dihedral : 6.026 50.469 4463 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.12 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.13), residues: 4053 helix: -3.11 (0.47), residues: 84 sheet: -0.65 (0.13), residues: 1428 loop : -1.37 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 706 HIS 0.009 0.002 HIS J 221 PHE 0.024 0.002 PHE H 652 TYR 0.021 0.002 TYR I 679 ARG 0.006 0.001 ARG H 229 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 1190) hydrogen bonds : angle 7.10613 ( 3282) SS BOND : bond 0.00425 ( 21) SS BOND : angle 1.37440 ( 42) covalent geometry : bond 0.00468 (31783) covalent geometry : angle 0.63741 (43326) *********************** 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 532 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 3.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 280 PHE cc_start: 0.9297 (m-80) cc_final: 0.8972 (m-80) REVERT: H 328 ILE cc_start: 0.9236 (mt) cc_final: 0.9031 (mt) REVERT: H 417 TYR cc_start: 0.8871 (t80) cc_final: 0.8579 (t80) REVERT: H 449 ASP cc_start: 0.8170 (t0) cc_final: 0.7762 (t0) REVERT: H 465 LEU cc_start: 0.9476 (mp) cc_final: 0.9109 (mt) REVERT: H 543 ASN cc_start: 0.9034 (t0) cc_final: 0.8655 (p0) REVERT: H 688 PHE cc_start: 0.7828 (t80) cc_final: 0.7413 (t80) REVERT: H 699 LEU cc_start: 0.8976 (tp) cc_final: 0.8487 (pp) REVERT: H 713 PHE cc_start: 0.9428 (m-10) cc_final: 0.9153 (m-10) REVERT: I 188 LEU cc_start: 0.9472 (mm) cc_final: 0.9195 (mt) REVERT: I 284 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8149 (mm-30) REVERT: I 347 TYR cc_start: 0.9269 (m-80) cc_final: 0.8839 (m-80) REVERT: I 385 MET cc_start: 0.8673 (pmm) cc_final: 0.8331 (pmm) REVERT: I 390 LYS cc_start: 0.9220 (tmtt) cc_final: 0.8855 (tptp) REVERT: I 532 TRP cc_start: 0.9356 (m100) cc_final: 0.8758 (m100) REVERT: I 541 LEU cc_start: 0.9529 (tp) cc_final: 0.9185 (tp) REVERT: I 594 GLN cc_start: 0.9343 (mp10) cc_final: 0.9051 (mp10) REVERT: J 154 ASP cc_start: 0.9540 (m-30) cc_final: 0.8951 (t0) REVERT: J 163 TRP cc_start: 0.8395 (t-100) cc_final: 0.7724 (t-100) REVERT: J 211 LEU cc_start: 0.9370 (tp) cc_final: 0.9167 (tp) REVERT: J 253 ASP cc_start: 0.8920 (p0) cc_final: 0.8715 (p0) REVERT: J 328 ILE cc_start: 0.9404 (mt) cc_final: 0.9123 (mt) REVERT: J 347 TYR cc_start: 0.9697 (m-10) cc_final: 0.9477 (m-10) REVERT: J 385 MET cc_start: 0.8596 (pmm) cc_final: 0.8290 (pmm) REVERT: J 434 ASP cc_start: 0.7956 (p0) cc_final: 0.7567 (p0) REVERT: J 449 ASP cc_start: 0.8372 (t0) cc_final: 0.8141 (t0) REVERT: J 658 GLN cc_start: 0.8035 (pm20) cc_final: 0.7367 (pm20) REVERT: K 188 LEU cc_start: 0.9515 (mm) cc_final: 0.9281 (mm) REVERT: K 257 VAL cc_start: 0.9526 (t) cc_final: 0.9213 (t) REVERT: K 278 GLU cc_start: 0.8899 (mp0) cc_final: 0.8686 (mp0) REVERT: K 334 ASN cc_start: 0.9412 (p0) cc_final: 0.8968 (p0) REVERT: K 347 TYR cc_start: 0.8986 (m-80) cc_final: 0.8598 (m-80) REVERT: K 713 PHE cc_start: 0.9614 (m-10) cc_final: 0.9243 (m-80) REVERT: L 139 LEU cc_start: 0.9568 (tp) cc_final: 0.9346 (tp) REVERT: L 167 ASN cc_start: 0.9192 (p0) cc_final: 0.8850 (p0) REVERT: L 185 ARG cc_start: 0.8744 (ttt180) cc_final: 0.8504 (ttt90) REVERT: L 254 TYR cc_start: 0.9011 (m-80) cc_final: 0.8659 (m-80) REVERT: L 315 GLN cc_start: 0.8999 (pp30) cc_final: 0.8768 (pm20) REVERT: L 541 LEU cc_start: 0.9255 (tp) cc_final: 0.8991 (tp) REVERT: M 166 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8526 (mmtm) REVERT: M 184 TYR cc_start: 0.8931 (m-10) cc_final: 0.8637 (m-10) REVERT: M 253 ASP cc_start: 0.9094 (p0) cc_final: 0.8757 (p0) REVERT: M 281 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8690 (tm-30) REVERT: M 328 ILE cc_start: 0.9070 (mt) cc_final: 0.8840 (mt) REVERT: N 356 ARG cc_start: 0.9208 (ttm110) cc_final: 0.8742 (ttm110) REVERT: N 371 ASN cc_start: 0.9500 (m110) cc_final: 0.9207 (m110) REVERT: N 376 LEU cc_start: 0.9368 (tp) cc_final: 0.9103 (tp) REVERT: N 385 MET cc_start: 0.8787 (pmm) cc_final: 0.8480 (pmm) REVERT: N 417 TYR cc_start: 0.7297 (t80) cc_final: 0.7021 (t80) REVERT: N 657 GLN cc_start: 0.9340 (pm20) cc_final: 0.8870 (pm20) outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.3828 time to fit residues: 339.7851 Evaluate side-chains 419 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 229 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 250 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 389 optimal weight: 30.0000 chunk 224 optimal weight: 0.3980 chunk 399 optimal weight: 10.0000 chunk 199 optimal weight: 7.9990 chunk 49 optimal weight: 0.4980 chunk 392 optimal weight: 7.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 230 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 275 ASN ** 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 599 GLN ** 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.085560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.062101 restraints weight = 117344.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.064303 restraints weight = 69093.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.065776 restraints weight = 47734.963| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31804 Z= 0.166 Angle : 0.593 8.472 43368 Z= 0.322 Chirality : 0.044 0.228 4788 Planarity : 0.004 0.066 5747 Dihedral : 5.779 47.427 4463 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.43 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 4053 helix: -3.11 (0.46), residues: 84 sheet: -0.48 (0.13), residues: 1414 loop : -1.31 (0.12), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 318 HIS 0.007 0.001 HIS J 221 PHE 0.022 0.002 PHE H 652 TYR 0.026 0.002 TYR H 184 ARG 0.005 0.000 ARG I 687 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 1190) hydrogen bonds : angle 6.84590 ( 3282) SS BOND : bond 0.00208 ( 21) SS BOND : angle 1.57449 ( 42) covalent geometry : bond 0.00360 (31783) covalent geometry : angle 0.59095 (43326) *********************** 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 541 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 3.801 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: H 280 PHE cc_start: 0.9267 (m-80) cc_final: 0.8922 (m-10) REVERT: H 328 ILE cc_start: 0.8950 (mt) cc_final: 0.8678 (mt) REVERT: H 417 TYR cc_start: 0.8822 (t80) cc_final: 0.8535 (t80) REVERT: H 465 LEU cc_start: 0.9440 (mp) cc_final: 0.9070 (mt) REVERT: H 688 PHE cc_start: 0.7810 (t80) cc_final: 0.7390 (t80) REVERT: H 699 LEU cc_start: 0.8968 (tp) cc_final: 0.8491 (pp) REVERT: H 713 PHE cc_start: 0.9441 (m-10) cc_final: 0.9185 (m-10) REVERT: I 188 LEU cc_start: 0.9471 (mm) cc_final: 0.9141 (mt) REVERT: I 247 THR cc_start: 0.9398 (m) cc_final: 0.9174 (p) REVERT: I 284 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8274 (mm-30) REVERT: I 347 TYR cc_start: 0.9281 (m-80) cc_final: 0.8785 (m-80) REVERT: I 385 MET cc_start: 0.8680 (pmm) cc_final: 0.8333 (pmm) REVERT: I 390 LYS cc_start: 0.9251 (tmtt) cc_final: 0.8861 (tptp) REVERT: I 532 TRP cc_start: 0.9369 (m100) cc_final: 0.8953 (m100) REVERT: I 541 LEU cc_start: 0.9546 (tp) cc_final: 0.9256 (tp) REVERT: I 594 GLN cc_start: 0.9301 (mp10) cc_final: 0.8839 (mp10) REVERT: J 154 ASP cc_start: 0.9539 (m-30) cc_final: 0.8888 (t0) REVERT: J 163 TRP cc_start: 0.8220 (t-100) cc_final: 0.7541 (t-100) REVERT: J 211 LEU cc_start: 0.9411 (tp) cc_final: 0.9192 (tp) REVERT: J 325 ASP cc_start: 0.8906 (t70) cc_final: 0.8704 (t70) REVERT: J 326 TYR cc_start: 0.9217 (m-10) cc_final: 0.8782 (m-10) REVERT: J 328 ILE cc_start: 0.9319 (mt) cc_final: 0.9041 (mt) REVERT: J 347 TYR cc_start: 0.9671 (m-10) cc_final: 0.9422 (m-10) REVERT: J 434 ASP cc_start: 0.7902 (p0) cc_final: 0.7562 (p0) REVERT: J 449 ASP cc_start: 0.8437 (t0) cc_final: 0.8163 (t0) REVERT: J 657 GLN cc_start: 0.7822 (tt0) cc_final: 0.7587 (tt0) REVERT: J 658 GLN cc_start: 0.7912 (pm20) cc_final: 0.7296 (pm20) REVERT: K 139 LEU cc_start: 0.9467 (tp) cc_final: 0.9251 (tp) REVERT: K 257 VAL cc_start: 0.9546 (t) cc_final: 0.9236 (t) REVERT: K 278 GLU cc_start: 0.8929 (mp0) cc_final: 0.8640 (mp0) REVERT: K 334 ASN cc_start: 0.9415 (p0) cc_final: 0.8977 (p0) REVERT: K 345 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8742 (tm-30) REVERT: K 347 TYR cc_start: 0.8952 (m-80) cc_final: 0.8543 (m-80) REVERT: K 385 MET cc_start: 0.8407 (pmm) cc_final: 0.8102 (pmm) REVERT: K 713 PHE cc_start: 0.9616 (m-10) cc_final: 0.9238 (m-80) REVERT: L 139 LEU cc_start: 0.9536 (tp) cc_final: 0.9309 (tp) REVERT: L 167 ASN cc_start: 0.9192 (p0) cc_final: 0.8986 (p0) REVERT: L 168 GLU cc_start: 0.9231 (mp0) cc_final: 0.8996 (mp0) REVERT: L 185 ARG cc_start: 0.8721 (ttt180) cc_final: 0.8326 (ttt180) REVERT: L 254 TYR cc_start: 0.9060 (m-80) cc_final: 0.8471 (m-10) REVERT: L 512 CYS cc_start: 0.7292 (t) cc_final: 0.7060 (t) REVERT: L 541 LEU cc_start: 0.9255 (tp) cc_final: 0.8968 (tp) REVERT: M 166 LYS cc_start: 0.8731 (mmtm) cc_final: 0.8455 (mmtm) REVERT: M 184 TYR cc_start: 0.8797 (m-10) cc_final: 0.8524 (m-10) REVERT: M 281 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8639 (tm-30) REVERT: M 417 TYR cc_start: 0.8293 (t80) cc_final: 0.8002 (t80) REVERT: N 356 ARG cc_start: 0.9176 (ttm110) cc_final: 0.8724 (ttm110) REVERT: N 371 ASN cc_start: 0.9483 (m110) cc_final: 0.9277 (m110) REVERT: N 385 MET cc_start: 0.8848 (pmm) cc_final: 0.8501 (pmm) REVERT: N 401 PHE cc_start: 0.8931 (m-80) cc_final: 0.8428 (m-80) REVERT: N 417 TYR cc_start: 0.7379 (t80) cc_final: 0.7092 (t80) REVERT: N 657 GLN cc_start: 0.9289 (pm20) cc_final: 0.8904 (pm20) outliers start: 0 outliers final: 0 residues processed: 541 average time/residue: 0.3817 time to fit residues: 341.6239 Evaluate side-chains 429 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 175 optimal weight: 5.9990 chunk 373 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 chunk 301 optimal weight: 10.0000 chunk 279 optimal weight: 30.0000 chunk 400 optimal weight: 6.9990 chunk 73 optimal weight: 30.0000 chunk 105 optimal weight: 30.0000 chunk 307 optimal weight: 40.0000 chunk 326 optimal weight: 9.9990 chunk 371 optimal weight: 0.9980 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 230 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 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 275 ASN ** I 345 GLN ** 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 599 GLN ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 ASN ** K 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 149 ASN ** 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** ** N 331 ASN ** 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 = 0.3350 r_free = 0.3350 target = 0.084083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.060886 restraints weight = 120880.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.062992 restraints weight = 71638.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.064398 restraints weight = 49764.666| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2361 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= 0.227 Angle : 0.642 8.055 43368 Z= 0.349 Chirality : 0.045 0.222 4788 Planarity : 0.005 0.116 5747 Dihedral : 5.951 47.521 4463 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.14 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.13), residues: 4053 helix: -3.02 (0.47), residues: 84 sheet: -0.55 (0.14), residues: 1393 loop : -1.28 (0.12), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 245 HIS 0.010 0.002 HIS M 221 PHE 0.023 0.002 PHE H 652 TYR 0.025 0.002 TYR I 254 ARG 0.006 0.001 ARG H 438 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 1190) hydrogen bonds : angle 6.90445 ( 3282) SS BOND : bond 0.00279 ( 21) SS BOND : angle 1.82789 ( 42) covalent geometry : bond 0.00483 (31783) covalent geometry : angle 0.63957 (43326) *********************** 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 524 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 3.278 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 328 ILE cc_start: 0.8925 (mt) cc_final: 0.8674 (mt) REVERT: H 417 TYR cc_start: 0.8761 (t80) cc_final: 0.7884 (t80) REVERT: H 465 LEU cc_start: 0.9427 (mp) cc_final: 0.9043 (mt) REVERT: H 543 ASN cc_start: 0.9041 (t0) cc_final: 0.8620 (p0) REVERT: H 688 PHE cc_start: 0.7859 (t80) cc_final: 0.7462 (t80) REVERT: H 699 LEU cc_start: 0.8995 (tp) cc_final: 0.8483 (pp) REVERT: H 713 PHE cc_start: 0.9442 (m-10) cc_final: 0.9185 (m-10) REVERT: I 188 LEU cc_start: 0.9494 (mm) cc_final: 0.9191 (mt) REVERT: I 243 ARG cc_start: 0.9281 (mmp80) cc_final: 0.9067 (mmm160) REVERT: I 259 ASN cc_start: 0.9357 (t0) cc_final: 0.9077 (t0) REVERT: I 315 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8427 (tm-30) REVERT: I 347 TYR cc_start: 0.9253 (m-80) cc_final: 0.8766 (m-80) REVERT: I 385 MET cc_start: 0.8828 (pmm) cc_final: 0.8470 (pmm) REVERT: I 390 LYS cc_start: 0.9230 (tmtt) cc_final: 0.8839 (tptp) REVERT: I 532 TRP cc_start: 0.9370 (m100) cc_final: 0.8856 (m100) REVERT: I 541 LEU cc_start: 0.9532 (tp) cc_final: 0.9198 (tp) REVERT: I 594 GLN cc_start: 0.9319 (mp10) cc_final: 0.9018 (mp10) REVERT: J 154 ASP cc_start: 0.9565 (m-30) cc_final: 0.8943 (t0) REVERT: J 163 TRP cc_start: 0.8342 (t-100) cc_final: 0.7568 (t-100) REVERT: J 253 ASP cc_start: 0.8908 (p0) cc_final: 0.8686 (p0) REVERT: J 328 ILE cc_start: 0.9309 (mt) cc_final: 0.9038 (mt) REVERT: J 347 TYR cc_start: 0.9674 (m-10) cc_final: 0.9452 (m-10) REVERT: J 385 MET cc_start: 0.8647 (pmm) cc_final: 0.8305 (pmm) REVERT: J 434 ASP cc_start: 0.7913 (p0) cc_final: 0.7454 (p0) REVERT: J 449 ASP cc_start: 0.8400 (t0) cc_final: 0.8155 (t0) REVERT: J 657 GLN cc_start: 0.7811 (tt0) cc_final: 0.7586 (tt0) REVERT: J 658 GLN cc_start: 0.7959 (pm20) cc_final: 0.7368 (pm20) REVERT: J 688 PHE cc_start: 0.7869 (t80) cc_final: 0.7461 (t80) REVERT: K 188 LEU cc_start: 0.9479 (mm) cc_final: 0.9234 (mm) REVERT: K 278 GLU cc_start: 0.8953 (mp0) cc_final: 0.8724 (mp0) REVERT: K 334 ASN cc_start: 0.9401 (p0) cc_final: 0.8989 (p0) REVERT: K 713 PHE cc_start: 0.9603 (m-10) cc_final: 0.9219 (m-80) REVERT: L 139 LEU cc_start: 0.9549 (tp) cc_final: 0.9343 (tp) REVERT: L 185 ARG cc_start: 0.8737 (ttt180) cc_final: 0.8462 (ttt90) REVERT: L 254 TYR cc_start: 0.9060 (m-80) cc_final: 0.8535 (m-80) REVERT: L 512 CYS cc_start: 0.7874 (t) cc_final: 0.7507 (t) REVERT: L 532 TRP cc_start: 0.9204 (m100) cc_final: 0.8738 (m100) REVERT: L 541 LEU cc_start: 0.9285 (tp) cc_final: 0.9043 (tp) REVERT: M 166 LYS cc_start: 0.8729 (mmtm) cc_final: 0.8421 (mmtm) REVERT: M 184 TYR cc_start: 0.8853 (m-10) cc_final: 0.8521 (m-10) REVERT: M 253 ASP cc_start: 0.9212 (p0) cc_final: 0.8905 (p0) REVERT: M 417 TYR cc_start: 0.8303 (t80) cc_final: 0.7991 (t80) REVERT: N 211 LEU cc_start: 0.9483 (tp) cc_final: 0.9275 (tp) REVERT: N 371 ASN cc_start: 0.9568 (m110) cc_final: 0.9307 (m110) REVERT: N 376 LEU cc_start: 0.9497 (tp) cc_final: 0.9206 (tp) REVERT: N 417 TYR cc_start: 0.7458 (t80) cc_final: 0.7136 (t80) REVERT: N 657 GLN cc_start: 0.9391 (pm20) cc_final: 0.8917 (pm20) outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.3628 time to fit residues: 318.2021 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 : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 391 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 266 optimal weight: 40.0000 chunk 49 optimal weight: 40.0000 chunk 214 optimal weight: 30.0000 chunk 393 optimal weight: 6.9990 chunk 366 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 230 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 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 221 HIS ** 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 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 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** 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 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 599 GLN ** 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 = 0.3348 r_free = 0.3348 target = 0.083895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.060690 restraints weight = 120742.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.062834 restraints weight = 71234.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.064269 restraints weight = 49316.366| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 31804 Z= 0.235 Angle : 0.646 7.018 43368 Z= 0.351 Chirality : 0.045 0.214 4788 Planarity : 0.005 0.088 5747 Dihedral : 6.002 47.309 4463 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.24 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 4053 helix: -3.03 (0.47), residues: 84 sheet: -0.64 (0.14), residues: 1407 loop : -1.32 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 163 HIS 0.009 0.002 HIS M 221 PHE 0.026 0.002 PHE H 652 TYR 0.028 0.002 TYR L 184 ARG 0.007 0.001 ARG J 150 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 1190) hydrogen bonds : angle 6.95053 ( 3282) SS BOND : bond 0.00398 ( 21) SS BOND : angle 1.63370 ( 42) covalent geometry : bond 0.00501 (31783) covalent geometry : angle 0.64440 (43326) *********************** 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 521 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 3.508 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: 0.8947 (mt) cc_final: 0.8707 (mt) REVERT: H 417 TYR cc_start: 0.8717 (t80) cc_final: 0.7841 (t80) REVERT: H 465 LEU cc_start: 0.9407 (mp) cc_final: 0.8932 (tp) REVERT: H 543 ASN cc_start: 0.9055 (t0) cc_final: 0.8620 (p0) REVERT: H 688 PHE cc_start: 0.7911 (t80) cc_final: 0.7516 (t80) REVERT: H 699 LEU cc_start: 0.8985 (tp) cc_final: 0.8446 (pp) REVERT: H 713 PHE cc_start: 0.9451 (m-10) cc_final: 0.9200 (m-10) REVERT: I 188 LEU cc_start: 0.9536 (mm) cc_final: 0.9194 (mt) REVERT: I 243 ARG cc_start: 0.9301 (mmp80) cc_final: 0.9079 (mmm160) REVERT: I 247 THR cc_start: 0.9379 (m) cc_final: 0.9152 (p) REVERT: I 253 ASP cc_start: 0.9048 (p0) cc_final: 0.8831 (p0) REVERT: I 259 ASN cc_start: 0.9290 (t0) cc_final: 0.9006 (t0) REVERT: I 347 TYR cc_start: 0.9267 (m-80) cc_final: 0.8741 (m-80) REVERT: I 385 MET cc_start: 0.8666 (pmm) cc_final: 0.8328 (pmm) REVERT: I 390 LYS cc_start: 0.9203 (tmtt) cc_final: 0.8797 (tptp) REVERT: I 532 TRP cc_start: 0.9344 (m100) cc_final: 0.8768 (m100) REVERT: I 594 GLN cc_start: 0.9328 (mp10) cc_final: 0.9029 (mp10) REVERT: J 154 ASP cc_start: 0.9530 (m-30) cc_final: 0.8923 (t0) REVERT: J 163 TRP cc_start: 0.8348 (t-100) cc_final: 0.7557 (t-100) REVERT: J 211 LEU cc_start: 0.9442 (tp) cc_final: 0.9196 (tp) REVERT: J 253 ASP cc_start: 0.8832 (p0) cc_final: 0.8569 (p0) REVERT: J 328 ILE cc_start: 0.9321 (mt) cc_final: 0.9084 (mt) REVERT: J 347 TYR cc_start: 0.9677 (m-10) cc_final: 0.9467 (m-10) REVERT: J 385 MET cc_start: 0.8551 (pmm) cc_final: 0.8182 (pmm) REVERT: J 434 ASP cc_start: 0.7847 (p0) cc_final: 0.7351 (p0) REVERT: J 449 ASP cc_start: 0.8378 (t0) cc_final: 0.8127 (t0) REVERT: J 657 GLN cc_start: 0.7861 (tt0) cc_final: 0.7622 (tt0) REVERT: J 658 GLN cc_start: 0.7999 (pm20) cc_final: 0.7423 (pm20) REVERT: J 688 PHE cc_start: 0.7933 (t80) cc_final: 0.7423 (t80) REVERT: K 139 LEU cc_start: 0.9506 (tp) cc_final: 0.9280 (tp) REVERT: K 211 LEU cc_start: 0.9091 (mm) cc_final: 0.8615 (tp) REVERT: K 253 ASP cc_start: 0.9160 (p0) cc_final: 0.8937 (p0) REVERT: K 278 GLU cc_start: 0.8878 (mp0) cc_final: 0.8660 (mp0) REVERT: K 334 ASN cc_start: 0.9419 (p0) cc_final: 0.8992 (p0) REVERT: K 347 TYR cc_start: 0.8786 (m-80) cc_final: 0.8392 (m-80) REVERT: K 385 MET cc_start: 0.8270 (pmm) cc_final: 0.7874 (pmm) REVERT: L 139 LEU cc_start: 0.9551 (tp) cc_final: 0.9336 (tp) REVERT: L 254 TYR cc_start: 0.9056 (m-80) cc_final: 0.8522 (m-80) REVERT: L 268 LEU cc_start: 0.9728 (tp) cc_final: 0.9508 (tp) REVERT: L 512 CYS cc_start: 0.7841 (t) cc_final: 0.7462 (t) REVERT: L 532 TRP cc_start: 0.9120 (m100) cc_final: 0.8907 (m100) REVERT: L 658 GLN cc_start: 0.7611 (pm20) cc_final: 0.6746 (pm20) REVERT: M 184 TYR cc_start: 0.8728 (m-10) cc_final: 0.8396 (m-10) REVERT: M 253 ASP cc_start: 0.9173 (p0) cc_final: 0.8831 (p0) REVERT: M 315 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8877 (tm-30) REVERT: M 417 TYR cc_start: 0.8300 (t80) cc_final: 0.7988 (t80) REVERT: N 356 ARG cc_start: 0.9099 (ttm110) cc_final: 0.8488 (mtm110) REVERT: N 371 ASN cc_start: 0.9533 (m110) cc_final: 0.9263 (m110) REVERT: N 376 LEU cc_start: 0.9430 (tp) cc_final: 0.9174 (tp) REVERT: N 385 MET cc_start: 0.8635 (pmm) cc_final: 0.8406 (pmm) REVERT: N 401 PHE cc_start: 0.9009 (m-80) cc_final: 0.8576 (m-80) REVERT: N 417 TYR cc_start: 0.7413 (t80) cc_final: 0.7040 (t80) REVERT: N 657 GLN cc_start: 0.9380 (pm20) cc_final: 0.8998 (pm20) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.3651 time to fit residues: 316.1193 Evaluate side-chains 409 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 385 optimal weight: 20.0000 chunk 335 optimal weight: 30.0000 chunk 82 optimal weight: 7.9990 chunk 346 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 296 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 300 optimal weight: 30.0000 chunk 264 optimal weight: 0.9980 chunk 329 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 230 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 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 225 GLN ** I 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 GLN ** 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 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 682 ASN ** L 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 427 GLN ** L 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 331 ASN ** 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 = 0.3372 r_free = 0.3372 target = 0.085173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.061495 restraints weight = 118103.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.063708 restraints weight = 69063.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.065198 restraints weight = 47600.184| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31804 Z= 0.179 Angle : 0.611 8.884 43368 Z= 0.331 Chirality : 0.045 0.219 4788 Planarity : 0.004 0.078 5747 Dihedral : 5.821 46.587 4463 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.50 % Favored : 94.47 % Rotamer: Outliers : 0.03 % Allowed : 1.19 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 4053 helix: -3.10 (0.47), residues: 84 sheet: -0.64 (0.13), residues: 1442 loop : -1.26 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 163 HIS 0.008 0.001 HIS J 221 PHE 0.025 0.002 PHE H 652 TYR 0.025 0.002 TYR L 184 ARG 0.013 0.001 ARG K 372 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 1190) hydrogen bonds : angle 6.79693 ( 3282) SS BOND : bond 0.00481 ( 21) SS BOND : angle 1.67153 ( 42) covalent geometry : bond 0.00392 (31783) covalent geometry : angle 0.60941 (43326) *********************** 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 524 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 523 time to evaluate : 3.517 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 211 LEU cc_start: 0.8650 (mt) cc_final: 0.7786 (tt) REVERT: H 222 LEU cc_start: 0.9371 (mt) cc_final: 0.9160 (mt) REVERT: H 328 ILE cc_start: 0.8922 (mt) cc_final: 0.8681 (mt) REVERT: H 417 TYR cc_start: 0.8718 (t80) cc_final: 0.7870 (t80) REVERT: H 452 HIS cc_start: 0.9164 (t-90) cc_final: 0.8909 (t-90) REVERT: H 465 LEU cc_start: 0.9406 (mp) cc_final: 0.8986 (mt) REVERT: H 543 ASN cc_start: 0.9062 (t0) cc_final: 0.8638 (p0) REVERT: H 688 PHE cc_start: 0.7973 (t80) cc_final: 0.7619 (t80) REVERT: H 699 LEU cc_start: 0.8962 (tp) cc_final: 0.8420 (pp) REVERT: H 703 SER cc_start: 0.8876 (p) cc_final: 0.8626 (m) REVERT: H 713 PHE cc_start: 0.9451 (m-10) cc_final: 0.9181 (m-10) REVERT: I 188 LEU cc_start: 0.9555 (mm) cc_final: 0.9275 (mt) REVERT: I 247 THR cc_start: 0.9396 (m) cc_final: 0.9153 (p) REVERT: I 253 ASP cc_start: 0.9082 (p0) cc_final: 0.8875 (p0) REVERT: I 259 ASN cc_start: 0.9245 (t0) cc_final: 0.8993 (t0) REVERT: I 347 TYR cc_start: 0.9243 (m-80) cc_final: 0.8669 (m-80) REVERT: I 385 MET cc_start: 0.8626 (pmm) cc_final: 0.8252 (pmm) REVERT: I 390 LYS cc_start: 0.9226 (tmtt) cc_final: 0.8820 (tptp) REVERT: I 532 TRP cc_start: 0.9344 (m100) cc_final: 0.8773 (m100) REVERT: I 594 GLN cc_start: 0.9303 (mp10) cc_final: 0.8843 (mp10) REVERT: J 154 ASP cc_start: 0.9512 (m-30) cc_final: 0.8855 (t0) REVERT: J 163 TRP cc_start: 0.8288 (t-100) cc_final: 0.7529 (t-100) REVERT: J 211 LEU cc_start: 0.9410 (tp) cc_final: 0.9137 (tp) REVERT: J 253 ASP cc_start: 0.8848 (p0) cc_final: 0.8607 (p0) REVERT: J 385 MET cc_start: 0.8671 (pmm) cc_final: 0.8417 (pmm) REVERT: J 434 ASP cc_start: 0.7846 (p0) cc_final: 0.7405 (p0) REVERT: J 449 ASP cc_start: 0.8419 (t0) cc_final: 0.8148 (t0) REVERT: J 657 GLN cc_start: 0.7786 (tt0) cc_final: 0.7477 (tt0) REVERT: J 658 GLN cc_start: 0.8019 (pm20) cc_final: 0.7452 (pm20) REVERT: J 688 PHE cc_start: 0.7832 (t80) cc_final: 0.7276 (t80) REVERT: K 139 LEU cc_start: 0.9495 (tp) cc_final: 0.9285 (tp) REVERT: K 211 LEU cc_start: 0.9111 (mm) cc_final: 0.8634 (tp) REVERT: K 278 GLU cc_start: 0.8880 (mp0) cc_final: 0.8631 (mp0) REVERT: K 334 ASN cc_start: 0.9405 (p0) cc_final: 0.8977 (p0) REVERT: K 347 TYR cc_start: 0.8878 (m-80) cc_final: 0.8491 (m-80) REVERT: K 385 MET cc_start: 0.8338 (pmm) cc_final: 0.7939 (pmm) REVERT: K 713 PHE cc_start: 0.9492 (m-80) cc_final: 0.9220 (m-80) REVERT: L 139 LEU cc_start: 0.9526 (tp) cc_final: 0.9302 (tp) REVERT: L 254 TYR cc_start: 0.9018 (m-80) cc_final: 0.8393 (m-80) REVERT: L 268 LEU cc_start: 0.9725 (tp) cc_final: 0.9522 (tp) REVERT: L 532 TRP cc_start: 0.9173 (m100) cc_final: 0.8845 (m100) REVERT: L 658 GLN cc_start: 0.7507 (pm20) cc_final: 0.6654 (pm20) REVERT: M 184 TYR cc_start: 0.8656 (m-10) cc_final: 0.8342 (m-10) REVERT: M 253 ASP cc_start: 0.9201 (p0) cc_final: 0.8872 (p0) REVERT: M 315 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8868 (tm-30) REVERT: M 417 TYR cc_start: 0.8260 (t80) cc_final: 0.7984 (t80) REVERT: N 253 ASP cc_start: 0.9201 (p0) cc_final: 0.8990 (p0) REVERT: N 356 ARG cc_start: 0.9048 (ttm110) cc_final: 0.8694 (mtm110) REVERT: N 371 ASN cc_start: 0.9529 (m110) cc_final: 0.9260 (m110) REVERT: N 376 LEU cc_start: 0.9414 (tp) cc_final: 0.9115 (tp) REVERT: N 385 MET cc_start: 0.8618 (pmm) cc_final: 0.8380 (pmm) REVERT: N 390 LYS cc_start: 0.9301 (tmtt) cc_final: 0.8994 (tptp) REVERT: N 417 TYR cc_start: 0.7257 (t80) cc_final: 0.6938 (t80) REVERT: N 657 GLN cc_start: 0.9301 (pm20) cc_final: 0.8988 (pm20) outliers start: 1 outliers final: 0 residues processed: 524 average time/residue: 0.3784 time to fit residues: 329.8869 Evaluate side-chains 422 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 313 optimal weight: 8.9990 chunk 389 optimal weight: 30.0000 chunk 182 optimal weight: 8.9990 chunk 335 optimal weight: 30.0000 chunk 263 optimal weight: 4.9990 chunk 387 optimal weight: 6.9990 chunk 401 optimal weight: 30.0000 chunk 63 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 230 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** 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 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 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** ** J 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 ASN ** K 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 230 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** ** N 331 ASN ** 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 = 0.3340 r_free = 0.3340 target = 0.083383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.060403 restraints weight = 121355.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.062505 restraints weight = 71450.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.063905 restraints weight = 49443.517| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 31804 Z= 0.258 Angle : 0.677 9.442 43368 Z= 0.366 Chirality : 0.046 0.219 4788 Planarity : 0.005 0.082 5747 Dihedral : 6.051 47.425 4463 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.76 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 4053 helix: -2.98 (0.49), residues: 84 sheet: -0.68 (0.13), residues: 1407 loop : -1.32 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP M 245 HIS 0.009 0.002 HIS J 221 PHE 0.025 0.002 PHE H 652 TYR 0.025 0.002 TYR H 254 ARG 0.014 0.001 ARG K 372 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 1190) hydrogen bonds : angle 6.95995 ( 3282) SS BOND : bond 0.00381 ( 21) SS BOND : angle 1.78431 ( 42) covalent geometry : bond 0.00552 (31783) covalent geometry : angle 0.67497 (43326) *********************** 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 496 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 3.251 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: H 222 LEU cc_start: 0.9365 (mt) cc_final: 0.9152 (mt) REVERT: H 328 ILE cc_start: 0.8949 (mt) cc_final: 0.8705 (mt) REVERT: H 417 TYR cc_start: 0.8697 (t80) cc_final: 0.7839 (t80) REVERT: H 465 LEU cc_start: 0.9391 (mp) cc_final: 0.8904 (tp) REVERT: H 543 ASN cc_start: 0.9086 (t0) cc_final: 0.8603 (p0) REVERT: H 688 PHE cc_start: 0.7988 (t80) cc_final: 0.7643 (t80) REVERT: H 699 LEU cc_start: 0.8990 (tp) cc_final: 0.8417 (pp) REVERT: H 713 PHE cc_start: 0.9456 (m-10) cc_final: 0.9193 (m-10) REVERT: I 188 LEU cc_start: 0.9544 (mm) cc_final: 0.9244 (mt) REVERT: I 243 ARG cc_start: 0.9363 (mmp80) cc_final: 0.9152 (mmm160) REVERT: I 247 THR cc_start: 0.9378 (m) cc_final: 0.9116 (p) REVERT: I 253 ASP cc_start: 0.9136 (p0) cc_final: 0.8919 (p0) REVERT: I 259 ASN cc_start: 0.9268 (t0) cc_final: 0.8994 (t0) REVERT: I 347 TYR cc_start: 0.9257 (m-80) cc_final: 0.8708 (m-80) REVERT: I 385 MET cc_start: 0.8632 (pmm) cc_final: 0.8373 (pmm) REVERT: I 390 LYS cc_start: 0.9168 (tmtt) cc_final: 0.8758 (tptp) REVERT: I 532 TRP cc_start: 0.9370 (m100) cc_final: 0.8694 (m100) REVERT: I 541 LEU cc_start: 0.9381 (tp) cc_final: 0.9175 (tp) REVERT: I 594 GLN cc_start: 0.9329 (mp10) cc_final: 0.9056 (mp10) REVERT: J 154 ASP cc_start: 0.9530 (m-30) cc_final: 0.8916 (t0) REVERT: J 163 TRP cc_start: 0.8342 (t-100) cc_final: 0.7508 (t-100) REVERT: J 253 ASP cc_start: 0.8771 (p0) cc_final: 0.8498 (p0) REVERT: J 347 TYR cc_start: 0.9732 (m-10) cc_final: 0.9488 (m-80) REVERT: J 385 MET cc_start: 0.8581 (pmm) cc_final: 0.8249 (pmm) REVERT: J 434 ASP cc_start: 0.7783 (p0) cc_final: 0.7237 (p0) REVERT: J 449 ASP cc_start: 0.8401 (t0) cc_final: 0.8120 (t0) REVERT: J 657 GLN cc_start: 0.7845 (tt0) cc_final: 0.7549 (tt0) REVERT: J 658 GLN cc_start: 0.8035 (pm20) cc_final: 0.7487 (pm20) REVERT: J 688 PHE cc_start: 0.7905 (t80) cc_final: 0.7363 (t80) REVERT: K 253 ASP cc_start: 0.9207 (p0) cc_final: 0.9001 (p0) REVERT: K 278 GLU cc_start: 0.8855 (mp0) cc_final: 0.8637 (mp0) REVERT: K 334 ASN cc_start: 0.9413 (p0) cc_final: 0.8825 (p0) REVERT: K 347 TYR cc_start: 0.8885 (m-80) cc_final: 0.8519 (m-80) REVERT: K 713 PHE cc_start: 0.9457 (m-80) cc_final: 0.9191 (m-80) REVERT: L 139 LEU cc_start: 0.9545 (tp) cc_final: 0.9321 (tp) REVERT: L 254 TYR cc_start: 0.9011 (m-80) cc_final: 0.8475 (m-80) REVERT: L 268 LEU cc_start: 0.9704 (tp) cc_final: 0.9471 (tp) REVERT: L 658 GLN cc_start: 0.7651 (pm20) cc_final: 0.6779 (pm20) REVERT: M 184 TYR cc_start: 0.8740 (m-10) cc_final: 0.8364 (m-10) REVERT: M 253 ASP cc_start: 0.9157 (p0) cc_final: 0.8799 (p0) REVERT: M 417 TYR cc_start: 0.8289 (t80) cc_final: 0.7985 (t80) REVERT: N 356 ARG cc_start: 0.9135 (ttm110) cc_final: 0.8569 (mtm110) REVERT: N 371 ASN cc_start: 0.9536 (m110) cc_final: 0.9259 (m110) REVERT: N 376 LEU cc_start: 0.9416 (tp) cc_final: 0.9137 (tp) REVERT: N 385 MET cc_start: 0.8580 (pmm) cc_final: 0.8350 (pmm) REVERT: N 401 PHE cc_start: 0.9090 (m-80) cc_final: 0.8635 (m-80) REVERT: N 417 TYR cc_start: 0.7349 (t80) cc_final: 0.7033 (t80) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.3602 time to fit residues: 298.4146 Evaluate side-chains 391 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 81 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 393 optimal weight: 10.0000 chunk 197 optimal weight: 0.5980 chunk 236 optimal weight: 1.9990 chunk 233 optimal weight: 8.9990 chunk 350 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 400 optimal weight: 20.0000 chunk 395 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 230 GLN H 266 GLN ** H 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN H 508 ASN ** H 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 225 GLN ** I 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 179 ASN K 371 ASN K 598 ASN ** 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 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.086442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.062729 restraints weight = 116258.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.065020 restraints weight = 67469.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.066560 restraints weight = 46101.003| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 31804 Z= 0.136 Angle : 0.596 8.250 43368 Z= 0.322 Chirality : 0.045 0.237 4788 Planarity : 0.004 0.078 5747 Dihedral : 5.674 44.672 4463 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.24 % Rotamer: Outliers : 0.03 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 4053 helix: -3.23 (0.58), residues: 42 sheet: -0.53 (0.13), residues: 1449 loop : -1.23 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP L 163 HIS 0.007 0.001 HIS M 221 PHE 0.024 0.002 PHE H 652 TYR 0.025 0.002 TYR H 254 ARG 0.012 0.000 ARG K 372 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 1190) hydrogen bonds : angle 6.60744 ( 3282) SS BOND : bond 0.00188 ( 21) SS BOND : angle 1.13166 ( 42) covalent geometry : bond 0.00306 (31783) covalent geometry : angle 0.59505 (43326) ********************** 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 535 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 534 time to evaluate : 3.333 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 280 PHE cc_start: 0.9085 (m-80) cc_final: 0.8743 (m-80) REVERT: H 328 ILE cc_start: 0.8890 (mt) cc_final: 0.8632 (mt) REVERT: H 417 TYR cc_start: 0.8701 (t80) cc_final: 0.7867 (t80) REVERT: H 449 ASP cc_start: 0.8071 (t0) cc_final: 0.7039 (t0) REVERT: H 452 HIS cc_start: 0.9193 (t-90) cc_final: 0.8905 (t-90) REVERT: H 465 LEU cc_start: 0.9368 (mp) cc_final: 0.8957 (mt) REVERT: H 543 ASN cc_start: 0.9095 (t0) cc_final: 0.8644 (p0) REVERT: H 688 PHE cc_start: 0.7878 (t80) cc_final: 0.7536 (t80) REVERT: H 699 LEU cc_start: 0.8950 (tp) cc_final: 0.8418 (pp) REVERT: H 703 SER cc_start: 0.8846 (p) cc_final: 0.8607 (m) REVERT: H 713 PHE cc_start: 0.9453 (m-10) cc_final: 0.9198 (m-10) REVERT: I 180 ILE cc_start: 0.9391 (mm) cc_final: 0.9110 (pt) REVERT: I 188 LEU cc_start: 0.9545 (mm) cc_final: 0.9279 (mt) REVERT: I 247 THR cc_start: 0.9401 (m) cc_final: 0.9101 (p) REVERT: I 253 ASP cc_start: 0.9104 (p0) cc_final: 0.8892 (p0) REVERT: I 259 ASN cc_start: 0.9211 (t0) cc_final: 0.8986 (t0) REVERT: I 281 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8705 (tm-30) REVERT: I 347 TYR cc_start: 0.9258 (m-80) cc_final: 0.8654 (m-80) REVERT: I 385 MET cc_start: 0.8711 (pmm) cc_final: 0.8343 (pmm) REVERT: I 390 LYS cc_start: 0.9240 (tmtt) cc_final: 0.8813 (tptp) REVERT: I 594 GLN cc_start: 0.9275 (mp10) cc_final: 0.8810 (mp10) REVERT: J 154 ASP cc_start: 0.9521 (m-30) cc_final: 0.8841 (t0) REVERT: J 163 TRP cc_start: 0.8196 (t-100) cc_final: 0.7486 (t-100) REVERT: J 211 LEU cc_start: 0.9455 (tp) cc_final: 0.9239 (tp) REVERT: J 253 ASP cc_start: 0.8873 (p0) cc_final: 0.8630 (p0) REVERT: J 325 ASP cc_start: 0.8929 (t70) cc_final: 0.8704 (t70) REVERT: J 347 TYR cc_start: 0.9712 (m-10) cc_final: 0.9456 (m-80) REVERT: J 385 MET cc_start: 0.8651 (pmm) cc_final: 0.8427 (pmm) REVERT: J 434 ASP cc_start: 0.7792 (p0) cc_final: 0.7420 (p0) REVERT: J 449 ASP cc_start: 0.8433 (t0) cc_final: 0.8138 (t0) REVERT: J 657 GLN cc_start: 0.7736 (tt0) cc_final: 0.7424 (tt0) REVERT: J 658 GLN cc_start: 0.7941 (pm20) cc_final: 0.7411 (pm20) REVERT: J 688 PHE cc_start: 0.7827 (t80) cc_final: 0.7262 (t80) REVERT: K 139 LEU cc_start: 0.9448 (tp) cc_final: 0.9223 (tp) REVERT: K 278 GLU cc_start: 0.8860 (mp0) cc_final: 0.8632 (mp0) REVERT: K 334 ASN cc_start: 0.9370 (p0) cc_final: 0.8958 (p0) REVERT: K 347 TYR cc_start: 0.8880 (m-80) cc_final: 0.8519 (m-80) REVERT: K 376 LEU cc_start: 0.9714 (tp) cc_final: 0.9425 (tp) REVERT: K 713 PHE cc_start: 0.9447 (m-80) cc_final: 0.9214 (m-80) REVERT: L 139 LEU cc_start: 0.9497 (tp) cc_final: 0.9258 (tp) REVERT: L 254 TYR cc_start: 0.9031 (m-80) cc_final: 0.8371 (m-80) REVERT: L 315 GLN cc_start: 0.9064 (pp30) cc_final: 0.8835 (tm-30) REVERT: L 373 ILE cc_start: 0.9588 (mp) cc_final: 0.9355 (tp) REVERT: L 481 LEU cc_start: 0.8714 (mt) cc_final: 0.8466 (mt) REVERT: M 139 LEU cc_start: 0.9398 (tp) cc_final: 0.9058 (tp) REVERT: M 184 TYR cc_start: 0.8601 (m-10) cc_final: 0.8256 (m-10) REVERT: M 253 ASP cc_start: 0.9166 (p0) cc_final: 0.8961 (p0) REVERT: M 417 TYR cc_start: 0.8252 (t80) cc_final: 0.7974 (t80) REVERT: N 371 ASN cc_start: 0.9509 (m110) cc_final: 0.9227 (m110) REVERT: N 376 LEU cc_start: 0.9415 (tp) cc_final: 0.9093 (tp) REVERT: N 385 MET cc_start: 0.8661 (pmm) cc_final: 0.8431 (pmm) REVERT: N 390 LYS cc_start: 0.9268 (tmtt) cc_final: 0.8950 (tptp) REVERT: N 401 PHE cc_start: 0.9067 (m-80) cc_final: 0.8613 (m-80) REVERT: N 417 TYR cc_start: 0.7282 (t80) cc_final: 0.6965 (t80) REVERT: N 657 GLN cc_start: 0.9167 (pm20) cc_final: 0.8606 (pm20) outliers start: 1 outliers final: 0 residues processed: 534 average time/residue: 0.3834 time to fit residues: 341.4804 Evaluate side-chains 429 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 3.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 71 optimal weight: 0.8980 chunk 158 optimal weight: 20.0000 chunk 165 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 chunk 152 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 294 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 43 optimal weight: 40.0000 chunk 403 optimal weight: 30.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 230 GLN ** H 277 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** ** J 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 ASN ** K 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 230 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** ** N 331 ASN ** 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 = 0.3378 r_free = 0.3378 target = 0.085514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.062012 restraints weight = 118130.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.064256 restraints weight = 68821.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.065785 restraints weight = 47233.005| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31804 Z= 0.175 Angle : 0.610 8.404 43368 Z= 0.329 Chirality : 0.045 0.203 4788 Planarity : 0.004 0.075 5747 Dihedral : 5.667 45.896 4463 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.58 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 4053 helix: -3.02 (0.47), residues: 84 sheet: -0.48 (0.13), residues: 1428 loop : -1.25 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP M 245 HIS 0.007 0.001 HIS L 221 PHE 0.024 0.002 PHE H 652 TYR 0.023 0.002 TYR H 254 ARG 0.011 0.001 ARG K 372 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 1190) hydrogen bonds : angle 6.58951 ( 3282) SS BOND : bond 0.00247 ( 21) SS BOND : angle 1.35211 ( 42) covalent geometry : bond 0.00383 (31783) covalent geometry : angle 0.60850 (43326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9409.13 seconds wall clock time: 166 minutes 19.46 seconds (9979.46 seconds total)