Starting phenix.real_space_refine on Thu Jan 23 20:08:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wyr_37936/01_2025/8wyr_37936.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wyr_37936/01_2025/8wyr_37936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wyr_37936/01_2025/8wyr_37936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wyr_37936/01_2025/8wyr_37936.map" model { file = "/net/cci-nas-00/data/ceres_data/8wyr_37936/01_2025/8wyr_37936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wyr_37936/01_2025/8wyr_37936.cif" } resolution = 3.39 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= 0.001 sd= 0.029 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 112 5.16 5 C 12931 2.51 5 N 3512 2.21 5 O 4055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 20612 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "B" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 18, 'TRANS': 211} Chain: "C" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1757 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 18, 'TRANS': 207} Chain: "D" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain: "E" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1757 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 18, 'TRANS': 207} Chain: "F" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain: "G" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 18, 'TRANS': 206} Chain: "H" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "J" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain breaks: 1 Chain: "K" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "L" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "M" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1669 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 8, 'TRANS': 204} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.34, per 1000 atoms: 0.74 Number of scatterers: 20612 At special positions: 0 Unit cell: (67.23, 170.15, 193.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 112 16.00 O 4055 8.00 N 3512 7.00 C 12931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.04 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS J 68 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS C 414 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.04 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.01 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS E 414 " distance=2.02 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.14 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 414 " - pdb=" SG CYS G 414 " distance=2.39 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.02 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.04 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 414 " - pdb=" SG CYS K 414 " distance=2.02 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 575 " - pdb=" SG CYS K 575 " distance=2.03 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=2.02 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 91 " distance=2.02 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.04 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 414 " - pdb=" SG CYS M 191 " distance=2.04 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.03 Simple disulfide: pdb=" SG CYS M 147 " - pdb=" SG CYS M 181 " distance=2.04 Simple disulfide: pdb=" SG CYS M 163 " - pdb=" SG CYS M 228 " distance=2.04 Simple disulfide: pdb=" SG CYS M 176 " - pdb=" SG CYS M 238 " distance=2.02 Simple disulfide: pdb=" SG CYS M 208 " - pdb=" SG CYS M 218 " distance=2.05 Simple disulfide: pdb=" SG CYS M 253 " - pdb=" SG CYS M 287 " distance=2.02 Simple disulfide: pdb=" SG CYS M 269 " - pdb=" SG CYS M 335 " distance=2.03 Simple disulfide: pdb=" SG CYS M 282 " - pdb=" SG CYS M 345 " distance=2.03 Simple disulfide: pdb=" SG CYS M 315 " - pdb=" SG CYS M 325 " distance=2.03 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 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG I 1 " - " ASN J 48 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " Time building additional restraints: 4.73 Conformation dependent library (CDL) restraints added in 2.9 seconds 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5016 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 66 sheets defined 13.4% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 353 through 360 removed outlier: 3.525A pdb=" N ILE A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 414 through 421 removed outlier: 3.881A pdb=" N TRP B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 466 Processing helix chain 'B' and resid 524 through 531 removed outlier: 3.968A pdb=" N GLY B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 460 through 467 Processing helix chain 'C' and resid 524 through 530 Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 460 through 465 Processing helix chain 'D' and resid 524 through 530 Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.828A pdb=" N GLY D 557 " --> pdb=" O LYS D 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 414 through 421 removed outlier: 4.315A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 467 removed outlier: 3.622A pdb=" N LEU E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 531 removed outlier: 3.796A pdb=" N GLY E 531 " --> pdb=" O GLU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 557 removed outlier: 4.153A pdb=" N GLY E 557 " --> pdb=" O LYS E 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 Processing helix chain 'F' and resid 414 through 421 removed outlier: 3.994A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 467 Processing helix chain 'F' and resid 524 through 530 removed outlier: 3.523A pdb=" N THR F 530 " --> pdb=" O GLU F 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 361 removed outlier: 3.629A pdb=" N THR G 360 " --> pdb=" O SER G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 420 removed outlier: 3.707A pdb=" N TRP G 418 " --> pdb=" O CYS G 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 467 removed outlier: 3.549A pdb=" N ARG G 467 " --> pdb=" O GLN G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 531 removed outlier: 3.842A pdb=" N GLY G 531 " --> pdb=" O GLU G 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 558 removed outlier: 4.070A pdb=" N GLY G 557 " --> pdb=" O ASP G 553 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS G 558 " --> pdb=" O LYS G 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 553 through 558' Processing helix chain 'H' and resid 355 through 360 Processing helix chain 'H' and resid 415 through 420 Processing helix chain 'H' and resid 460 through 466 Processing helix chain 'H' and resid 525 through 531 removed outlier: 3.669A pdb=" N THR H 530 " --> pdb=" O GLU H 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 68 Processing helix chain 'K' and resid 353 through 361 removed outlier: 3.572A pdb=" N THR K 360 " --> pdb=" O SER K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 419 Processing helix chain 'K' and resid 460 through 467 Processing helix chain 'K' and resid 524 through 531 removed outlier: 3.619A pdb=" N GLY K 531 " --> pdb=" O GLU K 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 359 Processing helix chain 'L' and resid 416 through 421 Processing helix chain 'L' and resid 460 through 465 Processing helix chain 'L' and resid 524 through 530 removed outlier: 3.540A pdb=" N TRP L 528 " --> pdb=" O SER L 524 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR L 530 " --> pdb=" O GLU L 526 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 3.730A pdb=" N ALA M 172 " --> pdb=" O SER M 168 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG M 177 " --> pdb=" O LYS M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 197 removed outlier: 4.056A pdb=" N GLY M 197 " --> pdb=" O HIS M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 286 Processing helix chain 'M' and resid 295 through 301 Processing helix chain 'M' and resid 336 through 340 removed outlier: 3.514A pdb=" N GLU M 339 " --> pdb=" O THR M 336 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP M 340 " --> pdb=" O HIS M 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 336 through 340' Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 347 removed outlier: 3.595A pdb=" N ARG A 346 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 363 through 364 removed outlier: 4.260A pdb=" N THR A 363 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 413 " --> pdb=" O THR A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 380 removed outlier: 3.690A pdb=" N THR A 379 " --> pdb=" O THR A 429 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.592A pdb=" N THR A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.929A pdb=" N GLN A 439 " --> pdb=" O CYS A 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 453 through 457 removed outlier: 5.608A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 453 through 457 removed outlier: 5.608A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.769A pdb=" N THR A 535 " --> pdb=" O MET A 489 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 548 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AB1, first strand: chain 'C' and resid 565 through 566 removed outlier: 6.913A pdb=" N LEU A 566 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N SER B 569 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N MET A 568 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AB3, first strand: chain 'B' and resid 381 through 382 Processing sheet with id=AB4, first strand: chain 'B' and resid 453 through 457 Processing sheet with id=AB5, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.642A pdb=" N VAL B 476 " --> pdb=" O ALA B 517 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AB7, first strand: chain 'C' and resid 346 through 348 Processing sheet with id=AB8, first strand: chain 'C' and resid 363 through 366 removed outlier: 4.198A pdb=" N THR C 363 " --> pdb=" O ILE C 413 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 389 through 390 removed outlier: 4.491A pdb=" N TRP C 382 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 424 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 441 " --> pdb=" O PHE C 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 456 through 457 Processing sheet with id=AC2, first strand: chain 'C' and resid 476 through 479 removed outlier: 5.696A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AC4, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AC5, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.647A pdb=" N LEU D 368 " --> pdb=" O PHE D 348 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR D 366 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 424 through 426 removed outlier: 3.575A pdb=" N GLN D 439 " --> pdb=" O CYS D 426 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 456 through 457 Processing sheet with id=AC8, first strand: chain 'D' and resid 470 through 471 Processing sheet with id=AC9, first strand: chain 'D' and resid 476 through 479 removed outlier: 5.219A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 493 through 494 removed outlier: 3.735A pdb=" N THR D 548 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 349 through 350 removed outlier: 3.803A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR E 363 " --> pdb=" O ILE E 413 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 379 through 380 Processing sheet with id=AD4, first strand: chain 'E' and resid 383 through 384 Processing sheet with id=AD5, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.695A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.695A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AD8, first strand: chain 'F' and resid 363 through 364 removed outlier: 3.896A pdb=" N THR F 363 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE F 413 " --> pdb=" O THR F 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'F' and resid 381 through 382 Processing sheet with id=AE1, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.780A pdb=" N THR F 477 " --> pdb=" O ASP F 453 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.780A pdb=" N THR F 477 " --> pdb=" O ASP F 453 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 493 through 494 removed outlier: 3.580A pdb=" N GLN F 493 " --> pdb=" O GLN F 490 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 565 through 568 removed outlier: 6.596A pdb=" N SER F 565 " --> pdb=" O LEU G 566 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N MET G 568 " --> pdb=" O SER F 565 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL F 567 " --> pdb=" O MET G 568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'G' and resid 346 through 349 removed outlier: 3.838A pdb=" N ARG G 346 " --> pdb=" O THR G 370 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR G 370 " --> pdb=" O ARG G 346 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 363 through 365 Processing sheet with id=AE7, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.641A pdb=" N THR G 477 " --> pdb=" O ASP G 453 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.641A pdb=" N THR G 477 " --> pdb=" O ASP G 453 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AF1, first strand: chain 'H' and resid 363 through 364 removed outlier: 4.045A pdb=" N THR H 363 " --> pdb=" O ILE H 413 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 424 through 425 removed outlier: 3.818A pdb=" N ILE H 441 " --> pdb=" O PHE H 424 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 455 through 457 Processing sheet with id=AF4, first strand: chain 'H' and resid 455 through 457 removed outlier: 5.283A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 493 through 494 removed outlier: 3.531A pdb=" N THR H 548 " --> pdb=" O VAL H 538 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 5 through 9 removed outlier: 5.670A pdb=" N VAL J 6 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER J 19 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL J 33 " --> pdb=" O LEU L 561 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASN L 563 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ARG J 35 " --> pdb=" O ASN L 563 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N SER L 565 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE J 37 " --> pdb=" O SER L 565 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL L 567 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE J 39 " --> pdb=" O VAL L 567 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER L 569 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL J 41 " --> pdb=" O SER L 569 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER K 565 " --> pdb=" O LEU L 566 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET L 568 " --> pdb=" O SER K 565 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL K 567 " --> pdb=" O MET L 568 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 74 through 77 removed outlier: 9.651A pdb=" N VAL L 547 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR J 84 " --> pdb=" O VAL L 547 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLU L 549 " --> pdb=" O THR J 84 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR J 86 " --> pdb=" O GLU L 549 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N THR L 551 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 112 through 115 Processing sheet with id=AF9, first strand: chain 'K' and resid 363 through 365 removed outlier: 3.792A pdb=" N ILE K 413 " --> pdb=" O THR K 363 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU K 365 " --> pdb=" O ALA K 411 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA K 411 " --> pdb=" O LEU K 365 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 382 through 383 Processing sheet with id=AG2, first strand: chain 'K' and resid 453 through 457 removed outlier: 5.628A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 453 through 457 removed outlier: 5.628A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 485 through 489 Processing sheet with id=AG5, first strand: chain 'L' and resid 347 through 348 removed outlier: 3.789A pdb=" N PHE L 348 " --> pdb=" O LEU L 368 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS L 367 " --> pdb=" O GLY L 409 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY L 409 " --> pdb=" O CYS L 367 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL L 369 " --> pdb=" O ALA L 407 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA L 407 " --> pdb=" O VAL L 369 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE L 396 " --> pdb=" O VAL L 408 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 389 through 390 removed outlier: 3.527A pdb=" N VAL L 390 " --> pdb=" O TRP L 382 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TRP L 382 " --> pdb=" O VAL L 390 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER L 381 " --> pdb=" O THR L 427 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS L 426 " --> pdb=" O GLN L 439 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN L 439 " --> pdb=" O CYS L 426 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 453 through 457 Processing sheet with id=AG8, first strand: chain 'L' and resid 453 through 457 removed outlier: 5.399A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'M' and resid 140 through 141 Processing sheet with id=AH1, first strand: chain 'M' and resid 140 through 141 Processing sheet with id=AH2, first strand: chain 'M' and resid 243 through 251 removed outlier: 4.138A pdb=" N ASP M 243 " --> pdb=" O LEU M 260 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY M 249 " --> pdb=" O SER M 254 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER M 254 " --> pdb=" O GLY M 249 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU M 257 " --> pdb=" O VAL M 268 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL M 268 " --> pdb=" O LEU M 257 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP M 309 " --> pdb=" O TRP M 265 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N SER M 267 " --> pdb=" O TRP M 309 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 243 through 251 removed outlier: 4.138A pdb=" N ASP M 243 " --> pdb=" O LEU M 260 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY M 249 " --> pdb=" O SER M 254 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER M 254 " --> pdb=" O GLY M 249 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY M 255 " --> pdb=" O VAL M 343 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1518 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: 7.93 Time building geometry restraints manager: 5.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3615 1.32 - 1.45: 5596 1.45 - 1.58: 11760 1.58 - 1.70: 3 1.70 - 1.83: 144 Bond restraints: 21118 Sorted by residual: bond pdb=" CA THR F 535 " pdb=" C THR F 535 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.19e-02 7.06e+03 2.48e+01 bond pdb=" CA LEU C 475 " pdb=" C LEU C 475 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.11e-02 8.12e+03 2.35e+01 bond pdb=" N VAL F 484 " pdb=" CA VAL F 484 " ideal model delta sigma weight residual 1.457 1.397 0.060 1.25e-02 6.40e+03 2.33e+01 bond pdb=" CA TYR F 534 " pdb=" C TYR F 534 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.20e-02 6.94e+03 2.17e+01 bond pdb=" CA CYS D 474 " pdb=" C CYS D 474 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.23e-02 6.61e+03 2.16e+01 ... (remaining 21113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 28013 2.72 - 5.44: 732 5.44 - 8.16: 112 8.16 - 10.88: 21 10.88 - 13.60: 4 Bond angle restraints: 28882 Sorted by residual: angle pdb=" N SER F 480 " pdb=" CA SER F 480 " pdb=" C SER F 480 " ideal model delta sigma weight residual 109.83 97.52 12.31 1.27e+00 6.20e-01 9.40e+01 angle pdb=" N ASP E 483 " pdb=" CA ASP E 483 " pdb=" C ASP E 483 " ideal model delta sigma weight residual 109.76 123.36 -13.60 1.59e+00 3.96e-01 7.32e+01 angle pdb=" N ASP D 483 " pdb=" CA ASP D 483 " pdb=" C ASP D 483 " ideal model delta sigma weight residual 110.24 121.28 -11.04 1.30e+00 5.92e-01 7.21e+01 angle pdb=" N PHE F 479 " pdb=" CA PHE F 479 " pdb=" C PHE F 479 " ideal model delta sigma weight residual 109.07 120.58 -11.51 1.52e+00 4.33e-01 5.73e+01 angle pdb=" N ALA F 482 " pdb=" CA ALA F 482 " pdb=" C ALA F 482 " ideal model delta sigma weight residual 112.97 105.12 7.85 1.06e+00 8.90e-01 5.49e+01 ... (remaining 28877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11296 17.76 - 35.53: 1315 35.53 - 53.29: 323 53.29 - 71.06: 53 71.06 - 88.82: 16 Dihedral angle restraints: 13003 sinusoidal: 5298 harmonic: 7705 Sorted by residual: dihedral pdb=" CB CYS M 269 " pdb=" SG CYS M 269 " pdb=" SG CYS M 335 " pdb=" CB CYS M 335 " ideal model delta sinusoidal sigma weight residual 93.00 173.35 -80.35 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS M 208 " pdb=" SG CYS M 208 " pdb=" SG CYS M 218 " pdb=" CB CYS M 218 " ideal model delta sinusoidal sigma weight residual -86.00 -6.70 -79.30 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS J 12 " pdb=" SG CYS J 12 " pdb=" SG CYS J 100 " pdb=" CB CYS J 100 " ideal model delta sinusoidal sigma weight residual -86.00 -154.00 68.00 1 1.00e+01 1.00e-02 6.00e+01 ... (remaining 13000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 3264 0.139 - 0.279: 119 0.279 - 0.418: 10 0.418 - 0.557: 2 0.557 - 0.697: 1 Chirality restraints: 3396 Sorted by residual: chirality pdb=" CA THR G 427 " pdb=" N THR G 427 " pdb=" C THR G 427 " pdb=" CB THR G 427 " both_signs ideal model delta sigma weight residual False 2.53 1.83 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" C1 NAG K 601 " pdb=" ND2 ASN K 563 " pdb=" C2 NAG K 601 " pdb=" O5 NAG K 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 563 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.48e+00 ... (remaining 3393 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 424 " 0.024 2.00e-02 2.50e+03 3.30e-02 1.90e+01 pdb=" CG PHE F 424 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE F 424 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE F 424 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE F 424 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 424 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE F 424 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 354 " 0.018 2.00e-02 2.50e+03 3.19e-02 1.79e+01 pdb=" CG PHE A 354 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 354 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 354 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 354 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 354 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 354 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO F 351 " 0.065 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO F 352 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO F 352 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 352 " 0.052 5.00e-02 4.00e+02 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4431 2.78 - 3.31: 18561 3.31 - 3.84: 34916 3.84 - 4.37: 39283 4.37 - 4.90: 68304 Nonbonded interactions: 165495 Sorted by model distance: nonbonded pdb=" OG SER K 565 " pdb=" O7 NAG K 601 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR F 363 " pdb=" O ILE F 413 " model vdw 2.265 3.040 nonbonded pdb=" O ASP G 416 " pdb=" OG SER G 420 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASP M 250 " pdb=" OH TYR M 301 " model vdw 2.289 3.040 nonbonded pdb=" O ALA D 448 " pdb=" OG SER D 480 " model vdw 2.299 3.040 ... (remaining 165490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 345 through 569 or resid 601)) selection = (chain 'B' and (resid 345 through 569 or resid 601)) selection = (chain 'C' and (resid 345 through 569 or resid 601)) selection = (chain 'D' and (resid 345 through 569 or resid 601)) selection = (chain 'E' and (resid 345 through 569 or resid 601)) selection = (chain 'F' and (resid 345 through 569 or resid 601)) selection = chain 'G' selection = (chain 'H' and (resid 345 through 569 or resid 601)) selection = (chain 'K' and (resid 345 through 569 or resid 601)) selection = (chain 'L' and (resid 345 through 569 or resid 601)) } 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 individual isotropic 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: 8.000 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: 2.850 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 49.040 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.007 0.078 21118 Z= 0.471 Angle : 1.049 13.602 28882 Z= 0.601 Chirality : 0.067 0.697 3396 Planarity : 0.010 0.120 3701 Dihedral : 15.720 88.822 7870 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.24 % Allowed : 23.67 % Favored : 75.10 % Cbeta Deviations : 0.04 % 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: -2.76 (0.15), residues: 2603 helix: -3.34 (0.19), residues: 292 sheet: -1.72 (0.18), residues: 700 loop : -1.59 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP E 418 HIS 0.022 0.002 HIS D 450 PHE 0.075 0.004 PHE F 424 TYR 0.058 0.003 TYR J 62 ARG 0.021 0.001 ARG H 461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 303 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 PHE cc_start: 0.7232 (t80) cc_final: 0.6941 (t80) REVERT: D 358 PHE cc_start: 0.7998 (t80) cc_final: 0.7791 (t80) REVERT: E 453 ASP cc_start: 0.7556 (m-30) cc_final: 0.7322 (t70) REVERT: E 483 ASP cc_start: 0.7725 (p0) cc_final: 0.7188 (p0) REVERT: E 485 PHE cc_start: 0.8279 (t80) cc_final: 0.7693 (t80) REVERT: F 500 TYR cc_start: 0.8027 (p90) cc_final: 0.7763 (p90) REVERT: F 530 THR cc_start: 0.8289 (p) cc_final: 0.7671 (p) REVERT: L 380 ILE cc_start: 0.5061 (OUTLIER) cc_final: 0.4795 (mt) REVERT: M 240 ASP cc_start: 0.8471 (t0) cc_final: 0.7475 (p0) outliers start: 29 outliers final: 16 residues processed: 323 average time/residue: 0.3434 time to fit residues: 168.5368 Evaluate side-chains 294 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 277 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain H residue 553 ASP Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain M residue 134 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 3.9990 chunk 195 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN B 395 ASN C 463 GLN ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN M 272 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.176243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.119119 restraints weight = 30226.596| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.63 r_work: 0.3391 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21118 Z= 0.235 Angle : 0.616 8.589 28882 Z= 0.327 Chirality : 0.046 0.429 3396 Planarity : 0.006 0.066 3701 Dihedral : 6.558 57.483 3103 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.20 % Allowed : 22.51 % Favored : 74.28 % 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: -2.36 (0.16), residues: 2603 helix: -2.59 (0.21), residues: 315 sheet: -1.54 (0.18), residues: 733 loop : -1.32 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 418 HIS 0.006 0.001 HIS F 400 PHE 0.022 0.002 PHE L 479 TYR 0.018 0.001 TYR F 534 ARG 0.008 0.000 ARG H 461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 317 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7661 (p0) cc_final: 0.7395 (p0) REVERT: A 487 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8061 (tm-30) REVERT: B 354 PHE cc_start: 0.7981 (t80) cc_final: 0.7737 (t80) REVERT: B 462 GLU cc_start: 0.8328 (mp0) cc_final: 0.7976 (mt-10) REVERT: B 490 GLN cc_start: 0.8342 (tm130) cc_final: 0.8035 (tm-30) REVERT: D 518 HIS cc_start: 0.7421 (m-70) cc_final: 0.7186 (m-70) REVERT: E 364 LYS cc_start: 0.7438 (mmtt) cc_final: 0.7209 (tppt) REVERT: E 418 TRP cc_start: 0.6595 (t60) cc_final: 0.6289 (t60) REVERT: E 453 ASP cc_start: 0.8182 (m-30) cc_final: 0.7391 (t70) REVERT: E 483 ASP cc_start: 0.7907 (p0) cc_final: 0.7461 (p0) REVERT: E 485 PHE cc_start: 0.8365 (t80) cc_final: 0.7560 (t80) REVERT: F 530 THR cc_start: 0.8630 (p) cc_final: 0.8376 (p) REVERT: H 364 LYS cc_start: 0.6551 (mmmm) cc_final: 0.6338 (mmmm) REVERT: H 525 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7620 (tm-30) REVERT: J 104 ASP cc_start: 0.8333 (t0) cc_final: 0.8110 (t0) REVERT: K 415 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8258 (mm-30) REVERT: K 443 ARG cc_start: 0.6232 (ttp80) cc_final: 0.5954 (ttp-110) REVERT: K 476 VAL cc_start: 0.9210 (t) cc_final: 0.8932 (m) outliers start: 75 outliers final: 40 residues processed: 379 average time/residue: 0.3291 time to fit residues: 191.3710 Evaluate side-chains 326 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 285 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 365 LEU Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 155 HIS Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 234 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 247 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 222 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** K 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** 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 = 0.4307 r_free = 0.4307 target = 0.175757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.114307 restraints weight = 30990.795| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.93 r_work: 0.3341 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21118 Z= 0.285 Angle : 0.609 8.993 28882 Z= 0.318 Chirality : 0.046 0.448 3396 Planarity : 0.005 0.061 3701 Dihedral : 5.961 51.508 3090 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.36 % Allowed : 21.87 % Favored : 73.77 % 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: -2.10 (0.16), residues: 2603 helix: -2.10 (0.23), residues: 316 sheet: -1.41 (0.18), residues: 738 loop : -1.19 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 418 HIS 0.007 0.001 HIS G 400 PHE 0.022 0.002 PHE L 479 TYR 0.016 0.002 TYR F 375 ARG 0.008 0.000 ARG H 461 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 291 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7800 (p0) cc_final: 0.7576 (p0) REVERT: A 487 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8153 (tm-30) REVERT: B 462 GLU cc_start: 0.8327 (mp0) cc_final: 0.8037 (mt-10) REVERT: B 480 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.7884 (p) REVERT: B 490 GLN cc_start: 0.8406 (tm130) cc_final: 0.7956 (tm-30) REVERT: D 450 HIS cc_start: 0.7851 (m170) cc_final: 0.7580 (m90) REVERT: D 468 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8067 (tm-30) REVERT: E 354 PHE cc_start: 0.7680 (t80) cc_final: 0.6953 (t80) REVERT: E 364 LYS cc_start: 0.7452 (mmtt) cc_final: 0.7206 (tppt) REVERT: E 418 TRP cc_start: 0.6625 (t60) cc_final: 0.6407 (t60) REVERT: E 483 ASP cc_start: 0.8007 (p0) cc_final: 0.7341 (p0) REVERT: E 485 PHE cc_start: 0.8400 (t80) cc_final: 0.7536 (t80) REVERT: F 388 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8277 (tp30) REVERT: F 530 THR cc_start: 0.8676 (p) cc_final: 0.8445 (p) REVERT: H 525 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7453 (tm-30) REVERT: H 529 ASN cc_start: 0.8262 (m110) cc_final: 0.7314 (m110) REVERT: J 104 ASP cc_start: 0.8437 (t0) cc_final: 0.8127 (t0) REVERT: L 380 ILE cc_start: 0.4757 (OUTLIER) cc_final: 0.4186 (mt) REVERT: L 382 TRP cc_start: 0.5402 (m100) cc_final: 0.5081 (m100) outliers start: 102 outliers final: 73 residues processed: 373 average time/residue: 0.3238 time to fit residues: 186.8113 Evaluate side-chains 342 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 266 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 365 LEU Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 526 GLU Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 480 SER Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 175 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 245 optimal weight: 0.0470 chunk 193 optimal weight: 40.0000 chunk 244 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 250 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** K 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** 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 = 0.4308 r_free = 0.4308 target = 0.175743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.117523 restraints weight = 30400.292| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.40 r_work: 0.3385 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21118 Z= 0.217 Angle : 0.576 10.404 28882 Z= 0.298 Chirality : 0.046 0.437 3396 Planarity : 0.005 0.060 3701 Dihedral : 5.738 51.912 3089 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.17 % Allowed : 21.70 % Favored : 73.13 % 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: -1.94 (0.16), residues: 2603 helix: -1.79 (0.25), residues: 316 sheet: -1.23 (0.19), residues: 738 loop : -1.17 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 418 HIS 0.007 0.001 HIS A 430 PHE 0.020 0.001 PHE A 354 TYR 0.015 0.001 TYR M 196 ARG 0.010 0.000 ARG H 461 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 300 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 462 GLU cc_start: 0.8242 (mp0) cc_final: 0.7998 (mt-10) REVERT: B 490 GLN cc_start: 0.8401 (tm130) cc_final: 0.7945 (tm-30) REVERT: D 450 HIS cc_start: 0.7902 (m170) cc_final: 0.7564 (m90) REVERT: D 468 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7416 (tm-30) REVERT: E 354 PHE cc_start: 0.7630 (t80) cc_final: 0.6976 (t80) REVERT: E 364 LYS cc_start: 0.7462 (mmtt) cc_final: 0.7234 (tppt) REVERT: E 483 ASP cc_start: 0.7897 (p0) cc_final: 0.7254 (p0) REVERT: E 485 PHE cc_start: 0.8345 (t80) cc_final: 0.7521 (t80) REVERT: F 388 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8276 (tp30) REVERT: F 530 THR cc_start: 0.8700 (p) cc_final: 0.8493 (p) REVERT: F 541 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7882 (mp0) REVERT: G 545 ASN cc_start: 0.8568 (t0) cc_final: 0.8299 (t0) REVERT: H 525 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7666 (tm-30) REVERT: J 104 ASP cc_start: 0.8437 (t0) cc_final: 0.8053 (t0) REVERT: J 123 MET cc_start: 0.8436 (mmm) cc_final: 0.8214 (mmm) REVERT: K 489 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8229 (mtp) REVERT: L 380 ILE cc_start: 0.4835 (OUTLIER) cc_final: 0.4385 (mt) REVERT: L 382 TRP cc_start: 0.5438 (m100) cc_final: 0.5107 (m100) REVERT: M 178 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8045 (pt0) outliers start: 121 outliers final: 83 residues processed: 400 average time/residue: 0.3207 time to fit residues: 199.8029 Evaluate side-chains 363 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 276 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 526 GLU Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 480 SER Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 541 GLU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 178 GLN Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 93 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 57 optimal weight: 0.1980 chunk 67 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 62 optimal weight: 0.0870 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 20.0000 chunk 203 optimal weight: 0.6980 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN C 439 GLN ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN H 430 HIS ** K 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 272 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.175911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.114530 restraints weight = 31171.253| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.60 r_work: 0.3353 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21118 Z= 0.259 Angle : 0.584 10.390 28882 Z= 0.301 Chirality : 0.046 0.452 3396 Planarity : 0.005 0.056 3701 Dihedral : 5.716 55.469 3089 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 5.21 % Allowed : 22.30 % Favored : 72.49 % 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: -1.79 (0.16), residues: 2603 helix: -1.56 (0.26), residues: 310 sheet: -1.09 (0.19), residues: 746 loop : -1.12 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 418 HIS 0.005 0.001 HIS A 518 PHE 0.023 0.002 PHE A 354 TYR 0.019 0.001 TYR F 534 ARG 0.010 0.000 ARG H 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 298 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 570 ASP cc_start: 0.8516 (t0) cc_final: 0.7822 (t0) REVERT: B 354 PHE cc_start: 0.8105 (t80) cc_final: 0.7718 (t80) REVERT: B 462 GLU cc_start: 0.8288 (mp0) cc_final: 0.8060 (mt-10) REVERT: B 480 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.7869 (p) REVERT: B 490 GLN cc_start: 0.8475 (tm130) cc_final: 0.7869 (tm-30) REVERT: B 568 MET cc_start: 0.8805 (ttm) cc_final: 0.8589 (ttm) REVERT: D 468 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8102 (tm-30) REVERT: E 354 PHE cc_start: 0.7555 (t80) cc_final: 0.6856 (t80) REVERT: E 364 LYS cc_start: 0.7456 (mmtt) cc_final: 0.7220 (tppt) REVERT: E 483 ASP cc_start: 0.7907 (p0) cc_final: 0.7247 (p0) REVERT: E 485 PHE cc_start: 0.8365 (t80) cc_final: 0.7531 (t80) REVERT: F 388 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8235 (tp30) REVERT: G 545 ASN cc_start: 0.8612 (t0) cc_final: 0.8186 (t0) REVERT: H 382 TRP cc_start: 0.3001 (OUTLIER) cc_final: -0.0504 (m100) REVERT: H 525 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7540 (tm-30) REVERT: J 104 ASP cc_start: 0.8544 (t0) cc_final: 0.8137 (t0) REVERT: J 107 LYS cc_start: 0.7860 (mmtp) cc_final: 0.7414 (mmtp) REVERT: J 123 MET cc_start: 0.8452 (mmm) cc_final: 0.8243 (mmm) REVERT: K 415 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8132 (mm-30) REVERT: K 489 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8198 (mtp) REVERT: K 508 GLU cc_start: 0.7558 (tp30) cc_final: 0.7249 (tt0) REVERT: L 380 ILE cc_start: 0.4880 (OUTLIER) cc_final: 0.4401 (mt) REVERT: L 532 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7240 (mp0) outliers start: 122 outliers final: 88 residues processed: 401 average time/residue: 0.3378 time to fit residues: 209.6159 Evaluate side-chains 375 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 280 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 568 MET Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 382 TRP Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 480 SER Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 532 GLU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 541 GLU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 242 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 220 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 237 optimal weight: 6.9990 chunk 160 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 GLN G 487 GLN ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** K 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 272 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.173698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.111649 restraints weight = 31071.529| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.58 r_work: 0.3307 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 21118 Z= 0.359 Angle : 0.625 11.657 28882 Z= 0.322 Chirality : 0.047 0.476 3396 Planarity : 0.005 0.058 3701 Dihedral : 5.745 52.429 3088 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 5.34 % Allowed : 22.73 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.81 (0.16), residues: 2603 helix: -1.53 (0.27), residues: 314 sheet: -1.14 (0.19), residues: 729 loop : -1.12 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 418 HIS 0.007 0.001 HIS A 518 PHE 0.025 0.002 PHE A 354 TYR 0.024 0.002 TYR J 62 ARG 0.010 0.000 ARG H 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 283 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7831 (p0) cc_final: 0.7395 (p0) REVERT: A 455 TYR cc_start: 0.8339 (m-80) cc_final: 0.8004 (m-80) REVERT: A 487 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8123 (tm-30) REVERT: A 570 ASP cc_start: 0.8681 (t0) cc_final: 0.8068 (t0) REVERT: B 354 PHE cc_start: 0.8172 (t80) cc_final: 0.7731 (t80) REVERT: B 462 GLU cc_start: 0.8368 (mp0) cc_final: 0.8108 (mt-10) REVERT: B 480 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.8018 (p) REVERT: B 490 GLN cc_start: 0.8519 (tm130) cc_final: 0.7928 (tm-30) REVERT: B 491 ARG cc_start: 0.8534 (ttm110) cc_final: 0.8165 (ttm110) REVERT: B 568 MET cc_start: 0.8870 (ttm) cc_final: 0.8644 (ttm) REVERT: C 363 THR cc_start: 0.7694 (m) cc_final: 0.6177 (m) REVERT: C 418 TRP cc_start: 0.6950 (t-100) cc_final: 0.6678 (t-100) REVERT: D 466 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8575 (mp) REVERT: D 468 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7659 (tm-30) REVERT: E 354 PHE cc_start: 0.7535 (t80) cc_final: 0.6870 (t80) REVERT: E 364 LYS cc_start: 0.7442 (mmtt) cc_final: 0.7180 (tppt) REVERT: E 483 ASP cc_start: 0.7906 (p0) cc_final: 0.7240 (p0) REVERT: E 485 PHE cc_start: 0.8400 (t80) cc_final: 0.7528 (t80) REVERT: F 388 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8278 (tp30) REVERT: F 410 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5703 (mp0) REVERT: G 545 ASN cc_start: 0.8569 (t0) cc_final: 0.8102 (t0) REVERT: H 382 TRP cc_start: 0.3167 (OUTLIER) cc_final: -0.0326 (m100) REVERT: H 415 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7685 (pp20) REVERT: J 16 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.7890 (ttp80) REVERT: J 104 ASP cc_start: 0.8597 (t0) cc_final: 0.8187 (t0) REVERT: J 107 LYS cc_start: 0.8074 (mmtp) cc_final: 0.7729 (mmtp) REVERT: K 379 THR cc_start: 0.4482 (OUTLIER) cc_final: 0.4237 (m) REVERT: K 489 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8242 (mtp) REVERT: K 508 GLU cc_start: 0.7639 (tp30) cc_final: 0.7322 (tt0) REVERT: L 380 ILE cc_start: 0.4983 (OUTLIER) cc_final: 0.3834 (mt) REVERT: L 382 TRP cc_start: 0.5621 (m100) cc_final: 0.5002 (m100) REVERT: L 532 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: M 178 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7973 (pt0) REVERT: M 318 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8292 (mp0) outliers start: 125 outliers final: 87 residues processed: 390 average time/residue: 0.3315 time to fit residues: 198.7892 Evaluate side-chains 363 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 265 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 382 TRP Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 379 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 532 GLU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 178 GLN Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 301 TYR Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 33 optimal weight: 0.4980 chunk 206 optimal weight: 0.9980 chunk 218 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 164 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 216 optimal weight: 50.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** 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 = 0.4305 r_free = 0.4305 target = 0.175216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.116986 restraints weight = 30085.570| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.42 r_work: 0.3366 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21118 Z= 0.219 Angle : 0.590 12.575 28882 Z= 0.302 Chirality : 0.046 0.443 3396 Planarity : 0.005 0.065 3701 Dihedral : 5.631 54.628 3088 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.44 % Allowed : 23.62 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.68 (0.16), residues: 2603 helix: -1.41 (0.27), residues: 322 sheet: -1.00 (0.19), residues: 729 loop : -1.07 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP H 418 HIS 0.006 0.001 HIS G 400 PHE 0.028 0.002 PHE A 354 TYR 0.020 0.001 TYR F 500 ARG 0.015 0.000 ARG H 461 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 293 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7770 (p0) cc_final: 0.7296 (p0) REVERT: A 455 TYR cc_start: 0.8251 (m-80) cc_final: 0.7874 (m-80) REVERT: A 487 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 570 ASP cc_start: 0.8559 (t0) cc_final: 0.7928 (t0) REVERT: B 354 PHE cc_start: 0.8125 (t80) cc_final: 0.7684 (t80) REVERT: B 462 GLU cc_start: 0.8259 (mp0) cc_final: 0.8010 (mt-10) REVERT: B 490 GLN cc_start: 0.8403 (tm130) cc_final: 0.7955 (tm-30) REVERT: B 568 MET cc_start: 0.8790 (ttm) cc_final: 0.8465 (ttm) REVERT: D 468 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7593 (tm-30) REVERT: D 499 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7730 (ttmm) REVERT: E 354 PHE cc_start: 0.7372 (t80) cc_final: 0.6880 (t80) REVERT: E 364 LYS cc_start: 0.7426 (mmtt) cc_final: 0.7173 (tppt) REVERT: E 483 ASP cc_start: 0.7875 (p0) cc_final: 0.7196 (p0) REVERT: E 485 PHE cc_start: 0.8354 (t80) cc_final: 0.7447 (t80) REVERT: F 388 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8194 (tp30) REVERT: G 545 ASN cc_start: 0.8456 (t0) cc_final: 0.8011 (t0) REVERT: H 382 TRP cc_start: 0.3179 (OUTLIER) cc_final: -0.0352 (m100) REVERT: H 415 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7579 (pp20) REVERT: H 529 ASN cc_start: 0.8211 (m110) cc_final: 0.7711 (m110) REVERT: J 16 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.7885 (ttp80) REVERT: J 71 CYS cc_start: 0.5955 (OUTLIER) cc_final: 0.5523 (m) REVERT: J 104 ASP cc_start: 0.8562 (t0) cc_final: 0.8145 (t0) REVERT: J 107 LYS cc_start: 0.7965 (mmtp) cc_final: 0.7479 (mmtp) REVERT: K 379 THR cc_start: 0.4471 (OUTLIER) cc_final: 0.4227 (m) REVERT: K 415 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8165 (mm-30) REVERT: K 489 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8314 (mtp) REVERT: K 508 GLU cc_start: 0.7567 (tp30) cc_final: 0.7299 (tt0) REVERT: L 380 ILE cc_start: 0.4953 (OUTLIER) cc_final: 0.3814 (mt) REVERT: L 382 TRP cc_start: 0.5546 (m100) cc_final: 0.4966 (m100) REVERT: L 532 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: M 246 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7177 (tp) outliers start: 104 outliers final: 77 residues processed: 382 average time/residue: 0.3308 time to fit residues: 194.6498 Evaluate side-chains 368 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 281 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 529 ASN Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 382 TRP Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 379 THR Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 480 SER Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 532 GLU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 199 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 236 optimal weight: 0.8980 chunk 159 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 HIS A 490 GLN B 385 GLN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN F 490 GLN F 545 ASN ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 272 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.172125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.113396 restraints weight = 30545.667| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.38 r_work: 0.3326 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.006 0.073 21118 Z= 0.393 Angle : 0.648 12.696 28882 Z= 0.333 Chirality : 0.048 0.488 3396 Planarity : 0.005 0.059 3701 Dihedral : 5.682 52.129 3086 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 5.38 % Allowed : 22.51 % Favored : 72.11 % 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: -1.76 (0.16), residues: 2603 helix: -1.42 (0.27), residues: 322 sheet: -1.13 (0.19), residues: 733 loop : -1.09 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 418 HIS 0.010 0.001 HIS A 400 PHE 0.028 0.002 PHE A 354 TYR 0.018 0.002 TYR F 500 ARG 0.007 0.001 ARG C 423 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 273 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7846 (p0) cc_final: 0.7271 (p0) REVERT: A 455 TYR cc_start: 0.8299 (m-80) cc_final: 0.7904 (m-80) REVERT: A 487 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 570 ASP cc_start: 0.8692 (t0) cc_final: 0.8081 (t0) REVERT: B 354 PHE cc_start: 0.8204 (t80) cc_final: 0.7716 (t80) REVERT: B 462 GLU cc_start: 0.8355 (mp0) cc_final: 0.8119 (mt-10) REVERT: B 480 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8223 (m) REVERT: B 483 ASP cc_start: 0.8524 (t0) cc_final: 0.8323 (t0) REVERT: B 490 GLN cc_start: 0.8498 (tm130) cc_final: 0.7925 (tm-30) REVERT: C 475 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8373 (pt) REVERT: C 529 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8541 (m110) REVERT: C 553 ASP cc_start: 0.8114 (t0) cc_final: 0.7681 (m-30) REVERT: D 468 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7608 (tm-30) REVERT: D 499 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7838 (ttmm) REVERT: E 354 PHE cc_start: 0.7564 (t80) cc_final: 0.6783 (t80) REVERT: E 364 LYS cc_start: 0.7436 (mmtt) cc_final: 0.7181 (tppt) REVERT: E 483 ASP cc_start: 0.7879 (p0) cc_final: 0.7216 (p0) REVERT: E 485 PHE cc_start: 0.8433 (t80) cc_final: 0.7512 (t80) REVERT: F 388 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8252 (tp30) REVERT: F 410 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5863 (mp0) REVERT: G 545 ASN cc_start: 0.8516 (t0) cc_final: 0.8064 (t0) REVERT: H 382 TRP cc_start: 0.3380 (OUTLIER) cc_final: -0.0149 (m100) REVERT: H 415 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7628 (pp20) REVERT: H 529 ASN cc_start: 0.8214 (m110) cc_final: 0.7878 (m110) REVERT: J 71 CYS cc_start: 0.6351 (OUTLIER) cc_final: 0.5861 (m) REVERT: J 104 ASP cc_start: 0.8663 (t0) cc_final: 0.8256 (t0) REVERT: J 107 LYS cc_start: 0.8153 (mmtp) cc_final: 0.7693 (mmtp) REVERT: K 379 THR cc_start: 0.4518 (OUTLIER) cc_final: 0.4274 (m) REVERT: K 415 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8206 (mm-30) REVERT: K 443 ARG cc_start: 0.5924 (ttp80) cc_final: 0.5718 (ttp-110) REVERT: K 489 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8221 (mtp) REVERT: K 508 GLU cc_start: 0.7685 (tp30) cc_final: 0.7330 (tt0) REVERT: L 380 ILE cc_start: 0.4969 (OUTLIER) cc_final: 0.3807 (mt) REVERT: L 382 TRP cc_start: 0.5654 (m100) cc_final: 0.5013 (m100) REVERT: L 532 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: M 318 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8181 (mp0) outliers start: 126 outliers final: 89 residues processed: 382 average time/residue: 0.3222 time to fit residues: 191.6786 Evaluate side-chains 363 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 261 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 382 TRP Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 526 GLU Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 379 THR Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 532 GLU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 187 THR Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 301 TYR Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 1 optimal weight: 0.9980 chunk 167 optimal weight: 0.5980 chunk 116 optimal weight: 0.4980 chunk 74 optimal weight: 10.0000 chunk 253 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 187 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 ASN D 545 ASN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** 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 = 0.4292 r_free = 0.4292 target = 0.174129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.115600 restraints weight = 30299.729| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.39 r_work: 0.3352 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21118 Z= 0.249 Angle : 0.613 13.905 28882 Z= 0.313 Chirality : 0.046 0.451 3396 Planarity : 0.005 0.059 3701 Dihedral : 5.627 54.158 3086 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.40 % Allowed : 23.37 % Favored : 72.23 % 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 (0.16), residues: 2603 helix: -1.31 (0.27), residues: 322 sheet: -0.98 (0.19), residues: 700 loop : -1.10 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 418 HIS 0.016 0.001 HIS A 400 PHE 0.018 0.002 PHE F 354 TYR 0.027 0.002 TYR G 534 ARG 0.007 0.000 ARG H 514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 286 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7708 (p0) cc_final: 0.7150 (p0) REVERT: A 455 TYR cc_start: 0.8245 (m-80) cc_final: 0.7876 (m-80) REVERT: A 487 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8101 (tm-30) REVERT: A 570 ASP cc_start: 0.8609 (t0) cc_final: 0.7976 (t0) REVERT: B 354 PHE cc_start: 0.8099 (t80) cc_final: 0.7723 (t80) REVERT: B 462 GLU cc_start: 0.8278 (mp0) cc_final: 0.8036 (mt-10) REVERT: B 490 GLN cc_start: 0.8341 (tm130) cc_final: 0.7798 (tm-30) REVERT: B 568 MET cc_start: 0.8945 (ttm) cc_final: 0.8744 (ttp) REVERT: C 475 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8235 (pt) REVERT: C 529 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8553 (m110) REVERT: C 553 ASP cc_start: 0.8089 (t0) cc_final: 0.7637 (m-30) REVERT: D 468 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7597 (tm-30) REVERT: D 499 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7752 (ttmm) REVERT: E 354 PHE cc_start: 0.7415 (t80) cc_final: 0.6668 (t80) REVERT: E 364 LYS cc_start: 0.7413 (mmtt) cc_final: 0.7165 (tppt) REVERT: E 483 ASP cc_start: 0.7907 (p0) cc_final: 0.7194 (p0) REVERT: E 485 PHE cc_start: 0.8393 (t80) cc_final: 0.7405 (t80) REVERT: F 388 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8197 (tp30) REVERT: F 410 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5873 (mp0) REVERT: G 545 ASN cc_start: 0.8469 (t0) cc_final: 0.8154 (t0) REVERT: H 382 TRP cc_start: 0.3246 (OUTLIER) cc_final: -0.0404 (m100) REVERT: H 415 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7594 (pp20) REVERT: H 529 ASN cc_start: 0.8207 (m110) cc_final: 0.7853 (m110) REVERT: J 16 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.7860 (ttp80) REVERT: J 71 CYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5689 (m) REVERT: J 104 ASP cc_start: 0.8591 (t0) cc_final: 0.8159 (t0) REVERT: J 107 LYS cc_start: 0.7998 (mmtp) cc_final: 0.7516 (mmtp) REVERT: K 379 THR cc_start: 0.4440 (OUTLIER) cc_final: 0.4196 (m) REVERT: K 415 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8200 (mm-30) REVERT: K 489 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8262 (mtp) REVERT: K 508 GLU cc_start: 0.7636 (tp30) cc_final: 0.7215 (tt0) REVERT: L 380 ILE cc_start: 0.4896 (OUTLIER) cc_final: 0.4398 (mt) REVERT: L 532 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7231 (mp0) outliers start: 103 outliers final: 80 residues processed: 376 average time/residue: 0.3189 time to fit residues: 185.4531 Evaluate side-chains 366 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 274 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 382 TRP Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 526 GLU Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 379 THR Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 480 SER Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 532 GLU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 187 THR Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 0.1980 chunk 241 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 173 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 chunk 233 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 HIS ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN E 393 HIS ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 272 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.177109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.116792 restraints weight = 31074.122| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.94 r_work: 0.3361 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21118 Z= 0.200 Angle : 0.593 14.402 28882 Z= 0.302 Chirality : 0.046 0.453 3396 Planarity : 0.005 0.059 3701 Dihedral : 5.510 59.488 3086 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.84 % Allowed : 23.84 % Favored : 72.32 % 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 (0.17), residues: 2603 helix: -1.15 (0.27), residues: 322 sheet: -0.91 (0.19), residues: 730 loop : -1.02 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 418 HIS 0.009 0.001 HIS A 400 PHE 0.036 0.002 PHE A 354 TYR 0.024 0.002 TYR F 534 ARG 0.009 0.000 ARG J 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 313 time to evaluate : 2.427 Fit side-chains revert: symmetry clash REVERT: A 354 PHE cc_start: 0.6971 (t80) cc_final: 0.6648 (t80) REVERT: A 453 ASP cc_start: 0.7631 (p0) cc_final: 0.7414 (p0) REVERT: A 487 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 518 HIS cc_start: 0.7541 (t70) cc_final: 0.7328 (m-70) REVERT: A 570 ASP cc_start: 0.8478 (t0) cc_final: 0.7831 (t0) REVERT: B 354 PHE cc_start: 0.8063 (t80) cc_final: 0.7667 (t80) REVERT: B 462 GLU cc_start: 0.8247 (mp0) cc_final: 0.7979 (mt-10) REVERT: B 490 GLN cc_start: 0.8284 (tm130) cc_final: 0.7786 (tm-30) REVERT: C 529 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8620 (m110) REVERT: C 553 ASP cc_start: 0.8118 (t0) cc_final: 0.7663 (m-30) REVERT: D 423 ARG cc_start: 0.8398 (mtp-110) cc_final: 0.8091 (mtp85) REVERT: D 468 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7544 (tm-30) REVERT: D 499 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7687 (ttmm) REVERT: E 354 PHE cc_start: 0.7295 (t80) cc_final: 0.6763 (t80) REVERT: E 364 LYS cc_start: 0.7419 (mmtt) cc_final: 0.7026 (tppt) REVERT: E 483 ASP cc_start: 0.7810 (p0) cc_final: 0.7081 (p0) REVERT: E 485 PHE cc_start: 0.8364 (t80) cc_final: 0.7423 (t80) REVERT: F 388 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8171 (tp30) REVERT: G 545 ASN cc_start: 0.8425 (t0) cc_final: 0.8118 (t0) REVERT: H 382 TRP cc_start: 0.3276 (OUTLIER) cc_final: -0.0276 (m100) REVERT: H 415 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7563 (pp20) REVERT: H 529 ASN cc_start: 0.8238 (m110) cc_final: 0.7697 (m110) REVERT: J 6 VAL cc_start: 0.8879 (t) cc_final: 0.8487 (p) REVERT: J 16 ARG cc_start: 0.8413 (ttm-80) cc_final: 0.7888 (ttp80) REVERT: J 71 CYS cc_start: 0.5840 (OUTLIER) cc_final: 0.5398 (m) REVERT: J 80 ASN cc_start: 0.8365 (m-40) cc_final: 0.7919 (m-40) REVERT: J 104 ASP cc_start: 0.8595 (t0) cc_final: 0.8147 (t0) REVERT: J 107 LYS cc_start: 0.7810 (mmtp) cc_final: 0.7321 (mmtp) REVERT: K 379 THR cc_start: 0.4316 (OUTLIER) cc_final: 0.4090 (m) REVERT: K 415 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8187 (mm-30) REVERT: K 476 VAL cc_start: 0.9087 (t) cc_final: 0.8853 (m) REVERT: K 500 TYR cc_start: 0.8470 (p90) cc_final: 0.7922 (p90) REVERT: K 508 GLU cc_start: 0.7575 (tp30) cc_final: 0.7190 (tt0) REVERT: L 532 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7176 (mp0) outliers start: 90 outliers final: 73 residues processed: 388 average time/residue: 0.3230 time to fit residues: 195.0279 Evaluate side-chains 367 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 286 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 382 TRP Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 379 THR Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 480 SER Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 532 GLU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 236 optimal weight: 0.2980 chunk 141 optimal weight: 8.9990 chunk 231 optimal weight: 3.9990 chunk 3 optimal weight: 30.0000 chunk 156 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 75 optimal weight: 0.0770 chunk 71 optimal weight: 0.0050 overall best weight: 1.0756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 272 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.175805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.114568 restraints weight = 31216.322| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.91 r_work: 0.3334 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21118 Z= 0.256 Angle : 0.620 14.764 28882 Z= 0.315 Chirality : 0.046 0.461 3396 Planarity : 0.005 0.061 3701 Dihedral : 5.372 59.885 3082 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.89 % Allowed : 24.48 % Favored : 71.64 % 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: -1.51 (0.16), residues: 2603 helix: -1.10 (0.28), residues: 320 sheet: -0.88 (0.19), residues: 734 loop : -1.00 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 418 HIS 0.007 0.001 HIS G 400 PHE 0.030 0.002 PHE A 354 TYR 0.031 0.002 TYR F 534 ARG 0.007 0.000 ARG C 423 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11278.50 seconds wall clock time: 201 minutes 42.48 seconds (12102.48 seconds total)