Starting phenix.real_space_refine on Fri Mar 22 23:54:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftn_3299/03_2024/5ftn_3299_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftn_3299/03_2024/5ftn_3299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftn_3299/03_2024/5ftn_3299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftn_3299/03_2024/5ftn_3299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftn_3299/03_2024/5ftn_3299_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftn_3299/03_2024/5ftn_3299_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 21882 2.51 5 N 6144 2.21 5 O 6690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34956 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5762 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5762 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 5762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5762 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 5762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5762 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5762 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 5762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5762 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 17.73, per 1000 atoms: 0.51 Number of scatterers: 34956 At special positions: 0 Unit cell: (165.62, 171.028, 123.032, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 36 15.00 Mg 12 11.99 O 6690 8.00 N 6144 7.00 C 21882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.51 Conformation dependent library (CDL) restraints added in 6.4 seconds 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 198 helices and 18 sheets defined 38.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.08 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.623A pdb=" N GLU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 135 through 138 Processing helix chain 'A' and resid 192 through 198 removed outlier: 3.980A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.611A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.645A pdb=" N LEU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 319 through 334 removed outlier: 3.754A pdb=" N ILE A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 387 removed outlier: 5.343A pdb=" N ASN A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 removed outlier: 3.717A pdb=" N ASN A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 424 removed outlier: 3.500A pdb=" N ARG A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.518A pdb=" N TRP A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.595A pdb=" N GLU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.818A pdb=" N LEU A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 removed outlier: 3.639A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 removed outlier: 4.063A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 Processing helix chain 'A' and resid 579 through 583 Processing helix chain 'A' and resid 601 through 609 Processing helix chain 'A' and resid 650 through 661 removed outlier: 3.659A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.802A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 706 removed outlier: 3.654A pdb=" N ARG A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.639A pdb=" N GLU A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 758 removed outlier: 3.830A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.624A pdb=" N GLU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 135 through 138 Processing helix chain 'B' and resid 192 through 198 removed outlier: 3.980A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.612A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.645A pdb=" N LEU B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 319 through 334 removed outlier: 3.754A pdb=" N ILE B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 387 removed outlier: 5.343A pdb=" N ASN B 387 " --> pdb=" O ILE B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 402 removed outlier: 3.717A pdb=" N ASN B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 449 through 457 removed outlier: 3.518A pdb=" N TRP B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.595A pdb=" N GLU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 506 removed outlier: 3.818A pdb=" N LEU B 504 " --> pdb=" O PRO B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 534 removed outlier: 3.639A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 removed outlier: 4.063A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 568 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 601 through 609 Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.658A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.802A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.654A pdb=" N ARG B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 704 " --> pdb=" O ARG B 700 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.639A pdb=" N GLU B 737 " --> pdb=" O ARG B 733 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 758 removed outlier: 3.830A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 removed outlier: 3.624A pdb=" N GLU C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 135 through 138 Processing helix chain 'C' and resid 192 through 198 removed outlier: 3.979A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.612A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 282 through 295 removed outlier: 3.645A pdb=" N LEU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 319 through 334 removed outlier: 3.753A pdb=" N ILE C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 387 removed outlier: 5.343A pdb=" N ASN C 387 " --> pdb=" O ILE C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 402 removed outlier: 3.716A pdb=" N ASN C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 424 removed outlier: 3.500A pdb=" N ARG C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 449 through 457 removed outlier: 3.518A pdb=" N TRP C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.596A pdb=" N GLU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 506 removed outlier: 3.817A pdb=" N LEU C 504 " --> pdb=" O PRO C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 534 removed outlier: 3.639A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 552 removed outlier: 4.063A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 Processing helix chain 'C' and resid 579 through 583 Processing helix chain 'C' and resid 601 through 609 Processing helix chain 'C' and resid 650 through 661 removed outlier: 3.659A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.802A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.654A pdb=" N ARG C 700 " --> pdb=" O LYS C 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 704 " --> pdb=" O ARG C 700 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 3.639A pdb=" N GLU C 737 " --> pdb=" O ARG C 733 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 758 removed outlier: 3.830A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 removed outlier: 3.623A pdb=" N GLU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 135 through 138 Processing helix chain 'D' and resid 192 through 198 removed outlier: 3.980A pdb=" N SER D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 219 removed outlier: 3.611A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.645A pdb=" N LEU D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 319 through 334 removed outlier: 3.754A pdb=" N ILE D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 334 " --> pdb=" O THR D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 339 No H-bonds generated for 'chain 'D' and resid 337 through 339' Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 387 removed outlier: 5.343A pdb=" N ASN D 387 " --> pdb=" O ILE D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 402 removed outlier: 3.717A pdb=" N ASN D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU D 402 " --> pdb=" O GLN D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 424 removed outlier: 3.500A pdb=" N ARG D 424 " --> pdb=" O LEU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 449 through 457 removed outlier: 3.518A pdb=" N TRP D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 498 removed outlier: 3.595A pdb=" N GLU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 506 removed outlier: 3.818A pdb=" N LEU D 504 " --> pdb=" O PRO D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 534 removed outlier: 3.639A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 552 removed outlier: 4.063A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 568 Processing helix chain 'D' and resid 579 through 583 Processing helix chain 'D' and resid 601 through 609 Processing helix chain 'D' and resid 650 through 661 removed outlier: 3.659A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.802A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.654A pdb=" N ARG D 700 " --> pdb=" O LYS D 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU D 704 " --> pdb=" O ARG D 700 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.639A pdb=" N GLU D 737 " --> pdb=" O ARG D 733 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 758 removed outlier: 3.831A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 removed outlier: 3.624A pdb=" N GLU E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 No H-bonds generated for 'chain 'E' and resid 87 through 90' Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 135 through 138 Processing helix chain 'E' and resid 192 through 198 removed outlier: 3.980A pdb=" N SER E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 219 removed outlier: 3.612A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 282 through 295 removed outlier: 3.645A pdb=" N LEU E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 319 through 334 removed outlier: 3.754A pdb=" N ILE E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 387 removed outlier: 5.343A pdb=" N ASN E 387 " --> pdb=" O ILE E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 402 removed outlier: 3.717A pdb=" N ASN E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU E 402 " --> pdb=" O GLN E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 424 removed outlier: 3.501A pdb=" N ARG E 424 " --> pdb=" O LEU E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 442 No H-bonds generated for 'chain 'E' and resid 439 through 442' Processing helix chain 'E' and resid 449 through 457 removed outlier: 3.518A pdb=" N TRP E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 498 removed outlier: 3.594A pdb=" N GLU E 491 " --> pdb=" O ARG E 487 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 506 removed outlier: 3.818A pdb=" N LEU E 504 " --> pdb=" O PRO E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 534 removed outlier: 3.639A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 552 removed outlier: 4.063A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 568 Processing helix chain 'E' and resid 579 through 583 Processing helix chain 'E' and resid 601 through 609 Processing helix chain 'E' and resid 650 through 661 removed outlier: 3.659A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.802A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 706 removed outlier: 3.654A pdb=" N ARG E 700 " --> pdb=" O LYS E 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU E 704 " --> pdb=" O ARG E 700 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 742 removed outlier: 3.639A pdb=" N GLU E 737 " --> pdb=" O ARG E 733 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 758 removed outlier: 3.830A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 removed outlier: 3.624A pdb=" N GLU F 48 " --> pdb=" O PRO F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 90 No H-bonds generated for 'chain 'F' and resid 87 through 90' Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 135 through 138 Processing helix chain 'F' and resid 192 through 198 removed outlier: 3.979A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 219 removed outlier: 3.612A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 225 Processing helix chain 'F' and resid 227 through 233 Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 282 through 295 removed outlier: 3.644A pdb=" N LEU F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 319 through 334 removed outlier: 3.754A pdb=" N ILE F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY F 334 " --> pdb=" O THR F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 339 No H-bonds generated for 'chain 'F' and resid 337 through 339' Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 387 removed outlier: 5.344A pdb=" N ASN F 387 " --> pdb=" O ILE F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 402 removed outlier: 3.716A pdb=" N ASN F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 424 removed outlier: 3.500A pdb=" N ARG F 424 " --> pdb=" O LEU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing helix chain 'F' and resid 449 through 457 removed outlier: 3.518A pdb=" N TRP F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 removed outlier: 3.596A pdb=" N GLU F 491 " --> pdb=" O ARG F 487 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 506 removed outlier: 3.818A pdb=" N LEU F 504 " --> pdb=" O PRO F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 534 removed outlier: 3.639A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 552 removed outlier: 4.063A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE F 552 " --> pdb=" O LEU F 548 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 568 Processing helix chain 'F' and resid 579 through 583 Processing helix chain 'F' and resid 601 through 609 Processing helix chain 'F' and resid 650 through 661 removed outlier: 3.658A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.802A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 706 removed outlier: 3.655A pdb=" N ARG F 700 " --> pdb=" O LYS F 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU F 704 " --> pdb=" O ARG F 700 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 742 removed outlier: 3.640A pdb=" N GLU F 737 " --> pdb=" O ARG F 733 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 758 removed outlier: 3.831A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 58 through 60 Processing sheet with id= B, first strand: chain 'A' and resid 366 through 369 removed outlier: 6.357A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE A 369 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR A 244 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY A 245 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR A 347 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.561A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 58 through 60 Processing sheet with id= E, first strand: chain 'B' and resid 366 through 369 removed outlier: 6.356A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE B 369 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR B 244 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY B 245 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 347 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.562A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 58 through 60 Processing sheet with id= H, first strand: chain 'C' and resid 366 through 369 removed outlier: 6.356A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE C 369 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR C 244 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY C 245 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR C 347 " --> pdb=" O GLY C 245 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.562A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 58 through 60 Processing sheet with id= K, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.357A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE D 369 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR D 244 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY D 245 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR D 347 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.561A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 58 through 60 Processing sheet with id= N, first strand: chain 'E' and resid 366 through 369 removed outlier: 6.357A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE E 369 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR E 244 " --> pdb=" O ILE E 369 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N GLY E 245 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR E 347 " --> pdb=" O GLY E 245 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.561A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 58 through 60 Processing sheet with id= Q, first strand: chain 'F' and resid 366 through 369 removed outlier: 6.357A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE F 369 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR F 244 " --> pdb=" O ILE F 369 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY F 245 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR F 347 " --> pdb=" O GLY F 245 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.561A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) 781 hydrogen bonds defined for protein. 2271 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: 11.24 Time building geometry restraints manager: 14.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 13719 1.39 - 1.56: 21435 1.56 - 1.73: 72 1.73 - 1.90: 288 1.90 - 2.07: 12 Bond restraints: 35526 Sorted by residual: bond pdb=" C4 AGS F 901 " pdb=" C5 AGS F 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.96e+01 bond pdb=" C4 AGS E 901 " pdb=" C5 AGS E 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.92e+01 bond pdb=" C4 AGS C 902 " pdb=" C5 AGS C 902 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 AGS F 902 " pdb=" C5 AGS F 902 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C4 AGS A 902 " pdb=" C5 AGS A 902 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.85e+01 ... (remaining 35521 not shown) Histogram of bond angle deviations from ideal: 99.17 - 107.28: 1586 107.28 - 115.40: 21464 115.40 - 123.51: 23584 123.51 - 131.63: 1360 131.63 - 139.74: 60 Bond angle restraints: 48054 Sorted by residual: angle pdb=" C5 AGS F 901 " pdb=" C4 AGS F 901 " pdb=" N3 AGS F 901 " ideal model delta sigma weight residual 126.80 118.60 8.20 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS C 901 " pdb=" C4 AGS C 901 " pdb=" N3 AGS C 901 " ideal model delta sigma weight residual 126.80 118.63 8.17 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS C 902 " pdb=" C4 AGS C 902 " pdb=" N3 AGS C 902 " ideal model delta sigma weight residual 126.80 118.64 8.16 7.41e-01 1.82e+00 1.21e+02 angle pdb=" C5 AGS A 901 " pdb=" C4 AGS A 901 " pdb=" N3 AGS A 901 " ideal model delta sigma weight residual 126.80 118.65 8.15 7.41e-01 1.82e+00 1.21e+02 angle pdb=" C5 AGS D 901 " pdb=" C4 AGS D 901 " pdb=" N3 AGS D 901 " ideal model delta sigma weight residual 126.80 118.65 8.15 7.41e-01 1.82e+00 1.21e+02 ... (remaining 48049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 20646 15.89 - 31.78: 1056 31.78 - 47.68: 276 47.68 - 63.57: 60 63.57 - 79.46: 30 Dihedral angle restraints: 22068 sinusoidal: 9348 harmonic: 12720 Sorted by residual: dihedral pdb=" CA ALA D 142 " pdb=" C ALA D 142 " pdb=" N TYR D 143 " pdb=" CA TYR D 143 " ideal model delta harmonic sigma weight residual -180.00 -133.07 -46.93 0 5.00e+00 4.00e-02 8.81e+01 dihedral pdb=" CA ALA A 142 " pdb=" C ALA A 142 " pdb=" N TYR A 143 " pdb=" CA TYR A 143 " ideal model delta harmonic sigma weight residual 180.00 -133.07 -46.93 0 5.00e+00 4.00e-02 8.81e+01 dihedral pdb=" CA ALA B 142 " pdb=" C ALA B 142 " pdb=" N TYR B 143 " pdb=" CA TYR B 143 " ideal model delta harmonic sigma weight residual -180.00 -133.08 -46.92 0 5.00e+00 4.00e-02 8.81e+01 ... (remaining 22065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4037 0.070 - 0.141: 1234 0.141 - 0.211: 129 0.211 - 0.282: 24 0.282 - 0.352: 12 Chirality restraints: 5436 Sorted by residual: chirality pdb=" CA LYS E 20 " pdb=" N LYS E 20 " pdb=" C LYS E 20 " pdb=" CB LYS E 20 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA LYS F 20 " pdb=" N LYS F 20 " pdb=" C LYS F 20 " pdb=" CB LYS F 20 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA LYS A 20 " pdb=" N LYS A 20 " pdb=" C LYS A 20 " pdb=" CB LYS A 20 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 5433 not shown) Planarity restraints: 6288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 169 " 0.051 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO B 170 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 169 " -0.051 5.00e-02 4.00e+02 7.59e-02 9.22e+00 pdb=" N PRO D 170 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 170 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 170 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 169 " 0.051 5.00e-02 4.00e+02 7.59e-02 9.22e+00 pdb=" N PRO A 170 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " 0.042 5.00e-02 4.00e+02 ... (remaining 6285 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 7408 2.77 - 3.30: 34920 3.30 - 3.83: 55586 3.83 - 4.37: 69409 4.37 - 4.90: 109733 Nonbonded interactions: 277056 Sorted by model distance: nonbonded pdb=" NE1 TRP E 476 " pdb=" OE1 GLU E 534 " model vdw 2.234 2.520 nonbonded pdb=" NE1 TRP B 476 " pdb=" OE1 GLU B 534 " model vdw 2.234 2.520 nonbonded pdb=" NE1 TRP C 476 " pdb=" OE1 GLU C 534 " model vdw 2.234 2.520 nonbonded pdb=" NE1 TRP F 476 " pdb=" OE1 GLU F 534 " model vdw 2.234 2.520 nonbonded pdb=" NE1 TRP A 476 " pdb=" OE1 GLU A 534 " model vdw 2.234 2.520 ... (remaining 277051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.610 Check model and map are aligned: 0.560 Set scattering table: 0.340 Process input model: 87.700 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 0.012 0.123 35526 Z= 0.773 Angle : 1.271 14.743 48054 Z= 0.780 Chirality : 0.067 0.352 5436 Planarity : 0.008 0.076 6288 Dihedral : 11.505 79.460 13824 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 22.42 Ramachandran Plot: Outliers : 0.95 % Allowed : 7.39 % Favored : 91.66 % Rotamer: Outliers : 0.32 % Allowed : 2.24 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.72 % 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: -4.38 (0.10), residues: 4398 helix: -3.94 (0.08), residues: 1728 sheet: -1.22 (0.21), residues: 390 loop : -2.31 (0.11), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.006 TRP A 551 HIS 0.010 0.002 HIS C 317 PHE 0.028 0.004 PHE B 290 TYR 0.029 0.004 TYR E 203 ARG 0.019 0.002 ARG E 766 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 798 time to evaluate : 4.155 Fit side-chains REVERT: A 46 MET cc_start: 0.2840 (mtp) cc_final: 0.2455 (mmm) REVERT: A 88 VAL cc_start: 0.4687 (m) cc_final: 0.4452 (m) REVERT: A 204 ASP cc_start: 0.8349 (m-30) cc_final: 0.7846 (p0) REVERT: A 217 LYS cc_start: 0.8964 (mttt) cc_final: 0.8644 (mtpt) REVERT: A 221 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 273 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7615 (tm-30) REVERT: A 320 VAL cc_start: 0.7659 (t) cc_final: 0.7456 (p) REVERT: A 484 ASP cc_start: 0.7891 (p0) cc_final: 0.7635 (p0) REVERT: A 560 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7391 (mtt180) REVERT: A 584 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7149 (tppt) REVERT: A 603 GLN cc_start: 0.8081 (tp40) cc_final: 0.7748 (tt0) REVERT: A 650 GLU cc_start: 0.7535 (pm20) cc_final: 0.7201 (tt0) REVERT: A 651 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7692 (mmmt) REVERT: A 764 GLN cc_start: 0.8020 (mp10) cc_final: 0.7418 (mt0) REVERT: B 46 MET cc_start: 0.2607 (mtp) cc_final: 0.2245 (mmm) REVERT: B 88 VAL cc_start: 0.4727 (m) cc_final: 0.4451 (m) REVERT: B 204 ASP cc_start: 0.8300 (m-30) cc_final: 0.7837 (p0) REVERT: B 217 LYS cc_start: 0.8991 (mttt) cc_final: 0.8689 (mtpt) REVERT: B 273 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7566 (tm-30) REVERT: B 335 LEU cc_start: 0.7518 (mt) cc_final: 0.7315 (mt) REVERT: B 484 ASP cc_start: 0.7850 (p0) cc_final: 0.7516 (p0) REVERT: B 508 MET cc_start: 0.7221 (ptm) cc_final: 0.6559 (ptm) REVERT: B 560 ARG cc_start: 0.7786 (ttm110) cc_final: 0.7132 (mtt180) REVERT: B 584 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7178 (tppt) REVERT: B 603 GLN cc_start: 0.8135 (tp40) cc_final: 0.7835 (mt0) REVERT: B 650 GLU cc_start: 0.7540 (pm20) cc_final: 0.7211 (tt0) REVERT: B 651 LYS cc_start: 0.8252 (ttpt) cc_final: 0.7724 (mmmt) REVERT: B 764 GLN cc_start: 0.8042 (mp10) cc_final: 0.7444 (mt0) REVERT: C 46 MET cc_start: 0.2703 (mtp) cc_final: 0.2263 (mmm) REVERT: C 88 VAL cc_start: 0.4662 (m) cc_final: 0.4309 (m) REVERT: C 204 ASP cc_start: 0.8345 (m-30) cc_final: 0.7937 (p0) REVERT: C 217 LYS cc_start: 0.9011 (mttt) cc_final: 0.8715 (mtpt) REVERT: C 273 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7614 (tm-30) REVERT: C 320 VAL cc_start: 0.7695 (t) cc_final: 0.7477 (p) REVERT: C 484 ASP cc_start: 0.7976 (p0) cc_final: 0.7750 (p0) REVERT: C 560 ARG cc_start: 0.7797 (ttm110) cc_final: 0.7092 (mtt180) REVERT: C 584 LYS cc_start: 0.7706 (ttmt) cc_final: 0.7046 (tppt) REVERT: C 603 GLN cc_start: 0.8109 (tp40) cc_final: 0.7859 (mt0) REVERT: C 650 GLU cc_start: 0.7541 (pm20) cc_final: 0.7224 (tt0) REVERT: C 651 LYS cc_start: 0.8278 (ttpt) cc_final: 0.7760 (mmmt) REVERT: C 764 GLN cc_start: 0.8102 (mp10) cc_final: 0.7544 (mt0) REVERT: D 46 MET cc_start: 0.2833 (mtp) cc_final: 0.2434 (mmm) REVERT: D 88 VAL cc_start: 0.4684 (m) cc_final: 0.4445 (m) REVERT: D 204 ASP cc_start: 0.8347 (m-30) cc_final: 0.7850 (p0) REVERT: D 217 LYS cc_start: 0.8964 (mttt) cc_final: 0.8643 (mtpt) REVERT: D 221 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7888 (mm-30) REVERT: D 273 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7597 (tm-30) REVERT: D 320 VAL cc_start: 0.7668 (t) cc_final: 0.7466 (p) REVERT: D 484 ASP cc_start: 0.7895 (p0) cc_final: 0.7640 (p0) REVERT: D 560 ARG cc_start: 0.7838 (ttm110) cc_final: 0.7395 (mtt180) REVERT: D 584 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7145 (tppt) REVERT: D 603 GLN cc_start: 0.8080 (tp40) cc_final: 0.7742 (tt0) REVERT: D 650 GLU cc_start: 0.7537 (pm20) cc_final: 0.7198 (tt0) REVERT: D 651 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7696 (mmmt) REVERT: D 764 GLN cc_start: 0.8013 (mp10) cc_final: 0.7417 (mt0) REVERT: E 46 MET cc_start: 0.2505 (mtp) cc_final: 0.2146 (mmm) REVERT: E 88 VAL cc_start: 0.4731 (m) cc_final: 0.4471 (m) REVERT: E 204 ASP cc_start: 0.8304 (m-30) cc_final: 0.7840 (p0) REVERT: E 217 LYS cc_start: 0.9000 (mttt) cc_final: 0.8751 (mtpt) REVERT: E 219 MET cc_start: 0.8212 (mtt) cc_final: 0.8011 (mtt) REVERT: E 273 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7597 (tm-30) REVERT: E 335 LEU cc_start: 0.7514 (mt) cc_final: 0.7304 (mt) REVERT: E 484 ASP cc_start: 0.7826 (p0) cc_final: 0.7512 (p0) REVERT: E 508 MET cc_start: 0.7204 (ptm) cc_final: 0.6552 (ptm) REVERT: E 560 ARG cc_start: 0.7781 (ttm110) cc_final: 0.7386 (mtt180) REVERT: E 584 LYS cc_start: 0.7789 (ttmt) cc_final: 0.7154 (tppt) REVERT: E 603 GLN cc_start: 0.8146 (tp40) cc_final: 0.7849 (mt0) REVERT: E 650 GLU cc_start: 0.7543 (pm20) cc_final: 0.7217 (tt0) REVERT: E 651 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7740 (mmmt) REVERT: E 764 GLN cc_start: 0.8047 (mp10) cc_final: 0.7446 (mt0) REVERT: F 46 MET cc_start: 0.2698 (mtp) cc_final: 0.2269 (mmm) REVERT: F 88 VAL cc_start: 0.4663 (m) cc_final: 0.4300 (m) REVERT: F 204 ASP cc_start: 0.8338 (m-30) cc_final: 0.7938 (p0) REVERT: F 217 LYS cc_start: 0.9016 (mttt) cc_final: 0.8718 (mtpt) REVERT: F 229 LEU cc_start: 0.8638 (mt) cc_final: 0.8388 (mt) REVERT: F 273 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7622 (tm-30) REVERT: F 484 ASP cc_start: 0.7974 (p0) cc_final: 0.7750 (p0) REVERT: F 560 ARG cc_start: 0.7804 (ttm110) cc_final: 0.7092 (mtt180) REVERT: F 584 LYS cc_start: 0.7719 (ttmt) cc_final: 0.7055 (tppt) REVERT: F 603 GLN cc_start: 0.8104 (tp40) cc_final: 0.7870 (mt0) REVERT: F 650 GLU cc_start: 0.7547 (pm20) cc_final: 0.7224 (tt0) REVERT: F 651 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7762 (mmmt) REVERT: F 764 GLN cc_start: 0.8097 (mp10) cc_final: 0.7503 (mt0) outliers start: 12 outliers final: 6 residues processed: 810 average time/residue: 0.5379 time to fit residues: 661.5546 Evaluate side-chains 443 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 437 time to evaluate : 3.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 0.4980 chunk 331 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 343 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 397 optimal weight: 6.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 660 ASN B 327 GLN B 660 ASN C 91 ASN C 327 GLN C 494 GLN C 660 ASN D 91 ASN D 327 GLN D 660 ASN E 91 ASN E 327 GLN E 494 GLN E 660 ASN F 91 ASN F 327 GLN F 494 GLN F 660 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35526 Z= 0.244 Angle : 0.810 9.240 48054 Z= 0.424 Chirality : 0.049 0.177 5436 Planarity : 0.007 0.092 6288 Dihedral : 9.898 53.247 5034 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.05 % Favored : 91.41 % Rotamer: Outliers : 2.40 % Allowed : 6.95 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.14 % 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: -2.56 (0.12), residues: 4398 helix: -1.86 (0.11), residues: 1740 sheet: -0.60 (0.23), residues: 408 loop : -1.72 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 551 HIS 0.004 0.001 HIS A 115 PHE 0.015 0.002 PHE D 139 TYR 0.021 0.002 TYR A 755 ARG 0.007 0.001 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 483 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.3005 (mtp) cc_final: 0.2477 (tpt) REVERT: A 64 ARG cc_start: 0.5363 (mmp-170) cc_final: 0.4999 (mmp-170) REVERT: A 204 ASP cc_start: 0.8380 (m-30) cc_final: 0.7942 (p0) REVERT: A 560 ARG cc_start: 0.7445 (ttm110) cc_final: 0.7002 (mtp180) REVERT: A 584 LYS cc_start: 0.7817 (ttmt) cc_final: 0.7133 (tppt) REVERT: A 650 GLU cc_start: 0.7323 (pm20) cc_final: 0.7062 (tt0) REVERT: A 651 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7778 (mmmt) REVERT: B 46 MET cc_start: 0.3013 (mtp) cc_final: 0.2527 (tpt) REVERT: B 204 ASP cc_start: 0.8274 (m-30) cc_final: 0.7853 (p0) REVERT: B 273 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7683 (tm-30) REVERT: B 434 ASP cc_start: 0.3971 (t70) cc_final: 0.3759 (p0) REVERT: B 504 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7462 (tp) REVERT: B 560 ARG cc_start: 0.7391 (ttm110) cc_final: 0.7053 (mtt180) REVERT: B 584 LYS cc_start: 0.7775 (ttmt) cc_final: 0.6810 (tptm) REVERT: B 650 GLU cc_start: 0.7369 (pm20) cc_final: 0.7120 (tt0) REVERT: B 651 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7807 (mmmt) REVERT: B 764 GLN cc_start: 0.8011 (mp10) cc_final: 0.7602 (mt0) REVERT: C 46 MET cc_start: 0.3139 (mtp) cc_final: 0.2700 (tpt) REVERT: C 204 ASP cc_start: 0.8371 (m-30) cc_final: 0.8001 (p0) REVERT: C 273 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7629 (tm-30) REVERT: C 560 ARG cc_start: 0.7391 (ttm110) cc_final: 0.7069 (mtt180) REVERT: C 561 GLU cc_start: 0.8028 (tt0) cc_final: 0.7796 (tp30) REVERT: C 584 LYS cc_start: 0.7717 (ttmt) cc_final: 0.7080 (tppt) REVERT: C 651 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7784 (mmmt) REVERT: C 675 LEU cc_start: 0.7939 (mt) cc_final: 0.7726 (mt) REVERT: D 46 MET cc_start: 0.3007 (mtp) cc_final: 0.2480 (tpt) REVERT: D 64 ARG cc_start: 0.5357 (mmp-170) cc_final: 0.4995 (mmp-170) REVERT: D 204 ASP cc_start: 0.8383 (m-30) cc_final: 0.7939 (p0) REVERT: D 560 ARG cc_start: 0.7446 (ttm110) cc_final: 0.7004 (mtp180) REVERT: D 561 GLU cc_start: 0.8087 (tt0) cc_final: 0.7814 (tp30) REVERT: D 584 LYS cc_start: 0.7809 (ttmt) cc_final: 0.7134 (tppt) REVERT: D 650 GLU cc_start: 0.7325 (pm20) cc_final: 0.7055 (tt0) REVERT: D 651 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7768 (mmmt) REVERT: E 46 MET cc_start: 0.3014 (mtp) cc_final: 0.2540 (tpt) REVERT: E 204 ASP cc_start: 0.8270 (m-30) cc_final: 0.7842 (p0) REVERT: E 273 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7685 (tm-30) REVERT: E 434 ASP cc_start: 0.3971 (t70) cc_final: 0.3760 (p0) REVERT: E 560 ARG cc_start: 0.7405 (ttm110) cc_final: 0.6975 (mtt180) REVERT: E 584 LYS cc_start: 0.7756 (ttmt) cc_final: 0.6788 (tptm) REVERT: E 603 GLN cc_start: 0.8010 (tp40) cc_final: 0.7809 (mt0) REVERT: E 651 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7812 (mmmt) REVERT: E 764 GLN cc_start: 0.8021 (mp10) cc_final: 0.7612 (mt0) REVERT: F 46 MET cc_start: 0.3102 (mtp) cc_final: 0.2665 (tpt) REVERT: F 204 ASP cc_start: 0.8371 (m-30) cc_final: 0.7997 (p0) REVERT: F 229 LEU cc_start: 0.8773 (mt) cc_final: 0.8548 (mt) REVERT: F 273 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7615 (tm-30) REVERT: F 560 ARG cc_start: 0.7398 (ttm110) cc_final: 0.7065 (mtt180) REVERT: F 561 GLU cc_start: 0.8028 (tt0) cc_final: 0.7803 (tp30) REVERT: F 584 LYS cc_start: 0.7711 (ttmt) cc_final: 0.7071 (tppt) REVERT: F 651 LYS cc_start: 0.8229 (ttpt) cc_final: 0.7790 (mmmt) REVERT: F 675 LEU cc_start: 0.7940 (mt) cc_final: 0.7688 (mt) outliers start: 90 outliers final: 59 residues processed: 544 average time/residue: 0.5011 time to fit residues: 434.5925 Evaluate side-chains 423 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 363 time to evaluate : 3.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 664 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 331 optimal weight: 20.0000 chunk 270 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 398 optimal weight: 8.9990 chunk 430 optimal weight: 20.0000 chunk 354 optimal weight: 9.9990 chunk 395 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 319 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 91 ASN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35526 Z= 0.268 Angle : 0.752 9.283 48054 Z= 0.386 Chirality : 0.049 0.191 5436 Planarity : 0.007 0.074 6288 Dihedral : 9.604 51.096 5034 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.87 % Favored : 90.59 % Rotamer: Outliers : 3.89 % Allowed : 10.60 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.93 (0.12), residues: 4398 helix: -0.96 (0.12), residues: 1752 sheet: -0.74 (0.21), residues: 528 loop : -1.64 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 551 HIS 0.005 0.001 HIS E 115 PHE 0.015 0.002 PHE C 506 TYR 0.014 0.002 TYR A 755 ARG 0.006 0.001 ARG E 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 381 time to evaluate : 4.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.2961 (mtp) cc_final: 0.2414 (tpt) REVERT: A 203 TYR cc_start: 0.7664 (m-10) cc_final: 0.7320 (m-10) REVERT: A 429 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7038 (tt) REVERT: A 498 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7552 (mp0) REVERT: A 560 ARG cc_start: 0.7461 (ttm110) cc_final: 0.7173 (mtt180) REVERT: A 561 GLU cc_start: 0.7909 (tt0) cc_final: 0.7690 (tp30) REVERT: A 584 LYS cc_start: 0.7767 (ttmt) cc_final: 0.7087 (tppt) REVERT: A 651 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7778 (mmmt) REVERT: B 46 MET cc_start: 0.2953 (mtp) cc_final: 0.2480 (tpt) REVERT: B 560 ARG cc_start: 0.7381 (ttm110) cc_final: 0.7091 (mtt180) REVERT: B 561 GLU cc_start: 0.8066 (tt0) cc_final: 0.7777 (tp30) REVERT: B 584 LYS cc_start: 0.7787 (ttmt) cc_final: 0.6798 (tptm) REVERT: B 650 GLU cc_start: 0.7405 (pm20) cc_final: 0.7178 (tt0) REVERT: B 651 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7821 (mmmt) REVERT: B 764 GLN cc_start: 0.8044 (mp10) cc_final: 0.7647 (mt0) REVERT: C 46 MET cc_start: 0.3031 (mtp) cc_final: 0.2512 (tpt) REVERT: C 203 TYR cc_start: 0.7704 (m-10) cc_final: 0.7350 (m-10) REVERT: C 273 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7696 (tm-30) REVERT: C 429 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7071 (tt) REVERT: C 560 ARG cc_start: 0.7432 (ttm110) cc_final: 0.7132 (mtt180) REVERT: C 561 GLU cc_start: 0.8033 (tt0) cc_final: 0.7802 (tp30) REVERT: C 584 LYS cc_start: 0.7743 (ttmt) cc_final: 0.6784 (tptm) REVERT: C 651 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7804 (mmmt) REVERT: D 46 MET cc_start: 0.2968 (mtp) cc_final: 0.2416 (tpt) REVERT: D 203 TYR cc_start: 0.7659 (m-10) cc_final: 0.7318 (m-10) REVERT: D 429 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7027 (tt) REVERT: D 498 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7550 (mp0) REVERT: D 560 ARG cc_start: 0.7444 (ttm110) cc_final: 0.7156 (mtt180) REVERT: D 561 GLU cc_start: 0.8046 (tt0) cc_final: 0.7798 (tp30) REVERT: D 584 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7086 (tppt) REVERT: D 651 LYS cc_start: 0.8182 (ttpt) cc_final: 0.7785 (mmmt) REVERT: E 46 MET cc_start: 0.2945 (mtp) cc_final: 0.2448 (tpt) REVERT: E 203 TYR cc_start: 0.7652 (m-10) cc_final: 0.6900 (m-80) REVERT: E 560 ARG cc_start: 0.7415 (ttm110) cc_final: 0.7114 (mtt180) REVERT: E 561 GLU cc_start: 0.8059 (tt0) cc_final: 0.7786 (tp30) REVERT: E 584 LYS cc_start: 0.7782 (ttmt) cc_final: 0.6799 (tptm) REVERT: E 651 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7798 (mmmt) REVERT: F 46 MET cc_start: 0.3076 (mtp) cc_final: 0.2570 (tpt) REVERT: F 203 TYR cc_start: 0.7707 (m-10) cc_final: 0.7331 (m-10) REVERT: F 273 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7673 (tm-30) REVERT: F 429 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7070 (tt) REVERT: F 560 ARG cc_start: 0.7431 (ttm110) cc_final: 0.7120 (mtt180) REVERT: F 561 GLU cc_start: 0.8036 (tt0) cc_final: 0.7806 (tp30) REVERT: F 584 LYS cc_start: 0.7739 (ttmt) cc_final: 0.6784 (tptm) REVERT: F 651 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7807 (mmmt) outliers start: 146 outliers final: 101 residues processed: 491 average time/residue: 0.4546 time to fit residues: 365.0941 Evaluate side-chains 443 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 338 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 707 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 8.9990 chunk 299 optimal weight: 30.0000 chunk 206 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 267 optimal weight: 9.9990 chunk 399 optimal weight: 7.9990 chunk 423 optimal weight: 30.0000 chunk 208 optimal weight: 10.0000 chunk 379 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN D 589 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 ASN E 589 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 35526 Z= 0.301 Angle : 0.751 9.101 48054 Z= 0.384 Chirality : 0.049 0.253 5436 Planarity : 0.007 0.075 6288 Dihedral : 9.367 50.625 5034 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.35 % Favored : 89.97 % Rotamer: Outliers : 4.93 % Allowed : 11.32 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 4398 helix: -0.63 (0.12), residues: 1758 sheet: -0.61 (0.22), residues: 516 loop : -1.58 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 551 HIS 0.006 0.001 HIS F 115 PHE 0.014 0.002 PHE C 506 TYR 0.017 0.003 TYR D 203 ARG 0.008 0.001 ARG F 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 341 time to evaluate : 3.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.2926 (mtp) cc_final: 0.2394 (tpt) REVERT: A 498 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7575 (mp0) REVERT: A 560 ARG cc_start: 0.7495 (ttm110) cc_final: 0.7196 (mtt180) REVERT: A 584 LYS cc_start: 0.7827 (ttmt) cc_final: 0.6898 (tptm) REVERT: A 651 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7809 (mmmt) REVERT: B 46 MET cc_start: 0.3016 (mtp) cc_final: 0.2525 (tpt) REVERT: B 366 GLU cc_start: 0.8237 (mp0) cc_final: 0.7957 (mt-10) REVERT: B 368 ASP cc_start: 0.8042 (t70) cc_final: 0.7816 (t70) REVERT: B 560 ARG cc_start: 0.7503 (ttm110) cc_final: 0.7158 (mtt180) REVERT: B 561 GLU cc_start: 0.8067 (tt0) cc_final: 0.7812 (tp30) REVERT: B 584 LYS cc_start: 0.7871 (ttmt) cc_final: 0.6920 (tptm) REVERT: B 650 GLU cc_start: 0.7398 (pm20) cc_final: 0.7120 (tt0) REVERT: B 651 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7839 (mmmt) REVERT: B 764 GLN cc_start: 0.8058 (mp10) cc_final: 0.7622 (mt0) REVERT: C 46 MET cc_start: 0.2855 (mtp) cc_final: 0.2411 (tpt) REVERT: C 560 ARG cc_start: 0.7413 (ttm110) cc_final: 0.7120 (mtt180) REVERT: C 561 GLU cc_start: 0.7992 (tt0) cc_final: 0.7777 (tp30) REVERT: C 584 LYS cc_start: 0.7817 (ttmt) cc_final: 0.6836 (tptm) REVERT: C 603 GLN cc_start: 0.8118 (tp40) cc_final: 0.7809 (mt0) REVERT: C 645 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8729 (mp) REVERT: C 651 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7821 (mmmt) REVERT: D 46 MET cc_start: 0.2928 (mtp) cc_final: 0.2392 (tpt) REVERT: D 498 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7569 (mp0) REVERT: D 560 ARG cc_start: 0.7489 (ttm110) cc_final: 0.7190 (mtt180) REVERT: D 561 GLU cc_start: 0.8079 (tt0) cc_final: 0.7817 (tp30) REVERT: D 584 LYS cc_start: 0.7823 (ttmt) cc_final: 0.6897 (tptm) REVERT: D 651 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7810 (mmmt) REVERT: E 46 MET cc_start: 0.2974 (mtp) cc_final: 0.2477 (tpt) REVERT: E 366 GLU cc_start: 0.8239 (mp0) cc_final: 0.7962 (mt-10) REVERT: E 368 ASP cc_start: 0.8047 (t70) cc_final: 0.7818 (t70) REVERT: E 560 ARG cc_start: 0.7509 (ttm110) cc_final: 0.7124 (mtt180) REVERT: E 561 GLU cc_start: 0.8074 (tt0) cc_final: 0.7844 (tp30) REVERT: E 584 LYS cc_start: 0.7854 (ttmt) cc_final: 0.6905 (tptm) REVERT: E 603 GLN cc_start: 0.8083 (tp40) cc_final: 0.7761 (mt0) REVERT: E 651 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7786 (mmmt) REVERT: F 46 MET cc_start: 0.2916 (mtp) cc_final: 0.2468 (tpt) REVERT: F 389 LYS cc_start: 0.7654 (ttmt) cc_final: 0.7441 (ttpt) REVERT: F 560 ARG cc_start: 0.7415 (ttm110) cc_final: 0.7098 (mtt180) REVERT: F 561 GLU cc_start: 0.7997 (tt0) cc_final: 0.7775 (tp30) REVERT: F 584 LYS cc_start: 0.7810 (ttmt) cc_final: 0.6837 (tptm) REVERT: F 603 GLN cc_start: 0.8107 (tp40) cc_final: 0.7799 (mt0) REVERT: F 645 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8726 (mp) REVERT: F 651 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7836 (mmmt) outliers start: 185 outliers final: 133 residues processed: 481 average time/residue: 0.4373 time to fit residues: 345.6132 Evaluate side-chains 462 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 327 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 298 PRO Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 298 PRO Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 645 ILE Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 707 ILE Chi-restraints excluded: chain F residue 730 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 6 optimal weight: 0.0370 chunk 315 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 361 optimal weight: 5.9990 chunk 292 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 216 optimal weight: 20.0000 chunk 380 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 overall best weight: 5.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 589 ASN ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN B 589 ASN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 589 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35526 Z= 0.258 Angle : 0.714 12.115 48054 Z= 0.361 Chirality : 0.047 0.185 5436 Planarity : 0.006 0.069 6288 Dihedral : 9.125 50.917 5034 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.94 % Favored : 90.38 % Rotamer: Outliers : 4.47 % Allowed : 12.14 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.34 (0.13), residues: 4398 helix: -0.18 (0.13), residues: 1710 sheet: -0.52 (0.22), residues: 522 loop : -1.55 (0.14), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 551 HIS 0.006 0.001 HIS A 115 PHE 0.013 0.002 PHE D 363 TYR 0.014 0.002 TYR D 203 ARG 0.007 0.001 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 363 time to evaluate : 3.648 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.2846 (mtp) cc_final: 0.2381 (tpt) REVERT: A 84 MET cc_start: 0.4168 (mtp) cc_final: 0.3859 (ptt) REVERT: A 404 HIS cc_start: 0.7145 (OUTLIER) cc_final: 0.6836 (m-70) REVERT: A 498 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7573 (mp0) REVERT: A 560 ARG cc_start: 0.7474 (ttm110) cc_final: 0.7247 (mtt180) REVERT: A 584 LYS cc_start: 0.7841 (ttmt) cc_final: 0.6911 (tptm) REVERT: A 645 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8691 (mp) REVERT: A 651 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7778 (mmmt) REVERT: B 46 MET cc_start: 0.2977 (mtp) cc_final: 0.2543 (tpt) REVERT: B 244 TYR cc_start: 0.8984 (p90) cc_final: 0.8589 (p90) REVERT: B 366 GLU cc_start: 0.8176 (mp0) cc_final: 0.7950 (mt-10) REVERT: B 368 ASP cc_start: 0.8036 (t70) cc_final: 0.7665 (t0) REVERT: B 560 ARG cc_start: 0.7413 (ttm110) cc_final: 0.7117 (mtt180) REVERT: B 561 GLU cc_start: 0.8069 (tt0) cc_final: 0.7830 (tp30) REVERT: B 584 LYS cc_start: 0.7916 (ttmt) cc_final: 0.6978 (tptm) REVERT: B 650 GLU cc_start: 0.7407 (pm20) cc_final: 0.7125 (tt0) REVERT: B 651 LYS cc_start: 0.8260 (ttpt) cc_final: 0.7843 (mmmt) REVERT: B 764 GLN cc_start: 0.8010 (mp10) cc_final: 0.7619 (mt0) REVERT: C 46 MET cc_start: 0.2748 (mtp) cc_final: 0.2313 (tpt) REVERT: C 244 TYR cc_start: 0.8951 (p90) cc_final: 0.8639 (p90) REVERT: C 368 ASP cc_start: 0.8019 (t70) cc_final: 0.7700 (t0) REVERT: C 498 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: C 560 ARG cc_start: 0.7427 (ttm110) cc_final: 0.7171 (mtt180) REVERT: C 584 LYS cc_start: 0.7855 (ttmt) cc_final: 0.6907 (tptm) REVERT: C 603 GLN cc_start: 0.8111 (tp40) cc_final: 0.7797 (mt0) REVERT: C 651 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7820 (mmmt) REVERT: D 46 MET cc_start: 0.2896 (mtp) cc_final: 0.2409 (tpt) REVERT: D 84 MET cc_start: 0.4132 (mtp) cc_final: 0.3833 (ptt) REVERT: D 404 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6836 (m-70) REVERT: D 498 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7565 (mp0) REVERT: D 560 ARG cc_start: 0.7469 (ttm110) cc_final: 0.7164 (mtt180) REVERT: D 561 GLU cc_start: 0.8074 (tt0) cc_final: 0.7829 (tp30) REVERT: D 584 LYS cc_start: 0.7840 (ttmt) cc_final: 0.6912 (tptm) REVERT: D 645 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8689 (mp) REVERT: D 651 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7768 (mmmt) REVERT: E 46 MET cc_start: 0.3008 (mtp) cc_final: 0.2557 (tpt) REVERT: E 244 TYR cc_start: 0.8988 (p90) cc_final: 0.8577 (p90) REVERT: E 366 GLU cc_start: 0.8183 (mp0) cc_final: 0.7961 (mt-10) REVERT: E 368 ASP cc_start: 0.8040 (t70) cc_final: 0.7674 (t0) REVERT: E 560 ARG cc_start: 0.7434 (ttm110) cc_final: 0.7148 (mtt180) REVERT: E 561 GLU cc_start: 0.8073 (tt0) cc_final: 0.7826 (tp30) REVERT: E 584 LYS cc_start: 0.7921 (ttmt) cc_final: 0.6981 (tptm) REVERT: E 651 LYS cc_start: 0.8169 (ttpt) cc_final: 0.7797 (mmmt) REVERT: F 46 MET cc_start: 0.2842 (mtp) cc_final: 0.2436 (tpt) REVERT: F 244 TYR cc_start: 0.8952 (p90) cc_final: 0.8641 (p90) REVERT: F 368 ASP cc_start: 0.8021 (t70) cc_final: 0.7707 (t0) REVERT: F 498 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: F 560 ARG cc_start: 0.7431 (ttm110) cc_final: 0.7198 (mtt180) REVERT: F 584 LYS cc_start: 0.7853 (ttmt) cc_final: 0.6910 (tptm) REVERT: F 603 GLN cc_start: 0.8109 (tp40) cc_final: 0.7799 (mt0) REVERT: F 651 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7819 (mmmt) outliers start: 168 outliers final: 127 residues processed: 479 average time/residue: 0.4566 time to fit residues: 358.3716 Evaluate side-chains 471 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 338 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 707 ILE Chi-restraints excluded: chain F residue 730 GLU Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 8.9990 chunk 381 optimal weight: 30.0000 chunk 83 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 423 optimal weight: 20.0000 chunk 351 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 222 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35526 Z= 0.265 Angle : 0.707 8.470 48054 Z= 0.358 Chirality : 0.047 0.183 5436 Planarity : 0.006 0.068 6288 Dihedral : 8.997 50.828 5034 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.25 % Favored : 90.06 % Rotamer: Outliers : 4.61 % Allowed : 12.38 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.21 (0.13), residues: 4398 helix: 0.03 (0.13), residues: 1710 sheet: -0.48 (0.23), residues: 516 loop : -1.55 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 551 HIS 0.006 0.001 HIS F 115 PHE 0.013 0.002 PHE C 363 TYR 0.010 0.002 TYR F 110 ARG 0.004 0.001 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 356 time to evaluate : 4.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 HIS cc_start: 0.7133 (OUTLIER) cc_final: 0.6845 (m-70) REVERT: A 498 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7564 (mp0) REVERT: A 584 LYS cc_start: 0.7918 (ttmt) cc_final: 0.6987 (tptm) REVERT: A 645 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8677 (mp) REVERT: A 651 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7747 (mmmt) REVERT: B 46 MET cc_start: 0.2967 (mtp) cc_final: 0.2541 (tpt) REVERT: B 368 ASP cc_start: 0.8042 (t70) cc_final: 0.7677 (t0) REVERT: B 560 ARG cc_start: 0.7377 (ttm110) cc_final: 0.7140 (mtt180) REVERT: B 561 GLU cc_start: 0.8058 (tt0) cc_final: 0.7837 (tp30) REVERT: B 584 LYS cc_start: 0.7819 (ttmt) cc_final: 0.6911 (tptm) REVERT: B 650 GLU cc_start: 0.7409 (pm20) cc_final: 0.7116 (tt0) REVERT: B 651 LYS cc_start: 0.8286 (ttpt) cc_final: 0.7865 (mmmt) REVERT: B 764 GLN cc_start: 0.8068 (mp10) cc_final: 0.7575 (mt0) REVERT: C 244 TYR cc_start: 0.8963 (p90) cc_final: 0.8628 (p90) REVERT: C 368 ASP cc_start: 0.8034 (t70) cc_final: 0.7674 (t0) REVERT: C 498 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: C 584 LYS cc_start: 0.7864 (ttmt) cc_final: 0.6928 (tptm) REVERT: C 603 GLN cc_start: 0.8078 (tp40) cc_final: 0.7753 (mt0) REVERT: C 645 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8709 (mp) REVERT: C 651 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7820 (mmmt) REVERT: D 404 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6858 (m-70) REVERT: D 498 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7544 (mp0) REVERT: D 560 ARG cc_start: 0.7430 (ttm110) cc_final: 0.7177 (mtt180) REVERT: D 561 GLU cc_start: 0.8078 (tt0) cc_final: 0.7845 (tp30) REVERT: D 584 LYS cc_start: 0.7891 (ttmt) cc_final: 0.6961 (tptm) REVERT: D 645 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8682 (mp) REVERT: D 651 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7751 (mmmt) REVERT: E 46 MET cc_start: 0.3005 (mtp) cc_final: 0.2555 (tpt) REVERT: E 368 ASP cc_start: 0.8051 (t70) cc_final: 0.7682 (t0) REVERT: E 560 ARG cc_start: 0.7394 (ttm110) cc_final: 0.7134 (mtt180) REVERT: E 561 GLU cc_start: 0.8074 (tt0) cc_final: 0.7847 (tp30) REVERT: E 584 LYS cc_start: 0.7822 (ttmt) cc_final: 0.6919 (tptm) REVERT: E 651 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7804 (mmmt) REVERT: F 244 TYR cc_start: 0.8961 (p90) cc_final: 0.8623 (p90) REVERT: F 368 ASP cc_start: 0.8036 (t70) cc_final: 0.7681 (t0) REVERT: F 498 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: F 560 ARG cc_start: 0.7374 (ttm110) cc_final: 0.7153 (mtt180) REVERT: F 584 LYS cc_start: 0.7857 (ttmt) cc_final: 0.6925 (tptm) REVERT: F 603 GLN cc_start: 0.8081 (tp40) cc_final: 0.7764 (mt0) REVERT: F 645 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8707 (mp) REVERT: F 651 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7819 (mmmt) outliers start: 173 outliers final: 142 residues processed: 472 average time/residue: 0.4377 time to fit residues: 339.2666 Evaluate side-chains 492 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 342 time to evaluate : 3.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 695 CYS Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 645 ILE Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 680 ASN Chi-restraints excluded: chain F residue 707 ILE Chi-restraints excluded: chain F residue 730 GLU Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 40.0000 chunk 47 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 309 optimal weight: 0.9990 chunk 239 optimal weight: 10.0000 chunk 356 optimal weight: 8.9990 chunk 236 optimal weight: 20.0000 chunk 422 optimal weight: 30.0000 chunk 264 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 194 optimal weight: 0.0170 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35526 Z= 0.227 Angle : 0.670 9.678 48054 Z= 0.339 Chirality : 0.046 0.184 5436 Planarity : 0.006 0.068 6288 Dihedral : 8.759 49.266 5034 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.39 % Favored : 90.93 % Rotamer: Outliers : 4.55 % Allowed : 12.75 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.07 (0.13), residues: 4398 helix: 0.22 (0.13), residues: 1716 sheet: -0.44 (0.22), residues: 516 loop : -1.55 (0.14), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 551 HIS 0.007 0.001 HIS F 115 PHE 0.015 0.001 PHE C 131 TYR 0.009 0.002 TYR B 110 ARG 0.003 0.000 ARG F 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 363 time to evaluate : 4.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.5423 (OUTLIER) cc_final: 0.4536 (tp) REVERT: A 229 LEU cc_start: 0.8505 (mm) cc_final: 0.8133 (mt) REVERT: A 404 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6788 (m-70) REVERT: A 498 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7535 (mp0) REVERT: A 584 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7070 (tppt) REVERT: A 651 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7754 (mmmt) REVERT: B 46 MET cc_start: 0.2961 (mtp) cc_final: 0.2520 (tpt) REVERT: B 244 TYR cc_start: 0.8956 (p90) cc_final: 0.8711 (p90) REVERT: B 368 ASP cc_start: 0.8012 (t70) cc_final: 0.7698 (t70) REVERT: B 561 GLU cc_start: 0.8036 (tt0) cc_final: 0.7830 (tp30) REVERT: B 584 LYS cc_start: 0.7804 (ttmt) cc_final: 0.6930 (tptm) REVERT: B 650 GLU cc_start: 0.7391 (pm20) cc_final: 0.7107 (tt0) REVERT: B 651 LYS cc_start: 0.8271 (ttpt) cc_final: 0.7857 (mmmt) REVERT: B 764 GLN cc_start: 0.8009 (mp10) cc_final: 0.7596 (mt0) REVERT: C 498 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: C 584 LYS cc_start: 0.7885 (ttmt) cc_final: 0.6925 (tptm) REVERT: C 603 GLN cc_start: 0.8125 (tp40) cc_final: 0.7763 (mt0) REVERT: C 651 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7833 (mmmt) REVERT: D 96 LEU cc_start: 0.5444 (OUTLIER) cc_final: 0.4555 (tp) REVERT: D 229 LEU cc_start: 0.8506 (mm) cc_final: 0.8144 (mt) REVERT: D 404 HIS cc_start: 0.7108 (OUTLIER) cc_final: 0.6824 (m-70) REVERT: D 498 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7525 (mp0) REVERT: D 560 ARG cc_start: 0.7444 (ttm110) cc_final: 0.7212 (mtp180) REVERT: D 561 GLU cc_start: 0.8073 (tt0) cc_final: 0.7853 (tp30) REVERT: D 584 LYS cc_start: 0.7877 (ttmt) cc_final: 0.7071 (tppt) REVERT: D 651 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7755 (mmmt) REVERT: E 46 MET cc_start: 0.3003 (mtp) cc_final: 0.2558 (tpt) REVERT: E 244 TYR cc_start: 0.8955 (p90) cc_final: 0.8711 (p90) REVERT: E 368 ASP cc_start: 0.8018 (t70) cc_final: 0.7700 (t70) REVERT: E 560 ARG cc_start: 0.7394 (ttm110) cc_final: 0.7170 (mtt180) REVERT: E 561 GLU cc_start: 0.8040 (tt0) cc_final: 0.7831 (tp30) REVERT: E 584 LYS cc_start: 0.7810 (ttmt) cc_final: 0.6931 (tptm) REVERT: E 651 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7808 (mmmt) REVERT: F 498 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: F 584 LYS cc_start: 0.7862 (ttmt) cc_final: 0.6913 (tptm) REVERT: F 651 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7827 (mmmt) outliers start: 171 outliers final: 145 residues processed: 484 average time/residue: 0.4319 time to fit residues: 346.5801 Evaluate side-chains 503 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 352 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 285 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 680 ASN Chi-restraints excluded: chain F residue 707 ILE Chi-restraints excluded: chain F residue 730 GLU Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 268 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 331 optimal weight: 6.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS F 603 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 35526 Z= 0.148 Angle : 0.607 7.986 48054 Z= 0.307 Chirality : 0.044 0.175 5436 Planarity : 0.005 0.070 6288 Dihedral : 8.202 48.186 5034 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.25 % Favored : 92.06 % Rotamer: Outliers : 3.06 % Allowed : 14.32 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.13), residues: 4398 helix: 0.54 (0.13), residues: 1704 sheet: -0.15 (0.23), residues: 504 loop : -1.38 (0.14), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 551 HIS 0.008 0.001 HIS C 115 PHE 0.019 0.001 PHE F 131 TYR 0.010 0.001 TYR F 244 ARG 0.005 0.000 ARG E 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 421 time to evaluate : 4.030 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.2776 (mtp) cc_final: 0.2301 (tpt) REVERT: A 84 MET cc_start: 0.4177 (mtp) cc_final: 0.3966 (ptt) REVERT: A 229 LEU cc_start: 0.8530 (mm) cc_final: 0.8196 (mt) REVERT: A 379 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7559 (mt-10) REVERT: A 404 HIS cc_start: 0.6978 (OUTLIER) cc_final: 0.6667 (m-70) REVERT: A 584 LYS cc_start: 0.7857 (ttmt) cc_final: 0.7047 (tppt) REVERT: A 651 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7795 (mmmt) REVERT: B 46 MET cc_start: 0.3156 (mtp) cc_final: 0.2701 (tpt) REVERT: B 204 ASP cc_start: 0.8293 (m-30) cc_final: 0.7914 (p0) REVERT: B 229 LEU cc_start: 0.8505 (mm) cc_final: 0.8161 (mt) REVERT: B 561 GLU cc_start: 0.8007 (tt0) cc_final: 0.7792 (tp30) REVERT: B 584 LYS cc_start: 0.7802 (ttmt) cc_final: 0.6903 (tptm) REVERT: B 650 GLU cc_start: 0.7344 (pm20) cc_final: 0.7135 (tt0) REVERT: B 651 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7831 (mmmt) REVERT: C 46 MET cc_start: 0.2801 (mtp) cc_final: 0.2401 (tpt) REVERT: C 498 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: C 584 LYS cc_start: 0.7786 (ttmt) cc_final: 0.6871 (tptm) REVERT: C 603 GLN cc_start: 0.8090 (tp40) cc_final: 0.7851 (mt0) REVERT: C 651 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7805 (mmmt) REVERT: D 46 MET cc_start: 0.2779 (mtp) cc_final: 0.2299 (tpt) REVERT: D 84 MET cc_start: 0.4088 (mtp) cc_final: 0.3835 (ptt) REVERT: D 229 LEU cc_start: 0.8530 (mm) cc_final: 0.8180 (mt) REVERT: D 379 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7562 (mt-10) REVERT: D 404 HIS cc_start: 0.6997 (OUTLIER) cc_final: 0.6675 (m-70) REVERT: D 584 LYS cc_start: 0.7856 (ttmt) cc_final: 0.7048 (tppt) REVERT: D 651 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7796 (mmmt) REVERT: E 46 MET cc_start: 0.3220 (mtp) cc_final: 0.2752 (tpt) REVERT: E 84 MET cc_start: 0.4070 (mtp) cc_final: 0.3823 (ptt) REVERT: E 204 ASP cc_start: 0.8397 (m-30) cc_final: 0.8091 (p0) REVERT: E 229 LEU cc_start: 0.8506 (mm) cc_final: 0.8168 (mt) REVERT: E 561 GLU cc_start: 0.8022 (tt0) cc_final: 0.7804 (tp30) REVERT: E 584 LYS cc_start: 0.7808 (ttmt) cc_final: 0.6911 (tptm) REVERT: E 651 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7752 (mmmt) REVERT: E 654 VAL cc_start: 0.8209 (t) cc_final: 0.8005 (m) REVERT: F 46 MET cc_start: 0.2958 (mtp) cc_final: 0.2571 (tpt) REVERT: F 498 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: F 584 LYS cc_start: 0.7793 (ttmt) cc_final: 0.6891 (tptm) REVERT: F 603 GLN cc_start: 0.8101 (tp40) cc_final: 0.7852 (mt0) REVERT: F 651 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7807 (mmmt) outliers start: 115 outliers final: 88 residues processed: 511 average time/residue: 0.4440 time to fit residues: 376.3527 Evaluate side-chains 462 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 370 time to evaluate : 4.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 695 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 285 ASN Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 9.9990 chunk 404 optimal weight: 20.0000 chunk 368 optimal weight: 5.9990 chunk 393 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 308 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 355 optimal weight: 0.9980 chunk 372 optimal weight: 7.9990 chunk 392 optimal weight: 0.8980 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN F 226 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35526 Z= 0.189 Angle : 0.628 8.123 48054 Z= 0.317 Chirality : 0.045 0.175 5436 Planarity : 0.005 0.071 6288 Dihedral : 8.208 47.972 5034 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.09 % Favored : 91.22 % Rotamer: Outliers : 3.51 % Allowed : 14.67 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 4398 helix: 0.54 (0.13), residues: 1734 sheet: -0.06 (0.23), residues: 504 loop : -1.34 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 551 HIS 0.007 0.001 HIS F 115 PHE 0.015 0.001 PHE C 131 TYR 0.009 0.002 TYR B 244 ARG 0.003 0.000 ARG F 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 364 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.2818 (mtp) cc_final: 0.2334 (tpt) REVERT: A 84 MET cc_start: 0.4220 (mtp) cc_final: 0.4007 (ptt) REVERT: A 96 LEU cc_start: 0.5158 (OUTLIER) cc_final: 0.4486 (tp) REVERT: A 229 LEU cc_start: 0.8539 (mm) cc_final: 0.8210 (mt) REVERT: A 404 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.6684 (m-70) REVERT: A 584 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7054 (tppt) REVERT: A 651 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7796 (mmmt) REVERT: B 46 MET cc_start: 0.3040 (mtp) cc_final: 0.2598 (tpt) REVERT: B 84 MET cc_start: 0.4009 (mtp) cc_final: 0.3748 (ptp) REVERT: B 204 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7930 (p0) REVERT: B 561 GLU cc_start: 0.8007 (tt0) cc_final: 0.7782 (tp30) REVERT: B 584 LYS cc_start: 0.7804 (ttmt) cc_final: 0.6903 (tptm) REVERT: B 650 GLU cc_start: 0.7383 (pm20) cc_final: 0.7169 (tt0) REVERT: B 651 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7850 (mmmt) REVERT: C 84 MET cc_start: 0.4608 (OUTLIER) cc_final: 0.4184 (ptt) REVERT: C 229 LEU cc_start: 0.8462 (mm) cc_final: 0.8124 (mt) REVERT: C 498 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: C 584 LYS cc_start: 0.7821 (ttmt) cc_final: 0.6927 (tptm) REVERT: C 651 LYS cc_start: 0.8196 (ttpt) cc_final: 0.7823 (mmmt) REVERT: D 46 MET cc_start: 0.2810 (mtp) cc_final: 0.2332 (tpt) REVERT: D 84 MET cc_start: 0.4067 (mtp) cc_final: 0.3837 (ptt) REVERT: D 96 LEU cc_start: 0.5215 (OUTLIER) cc_final: 0.4528 (tp) REVERT: D 229 LEU cc_start: 0.8548 (mm) cc_final: 0.8163 (mt) REVERT: D 404 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6676 (m-70) REVERT: D 584 LYS cc_start: 0.7884 (ttmt) cc_final: 0.7063 (tppt) REVERT: D 651 LYS cc_start: 0.8169 (ttpt) cc_final: 0.7799 (mmmt) REVERT: E 46 MET cc_start: 0.2980 (mtp) cc_final: 0.2536 (tpt) REVERT: E 561 GLU cc_start: 0.8035 (tt0) cc_final: 0.7792 (tp30) REVERT: E 584 LYS cc_start: 0.7810 (ttmt) cc_final: 0.6900 (tptm) REVERT: E 651 LYS cc_start: 0.8199 (ttpt) cc_final: 0.7839 (mmmt) REVERT: F 84 MET cc_start: 0.4652 (OUTLIER) cc_final: 0.4204 (ptt) REVERT: F 498 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: F 584 LYS cc_start: 0.7822 (ttmt) cc_final: 0.6930 (tptm) REVERT: F 603 GLN cc_start: 0.8135 (tp40) cc_final: 0.7830 (mt0) REVERT: F 651 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7823 (mmmt) outliers start: 132 outliers final: 110 residues processed: 459 average time/residue: 0.4313 time to fit residues: 329.2019 Evaluate side-chains 476 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 357 time to evaluate : 3.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 695 CYS Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 285 ASN Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 384 HIS Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 9.9990 chunk 415 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 436 optimal weight: 30.0000 chunk 401 optimal weight: 5.9990 chunk 347 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 chunk 213 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 285 ASN ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 35526 Z= 0.256 Angle : 0.677 8.823 48054 Z= 0.339 Chirality : 0.047 0.181 5436 Planarity : 0.006 0.070 6288 Dihedral : 8.490 48.735 5034 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.37 % Favored : 91.00 % Rotamer: Outliers : 3.75 % Allowed : 14.54 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4398 helix: 0.42 (0.13), residues: 1746 sheet: -0.18 (0.23), residues: 498 loop : -1.39 (0.14), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 551 HIS 0.007 0.001 HIS F 115 PHE 0.017 0.002 PHE C 131 TYR 0.012 0.002 TYR E 244 ARG 0.004 0.001 ARG C 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 347 time to evaluate : 4.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.5245 (OUTLIER) cc_final: 0.4576 (tp) REVERT: A 229 LEU cc_start: 0.8509 (mm) cc_final: 0.8130 (mt) REVERT: A 404 HIS cc_start: 0.7055 (OUTLIER) cc_final: 0.6789 (m-70) REVERT: A 584 LYS cc_start: 0.7868 (ttmt) cc_final: 0.7046 (tppt) REVERT: A 651 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7800 (mmmt) REVERT: B 46 MET cc_start: 0.2859 (mtp) cc_final: 0.2457 (tpt) REVERT: B 561 GLU cc_start: 0.8017 (tt0) cc_final: 0.7807 (tp30) REVERT: B 584 LYS cc_start: 0.7843 (ttmt) cc_final: 0.6921 (tptm) REVERT: B 650 GLU cc_start: 0.7394 (pm20) cc_final: 0.7175 (tt0) REVERT: B 651 LYS cc_start: 0.8281 (ttpt) cc_final: 0.7837 (mmmt) REVERT: C 84 MET cc_start: 0.4578 (OUTLIER) cc_final: 0.4119 (ptt) REVERT: C 498 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: C 584 LYS cc_start: 0.7888 (ttmt) cc_final: 0.6974 (tptm) REVERT: C 651 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7819 (mmmt) REVERT: D 96 LEU cc_start: 0.5254 (OUTLIER) cc_final: 0.4582 (tp) REVERT: D 229 LEU cc_start: 0.8534 (mm) cc_final: 0.8153 (mt) REVERT: D 404 HIS cc_start: 0.7053 (OUTLIER) cc_final: 0.6785 (m-70) REVERT: D 584 LYS cc_start: 0.7874 (ttmt) cc_final: 0.7053 (tppt) REVERT: D 651 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7793 (mmmt) REVERT: E 46 MET cc_start: 0.2890 (mtp) cc_final: 0.2500 (tpt) REVERT: E 561 GLU cc_start: 0.8031 (tt0) cc_final: 0.7809 (tp30) REVERT: E 584 LYS cc_start: 0.7834 (ttmt) cc_final: 0.6925 (tptm) REVERT: E 651 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7827 (mmmt) REVERT: F 84 MET cc_start: 0.4576 (OUTLIER) cc_final: 0.4126 (ptt) REVERT: F 498 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: F 584 LYS cc_start: 0.7885 (ttmt) cc_final: 0.6975 (tptm) REVERT: F 651 LYS cc_start: 0.8203 (ttpt) cc_final: 0.7823 (mmmt) outliers start: 141 outliers final: 128 residues processed: 447 average time/residue: 0.4240 time to fit residues: 319.3075 Evaluate side-chains 476 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 340 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 384 HIS Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 703 ILE Chi-restraints excluded: chain F residue 707 ILE Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 10.0000 chunk 370 optimal weight: 0.0670 chunk 106 optimal weight: 4.9990 chunk 320 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 348 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 357 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 285 ASN ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.173891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131253 restraints weight = 52866.391| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.00 r_work: 0.3297 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 35526 Z= 0.258 Angle : 0.859 59.200 48054 Z= 0.481 Chirality : 0.046 0.234 5436 Planarity : 0.006 0.069 6288 Dihedral : 8.491 48.708 5034 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.39 % Favored : 90.95 % Rotamer: Outliers : 3.83 % Allowed : 14.75 % Favored : 81.42 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 4398 helix: 0.37 (0.13), residues: 1764 sheet: -0.19 (0.23), residues: 498 loop : -1.43 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 551 HIS 0.007 0.001 HIS F 115 PHE 0.016 0.001 PHE C 131 TYR 0.099 0.002 TYR E 203 ARG 0.004 0.000 ARG F 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7681.41 seconds wall clock time: 138 minutes 44.97 seconds (8324.97 seconds total)