Starting phenix.real_space_refine on Thu Mar 5 17:29:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kdd_22819/03_2026/7kdd_22819.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kdd_22819/03_2026/7kdd_22819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kdd_22819/03_2026/7kdd_22819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kdd_22819/03_2026/7kdd_22819.map" model { file = "/net/cci-nas-00/data/ceres_data/7kdd_22819/03_2026/7kdd_22819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kdd_22819/03_2026/7kdd_22819.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5289 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 102 5.16 5 C 12435 2.51 5 N 3336 2.21 5 O 3867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19741 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4646 Classifications: {'peptide': 571} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 556} Chain breaks: 2 Chain: "D" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 998 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "B" Number of atoms: 4646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4646 Classifications: {'peptide': 571} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 556} Chain breaks: 2 Chain: "F" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 998 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "C" Number of atoms: 4646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4646 Classifications: {'peptide': 571} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 556} Chain breaks: 2 Chain: "H" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 998 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "A" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 141 Unusual residues: {' CA': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 4.89, per 1000 atoms: 0.25 Number of scatterers: 19741 At special positions: 0 Unit cell: (136.224, 140.352, 188.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 102 16.00 O 3867 8.00 N 3336 7.00 C 12435 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 250 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 391 " distance=2.04 Simple disulfide: pdb=" SG CYS A 574 " - pdb=" SG CYS A 611 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 250 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 391 " distance=2.03 Simple disulfide: pdb=" SG CYS B 574 " - pdb=" SG CYS B 611 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 507 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 250 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 391 " distance=2.04 Simple disulfide: pdb=" SG CYS C 574 " - pdb=" SG CYS C 611 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 281 " " NAG A1002 " - " ASN A 286 " " NAG A1003 " - " ASN A 302 " " NAG A1004 " - " ASN A 341 " " NAG A1005 " - " ASN A 383 " " NAG A1006 " - " ASN A 405 " " NAG A1007 " - " ASN A 409 " " NAG A1008 " - " ASN A 417 " " NAG A1009 " - " ASN A 555 " " NAG A1010 " - " ASN A 586 " " NAG B1001 " - " ASN B 281 " " NAG B1002 " - " ASN B 286 " " NAG B1003 " - " ASN B 302 " " NAG B1004 " - " ASN B 341 " " NAG B1005 " - " ASN B 383 " " NAG B1006 " - " ASN B 405 " " NAG B1007 " - " ASN B 409 " " NAG B1008 " - " ASN B 417 " " NAG B1009 " - " ASN B 555 " " NAG B1010 " - " ASN B 586 " " NAG C1001 " - " ASN C 281 " " NAG C1002 " - " ASN C 286 " " NAG C1003 " - " ASN C 302 " " NAG C1004 " - " ASN C 341 " " NAG C1005 " - " ASN C 383 " " NAG C1006 " - " ASN C 405 " " NAG C1007 " - " ASN C 409 " " NAG C1008 " - " ASN C 417 " " NAG C1009 " - " ASN C 555 " " NAG C1010 " - " ASN C 586 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4572 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 64 sheets defined 15.8% alpha, 65.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.554A pdb=" N VAL A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 392 through 407 removed outlier: 3.594A pdb=" N GLN A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 406 " --> pdb=" O GLN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 521 removed outlier: 3.743A pdb=" N GLN A 485 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A 500 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 removed outlier: 3.632A pdb=" N ILE A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'A' and resid 668 through 674 Processing helix chain 'A' and resid 679 through 692 removed outlier: 3.684A pdb=" N SER A 689 " --> pdb=" O ARG A 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.951A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.590A pdb=" N VAL B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 407 removed outlier: 4.078A pdb=" N GLN B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 521 removed outlier: 3.832A pdb=" N GLN B 485 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE B 486 " --> pdb=" O ALA B 482 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 500 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 505 " --> pdb=" O GLN B 501 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 534 removed outlier: 3.673A pdb=" N ILE B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 642 Processing helix chain 'B' and resid 668 through 674 Processing helix chain 'B' and resid 680 through 692 removed outlier: 3.796A pdb=" N GLU B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 689 " --> pdb=" O ARG B 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.803A pdb=" N GLN F 65 " --> pdb=" O GLN F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.950A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 183 removed outlier: 3.573A pdb=" N ILE C 176 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS C 177 " --> pdb=" O MET C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.637A pdb=" N VAL C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 391 No H-bonds generated for 'chain 'C' and resid 389 through 391' Processing helix chain 'C' and resid 392 through 407 removed outlier: 3.646A pdb=" N GLN C 402 " --> pdb=" O ASN C 398 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE C 403 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR C 406 " --> pdb=" O GLN C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 521 removed outlier: 3.701A pdb=" N GLN C 485 " --> pdb=" O TYR C 481 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE C 486 " --> pdb=" O ALA C 482 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 497 " --> pdb=" O GLY C 493 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA C 500 " --> pdb=" O ASN C 496 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 503 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 505 " --> pdb=" O GLN C 501 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU C 515 " --> pdb=" O ARG C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 534 removed outlier: 3.567A pdb=" N ILE C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 642 Processing helix chain 'C' and resid 668 through 674 Processing helix chain 'C' and resid 679 through 692 removed outlier: 3.681A pdb=" N SER C 689 " --> pdb=" O ARG C 685 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.726A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 74 through 77 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.178A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 538 through 540 removed outlier: 4.610A pdb=" N ALA A 538 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG A 92 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 582 " --> pdb=" O GLN A 591 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA3, first strand: chain 'A' and resid 373 through 375 removed outlier: 3.723A pdb=" N ALA A 373 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS A 365 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHE A 348 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS A 130 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY A 124 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE A 356 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP A 122 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU A 123 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 127 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 428 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 375 removed outlier: 3.723A pdb=" N ALA A 373 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS A 365 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHE A 348 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS A 130 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY A 124 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE A 356 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP A 122 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU A 123 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 127 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 428 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 214 through 215 removed outlier: 3.614A pdb=" N ASN A 249 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 146 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 214 through 215 Processing sheet with id=AA7, first strand: chain 'A' and resid 214 through 215 removed outlier: 3.614A pdb=" N ASN A 249 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 146 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR A 168 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 147 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR A 166 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 149 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A 164 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG A 151 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR A 159 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N TYR C 201 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N LEU A 161 " --> pdb=" O TYR C 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 214 through 215 removed outlier: 3.614A pdb=" N ASN A 249 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 146 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYS A 139 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP A 335 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 306 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 318 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR A 304 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG A 320 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 242 through 245 removed outlier: 6.763A pdb=" N LYS A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR A 168 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 147 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR A 166 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 149 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A 164 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG A 151 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR A 159 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N TYR C 201 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N LEU A 161 " --> pdb=" O TYR C 201 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 242 through 245 removed outlier: 3.795A pdb=" N VAL A 146 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 249 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 242 through 245 removed outlier: 3.795A pdb=" N VAL A 146 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 249 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 242 through 245 removed outlier: 7.448A pdb=" N LYS A 139 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP A 335 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 306 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 318 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR A 304 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG A 320 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 273 through 274 removed outlier: 3.614A pdb=" N ASN A 249 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 146 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=AB6, first strand: chain 'A' and resid 273 through 274 removed outlier: 3.614A pdb=" N ASN A 249 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 146 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR A 168 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 147 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR A 166 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 149 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A 164 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG A 151 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR A 159 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N TYR C 201 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N LEU A 161 " --> pdb=" O TYR C 201 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 273 through 274 removed outlier: 3.614A pdb=" N ASN A 249 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 146 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYS A 139 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP A 335 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 306 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 318 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR A 304 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG A 320 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 297 through 306 removed outlier: 6.813A pdb=" N ARG A 320 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR A 304 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 318 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 306 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP A 335 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYS A 139 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 297 through 306 removed outlier: 6.813A pdb=" N ARG A 320 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR A 304 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 318 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 306 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP A 335 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYS A 139 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR A 168 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 147 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR A 166 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 149 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A 164 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG A 151 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR A 159 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N TYR C 201 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N LEU A 161 " --> pdb=" O TYR C 201 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 297 through 306 removed outlier: 6.813A pdb=" N ARG A 320 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR A 304 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 318 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 306 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP A 335 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYS A 139 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 146 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 249 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 297 through 306 removed outlier: 6.813A pdb=" N ARG A 320 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR A 304 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 318 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 306 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP A 335 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYS A 139 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 146 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 249 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 188 through 191 removed outlier: 6.420A pdb=" N THR A 159 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N TYR C 201 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N LEU A 161 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG A 151 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A 164 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 149 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR A 166 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 147 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR A 168 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 188 through 191 removed outlier: 6.420A pdb=" N THR A 159 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N TYR C 201 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N LEU A 161 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG A 151 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A 164 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 149 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR A 166 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 147 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR A 168 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 146 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 249 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 188 through 191 removed outlier: 6.420A pdb=" N THR A 159 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N TYR C 201 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N LEU A 161 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG A 151 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A 164 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 149 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR A 166 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 147 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR A 168 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 146 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 249 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 188 through 191 removed outlier: 6.420A pdb=" N THR A 159 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N TYR C 201 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N LEU A 161 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG A 151 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A 164 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 149 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR A 166 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 147 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR A 168 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYS A 139 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP A 335 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 306 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 318 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR A 304 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG A 320 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.542A pdb=" N MET A 211 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 189 through 191 removed outlier: 4.579A pdb=" N ARG B 151 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 243 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 573 through 575 Processing sheet with id=AD1, first strand: chain 'A' and resid 617 through 620 removed outlier: 3.683A pdb=" N GLU A 627 " --> pdb=" O ARG A 635 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG A 635 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL A 629 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 643 through 644 removed outlier: 6.368A pdb=" N SER A 643 " --> pdb=" O ARG B 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.500A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.622A pdb=" N ALA D 92 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 68 through 72 removed outlier: 3.756A pdb=" N THR D 71 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.487A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AD8, first strand: chain 'E' and resid 17 through 23 removed outlier: 3.553A pdb=" N VAL E 18 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER E 64 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 538 through 540 removed outlier: 4.752A pdb=" N ALA B 538 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG B 92 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 582 " --> pdb=" O GLN B 591 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.644A pdb=" N ALA B 373 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS B 365 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE B 348 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS B 130 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 350 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY B 124 " --> pdb=" O ARG B 354 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE B 356 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ASP B 122 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU B 123 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 127 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.644A pdb=" N ALA B 373 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS B 365 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE B 348 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS B 130 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 350 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY B 124 " --> pdb=" O ARG B 354 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE B 356 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ASP B 122 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU B 123 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 127 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 167 through 169 removed outlier: 3.770A pdb=" N VAL B 146 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 214 through 215 removed outlier: 3.770A pdb=" N VAL B 146 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LYS B 139 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASP B 335 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 316 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B 306 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 318 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B 304 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG B 320 " --> pdb=" O ASN B 302 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 184 through 186 removed outlier: 3.887A pdb=" N CYS B 185 " --> pdb=" O MET B 211 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET B 211 " --> pdb=" O CYS B 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'B' and resid 188 through 191 removed outlier: 7.034A pdb=" N TYR B 201 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 574 through 575 removed outlier: 3.763A pdb=" N GLU B 609 " --> pdb=" O CYS B 574 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 617 through 620 removed outlier: 4.371A pdb=" N GLU B 627 " --> pdb=" O ARG B 635 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ARG B 635 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL B 629 " --> pdb=" O PHE B 633 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N PHE B 633 " --> pdb=" O VAL B 629 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 643 through 644 removed outlier: 6.317A pdb=" N SER B 643 " --> pdb=" O ARG C 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.537A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.674A pdb=" N ALA F 92 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 17 through 19 removed outlier: 3.878A pdb=" N LEU F 83 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR F 80 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR F 71 " --> pdb=" O TYR F 80 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.513A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AF6, first strand: chain 'G' and resid 17 through 23 removed outlier: 3.636A pdb=" N VAL G 18 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 538 through 540 removed outlier: 4.597A pdb=" N ALA C 538 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG C 92 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 582 " --> pdb=" O GLN C 591 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 373 through 375 removed outlier: 3.526A pdb=" N ALA C 373 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS C 365 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N PHE C 348 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS C 130 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 354 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY C 124 " --> pdb=" O ARG C 354 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU C 123 " --> pdb=" O ILE C 434 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 127 " --> pdb=" O PHE C 430 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL C 428 " --> pdb=" O TYR C 129 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 373 through 375 removed outlier: 3.526A pdb=" N ALA C 373 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS C 365 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N PHE C 348 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS C 130 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 354 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY C 124 " --> pdb=" O ARG C 354 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU C 123 " --> pdb=" O ILE C 434 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 127 " --> pdb=" O PHE C 430 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL C 428 " --> pdb=" O TYR C 129 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.553A pdb=" N VAL C 146 " --> pdb=" O ASN C 249 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 214 through 215 removed outlier: 3.553A pdb=" N VAL C 146 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LYS C 139 " --> pdb=" O ASP C 335 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP C 335 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU C 316 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL C 306 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR C 318 " --> pdb=" O THR C 304 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 304 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG C 320 " --> pdb=" O ASN C 302 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 184 through 186 Processing sheet with id=AG4, first strand: chain 'C' and resid 573 through 575 Processing sheet with id=AG5, first strand: chain 'C' and resid 617 through 620 removed outlier: 3.773A pdb=" N GLU C 627 " --> pdb=" O ARG C 635 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG C 635 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL C 629 " --> pdb=" O PHE C 633 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE C 633 " --> pdb=" O VAL C 629 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.685A pdb=" N ALA H 92 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 18 through 21 removed outlier: 3.982A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET H 81 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.521A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AH1, first strand: chain 'I' and resid 17 through 23 removed outlier: 3.610A pdb=" N VAL I 18 " --> pdb=" O ILE I 76 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 2643 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: 4.85 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3171 1.31 - 1.44: 5751 1.44 - 1.56: 11082 1.56 - 1.69: 0 1.69 - 1.82: 159 Bond restraints: 20163 Sorted by residual: bond pdb=" C7 NAG A1004 " pdb=" N2 NAG A1004 " ideal model delta sigma weight residual 1.346 1.473 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C7 NAG B1004 " pdb=" N2 NAG B1004 " ideal model delta sigma weight residual 1.346 1.473 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C7 NAG C1004 " pdb=" N2 NAG C1004 " ideal model delta sigma weight residual 1.346 1.472 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C7 NAG B1009 " pdb=" N2 NAG B1009 " ideal model delta sigma weight residual 1.346 1.472 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C7 NAG C1009 " pdb=" N2 NAG C1009 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.92e+01 ... (remaining 20158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 26333 1.77 - 3.53: 768 3.53 - 5.30: 193 5.30 - 7.06: 35 7.06 - 8.83: 4 Bond angle restraints: 27333 Sorted by residual: angle pdb=" C ARG D 12 " pdb=" N LYS D 13 " pdb=" CA LYS D 13 " ideal model delta sigma weight residual 120.49 125.18 -4.69 1.42e+00 4.96e-01 1.09e+01 angle pdb=" C TYR C 408 " pdb=" N ASN C 409 " pdb=" CA ASN C 409 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.55e+00 angle pdb=" C TYR A 408 " pdb=" N ASN A 409 " pdb=" CA ASN A 409 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.91e+00 angle pdb=" C TYR B 408 " pdb=" N ASN B 409 " pdb=" CA ASN B 409 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.26e+00 angle pdb=" C LYS B 378 " pdb=" N LYS B 379 " pdb=" CA LYS B 379 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.12e+00 ... (remaining 27328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11309 17.95 - 35.89: 912 35.89 - 53.84: 143 53.84 - 71.78: 24 71.78 - 89.73: 11 Dihedral angle restraints: 12399 sinusoidal: 5262 harmonic: 7137 Sorted by residual: dihedral pdb=" CB CYS B 574 " pdb=" SG CYS B 574 " pdb=" SG CYS B 611 " pdb=" CB CYS B 611 " ideal model delta sinusoidal sigma weight residual 93.00 158.65 -65.65 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CA ASP G 51 " pdb=" C ASP G 51 " pdb=" N ASN G 52 " pdb=" CA ASN G 52 " ideal model delta harmonic sigma weight residual -180.00 -143.48 -36.52 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" CA ASP I 51 " pdb=" C ASP I 51 " pdb=" N ASN I 52 " pdb=" CA ASN I 52 " ideal model delta harmonic sigma weight residual -180.00 -146.90 -33.10 0 5.00e+00 4.00e-02 4.38e+01 ... (remaining 12396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2961 0.106 - 0.212: 143 0.212 - 0.318: 0 0.318 - 0.423: 0 0.423 - 0.529: 1 Chirality restraints: 3105 Sorted by residual: chirality pdb=" C1 NAG B1004 " pdb=" ND2 ASN B 341 " pdb=" C2 NAG B1004 " pdb=" O5 NAG B1004 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" CB THR C 210 " pdb=" CA THR C 210 " pdb=" OG1 THR C 210 " pdb=" CG2 THR C 210 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" C5 NAG B1008 " pdb=" C4 NAG B1008 " pdb=" C6 NAG B1008 " pdb=" O5 NAG B1008 " both_signs ideal model delta sigma weight residual False -2.41 -2.60 0.19 2.00e-01 2.50e+01 9.18e-01 ... (remaining 3102 not shown) Planarity restraints: 3486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO H 14 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 13 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO D 14 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 13 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO F 14 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO F 14 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 14 " -0.021 5.00e-02 4.00e+02 ... (remaining 3483 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 228 2.63 - 3.19: 17122 3.19 - 3.76: 26392 3.76 - 4.33: 36684 4.33 - 4.90: 63924 Nonbonded interactions: 144350 Sorted by model distance: nonbonded pdb=" OD2 ASP F 73 " pdb=" OG1 THR F 76 " model vdw 2.056 3.040 nonbonded pdb=" OD2 ASP H 73 " pdb=" OG1 THR H 76 " model vdw 2.120 3.040 nonbonded pdb=" OH TYR H 33 " pdb=" O LEU H 112 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR A 667 " pdb=" O ARG C 131 " model vdw 2.205 3.040 nonbonded pdb=" NE2 GLN H 6 " pdb=" O TYR H 94 " model vdw 2.212 3.120 ... (remaining 144345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 87 through 1010) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.900 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.009 0.127 20211 Z= 0.415 Angle : 0.766 17.904 27459 Z= 0.368 Chirality : 0.048 0.529 3105 Planarity : 0.004 0.045 3456 Dihedral : 12.916 89.729 7773 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.44 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.17), residues: 2406 helix: -0.28 (0.31), residues: 291 sheet: -1.16 (0.19), residues: 795 loop : -2.08 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 311 TYR 0.018 0.001 TYR A 155 PHE 0.008 0.001 PHE E 100 TRP 0.018 0.001 TRP A 233 HIS 0.008 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00852 (20163) covalent geometry : angle 0.75330 (27333) SS BOND : bond 0.00225 ( 18) SS BOND : angle 1.20970 ( 36) hydrogen bonds : bond 0.22533 ( 614) hydrogen bonds : angle 9.11000 ( 2643) link_NAG-ASN : bond 0.00425 ( 30) link_NAG-ASN : angle 2.50279 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 612 GLN cc_start: 0.8208 (tp40) cc_final: 0.7789 (tp-100) REVERT: A 679 ASP cc_start: 0.7921 (t0) cc_final: 0.7527 (p0) REVERT: D 23 LYS cc_start: 0.8016 (tmtt) cc_final: 0.7785 (tptt) REVERT: D 73 ASP cc_start: 0.7569 (t0) cc_final: 0.7144 (t0) REVERT: D 76 THR cc_start: 0.8514 (p) cc_final: 0.8253 (p) REVERT: D 81 MET cc_start: 0.8315 (ptm) cc_final: 0.8017 (ptm) REVERT: D 126 MET cc_start: 0.8119 (tpt) cc_final: 0.7655 (tpt) REVERT: E 5 THR cc_start: 0.8763 (m) cc_final: 0.8479 (p) REVERT: B 111 CYS cc_start: 0.3255 (p) cc_final: 0.2876 (p) REVERT: B 338 ASP cc_start: 0.7941 (t0) cc_final: 0.7708 (t0) REVERT: F 23 LYS cc_start: 0.8402 (tmtt) cc_final: 0.8045 (tmtt) REVERT: G 84 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7610 (mp0) REVERT: C 214 MET cc_start: 0.7805 (ptp) cc_final: 0.7534 (ptp) REVERT: C 233 TRP cc_start: 0.7295 (p-90) cc_final: 0.6748 (p-90) REVERT: H 54 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8578 (tm-30) REVERT: H 73 ASP cc_start: 0.7599 (t70) cc_final: 0.7260 (t0) REVERT: H 76 THR cc_start: 0.8573 (p) cc_final: 0.8366 (p) REVERT: H 81 MET cc_start: 0.8134 (ptm) cc_final: 0.7817 (ptm) REVERT: H 123 GLN cc_start: 0.8619 (pm20) cc_final: 0.8352 (pm20) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1432 time to fit residues: 61.8893 Evaluate side-chains 234 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 0.0670 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 235 optimal weight: 1.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 123 GLN E 39 GLN B 692 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.083449 restraints weight = 32774.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.086800 restraints weight = 17073.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.088930 restraints weight = 11720.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.090219 restraints weight = 9369.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.090921 restraints weight = 8213.249| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20211 Z= 0.136 Angle : 0.612 16.823 27459 Z= 0.316 Chirality : 0.046 0.495 3105 Planarity : 0.004 0.043 3456 Dihedral : 5.401 40.116 3327 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.77 % Favored : 93.10 % Rotamer: Outliers : 0.65 % Allowed : 9.35 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.17), residues: 2406 helix: 0.50 (0.31), residues: 294 sheet: -0.98 (0.19), residues: 798 loop : -2.02 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 62 TYR 0.021 0.001 TYR A 408 PHE 0.015 0.001 PHE C 633 TRP 0.016 0.001 TRP A 334 HIS 0.006 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00308 (20163) covalent geometry : angle 0.59520 (27333) SS BOND : bond 0.00269 ( 18) SS BOND : angle 0.95871 ( 36) hydrogen bonds : bond 0.05386 ( 614) hydrogen bonds : angle 5.17481 ( 2643) link_NAG-ASN : bond 0.00397 ( 30) link_NAG-ASN : angle 2.51553 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 256 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.7956 (t0) cc_final: 0.7714 (t0) REVERT: A 589 TYR cc_start: 0.4045 (OUTLIER) cc_final: 0.2613 (t80) REVERT: A 612 GLN cc_start: 0.8174 (tp40) cc_final: 0.7756 (tp-100) REVERT: D 23 LYS cc_start: 0.8007 (tmtt) cc_final: 0.7501 (tmtt) REVERT: D 73 ASP cc_start: 0.7530 (t0) cc_final: 0.7029 (t0) REVERT: D 76 THR cc_start: 0.8498 (p) cc_final: 0.8168 (p) REVERT: D 126 MET cc_start: 0.7936 (tpt) cc_final: 0.7464 (tpt) REVERT: E 5 THR cc_start: 0.8803 (m) cc_final: 0.8474 (p) REVERT: B 338 ASP cc_start: 0.7885 (t0) cc_final: 0.7525 (t0) REVERT: F 73 ASP cc_start: 0.7684 (t0) cc_final: 0.7305 (t0) REVERT: F 126 MET cc_start: 0.7414 (tpt) cc_final: 0.7102 (tpt) REVERT: G 84 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7608 (mp0) REVERT: C 233 TRP cc_start: 0.7291 (p-90) cc_final: 0.6944 (p-90) REVERT: C 642 ILE cc_start: 0.7701 (mp) cc_final: 0.7496 (mp) REVERT: H 81 MET cc_start: 0.8222 (ptm) cc_final: 0.7798 (ptm) REVERT: H 123 GLN cc_start: 0.8677 (pm20) cc_final: 0.8321 (pm20) REVERT: I 32 ASN cc_start: 0.8548 (m-40) cc_final: 0.8312 (m-40) outliers start: 14 outliers final: 7 residues processed: 259 average time/residue: 0.1356 time to fit residues: 55.2094 Evaluate side-chains 241 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 233 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain I residue 98 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 160 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN C 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.080835 restraints weight = 33087.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.084103 restraints weight = 17243.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.086174 restraints weight = 11842.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.087435 restraints weight = 9494.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.088196 restraints weight = 8324.467| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 20211 Z= 0.211 Angle : 0.643 16.122 27459 Z= 0.331 Chirality : 0.047 0.476 3105 Planarity : 0.004 0.041 3456 Dihedral : 5.314 40.398 3327 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.94 % Favored : 91.90 % Rotamer: Outliers : 1.68 % Allowed : 12.81 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.16), residues: 2406 helix: 0.31 (0.29), residues: 312 sheet: -1.05 (0.18), residues: 795 loop : -2.05 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 38 TYR 0.024 0.001 TYR A 408 PHE 0.012 0.001 PHE A 266 TRP 0.015 0.002 TRP A 334 HIS 0.008 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00505 (20163) covalent geometry : angle 0.62498 (27333) SS BOND : bond 0.00285 ( 18) SS BOND : angle 1.00962 ( 36) hydrogen bonds : bond 0.05585 ( 614) hydrogen bonds : angle 5.01579 ( 2643) link_NAG-ASN : bond 0.00535 ( 30) link_NAG-ASN : angle 2.64241 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8799 (ttm) cc_final: 0.8571 (ttm) REVERT: A 362 ASP cc_start: 0.8069 (t0) cc_final: 0.7732 (t0) REVERT: A 589 TYR cc_start: 0.3976 (OUTLIER) cc_final: 0.2807 (t80) REVERT: D 23 LYS cc_start: 0.8010 (tmtt) cc_final: 0.7510 (tmtt) REVERT: D 73 ASP cc_start: 0.7566 (t0) cc_final: 0.7102 (t0) REVERT: D 126 MET cc_start: 0.7981 (tpt) cc_final: 0.7558 (tpt) REVERT: E 5 THR cc_start: 0.8820 (m) cc_final: 0.8503 (p) REVERT: B 338 ASP cc_start: 0.7928 (t0) cc_final: 0.7508 (t0) REVERT: B 648 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8119 (ttt) REVERT: F 19 LYS cc_start: 0.8186 (tptm) cc_final: 0.7824 (tppt) REVERT: F 23 LYS cc_start: 0.7963 (tmtt) cc_final: 0.7585 (tmtt) REVERT: F 30 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8697 (mttt) REVERT: F 73 ASP cc_start: 0.7787 (t0) cc_final: 0.7347 (t0) REVERT: G 79 LEU cc_start: 0.8864 (pp) cc_final: 0.8644 (pp) REVERT: G 84 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7984 (mp0) REVERT: C 338 ASP cc_start: 0.8101 (t0) cc_final: 0.7882 (t0) REVERT: C 362 ASP cc_start: 0.7844 (t0) cc_final: 0.7581 (t0) REVERT: C 589 TYR cc_start: 0.4551 (OUTLIER) cc_final: 0.3736 (t80) REVERT: C 642 ILE cc_start: 0.7761 (mp) cc_final: 0.7551 (mp) REVERT: H 81 MET cc_start: 0.8368 (ptm) cc_final: 0.7833 (ptm) outliers start: 36 outliers final: 26 residues processed: 263 average time/residue: 0.1489 time to fit residues: 60.6565 Evaluate side-chains 263 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 188 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN C 583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.115961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.080074 restraints weight = 33079.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.083154 restraints weight = 18035.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.085117 restraints weight = 12680.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.086316 restraints weight = 10300.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.086989 restraints weight = 9096.496| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 20211 Z= 0.236 Angle : 0.657 15.402 27459 Z= 0.341 Chirality : 0.047 0.469 3105 Planarity : 0.004 0.041 3456 Dihedral : 5.396 48.852 3327 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.31 % Favored : 91.56 % Rotamer: Outliers : 3.60 % Allowed : 13.74 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.16), residues: 2406 helix: 0.44 (0.30), residues: 294 sheet: -1.04 (0.18), residues: 792 loop : -2.08 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 354 TYR 0.025 0.001 TYR A 408 PHE 0.016 0.001 PHE B 309 TRP 0.014 0.002 TRP A 334 HIS 0.008 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00568 (20163) covalent geometry : angle 0.64215 (27333) SS BOND : bond 0.00283 ( 18) SS BOND : angle 1.02031 ( 36) hydrogen bonds : bond 0.05655 ( 614) hydrogen bonds : angle 4.93355 ( 2643) link_NAG-ASN : bond 0.00430 ( 30) link_NAG-ASN : angle 2.47739 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 246 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8782 (ttm) cc_final: 0.8574 (ttm) REVERT: A 362 ASP cc_start: 0.8116 (t0) cc_final: 0.7767 (t0) REVERT: A 589 TYR cc_start: 0.3974 (OUTLIER) cc_final: 0.2791 (t80) REVERT: D 19 LYS cc_start: 0.8547 (mmmm) cc_final: 0.8220 (mmmm) REVERT: D 23 LYS cc_start: 0.7969 (tmtt) cc_final: 0.7421 (tmtt) REVERT: D 73 ASP cc_start: 0.7629 (t0) cc_final: 0.7320 (t0) REVERT: D 126 MET cc_start: 0.7850 (tpt) cc_final: 0.7432 (tpt) REVERT: E 5 THR cc_start: 0.8821 (m) cc_final: 0.8505 (p) REVERT: E 51 ASP cc_start: 0.6792 (m-30) cc_final: 0.6325 (m-30) REVERT: B 338 ASP cc_start: 0.7997 (t0) cc_final: 0.7606 (t0) REVERT: B 389 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8868 (pp) REVERT: F 23 LYS cc_start: 0.7949 (tmtt) cc_final: 0.7486 (tmtt) REVERT: F 30 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8725 (mttt) REVERT: F 73 ASP cc_start: 0.7955 (t0) cc_final: 0.7507 (t0) REVERT: F 86 LEU cc_start: 0.9112 (mt) cc_final: 0.8885 (mp) REVERT: G 32 ASN cc_start: 0.8800 (m110) cc_final: 0.8404 (m-40) REVERT: G 84 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8014 (mp0) REVERT: C 295 ASP cc_start: 0.8107 (t0) cc_final: 0.7876 (t0) REVERT: C 362 ASP cc_start: 0.7842 (t0) cc_final: 0.7553 (t0) REVERT: C 589 TYR cc_start: 0.4589 (OUTLIER) cc_final: 0.3851 (t80) REVERT: H 73 ASP cc_start: 0.7630 (t0) cc_final: 0.7409 (t0) REVERT: H 81 MET cc_start: 0.8333 (ptm) cc_final: 0.7814 (ptm) outliers start: 77 outliers final: 45 residues processed: 301 average time/residue: 0.1448 time to fit residues: 67.5083 Evaluate side-chains 283 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 182 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN D 62 GLN ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.082512 restraints weight = 32569.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.085896 restraints weight = 16835.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.088038 restraints weight = 11417.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.089340 restraints weight = 9072.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.090054 restraints weight = 7916.389| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20211 Z= 0.132 Angle : 0.587 14.713 27459 Z= 0.302 Chirality : 0.045 0.445 3105 Planarity : 0.004 0.043 3456 Dihedral : 4.927 48.003 3327 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.23 % Favored : 93.68 % Rotamer: Outliers : 3.32 % Allowed : 14.63 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.16), residues: 2406 helix: 0.78 (0.30), residues: 294 sheet: -0.84 (0.19), residues: 780 loop : -2.00 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 354 TYR 0.020 0.001 TYR A 408 PHE 0.012 0.001 PHE A 266 TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00306 (20163) covalent geometry : angle 0.57142 (27333) SS BOND : bond 0.00252 ( 18) SS BOND : angle 0.77911 ( 36) hydrogen bonds : bond 0.04725 ( 614) hydrogen bonds : angle 4.57346 ( 2643) link_NAG-ASN : bond 0.00417 ( 30) link_NAG-ASN : angle 2.35540 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 262 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8817 (ttm) cc_final: 0.8603 (ttm) REVERT: A 155 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6174 (m-80) REVERT: A 244 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: A 362 ASP cc_start: 0.8047 (t0) cc_final: 0.7691 (t0) REVERT: A 420 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8594 (p) REVERT: A 589 TYR cc_start: 0.4091 (OUTLIER) cc_final: 0.3004 (t80) REVERT: A 636 MET cc_start: 0.8574 (mmm) cc_final: 0.8095 (mmm) REVERT: D 19 LYS cc_start: 0.8502 (mmmm) cc_final: 0.8285 (mmmm) REVERT: D 23 LYS cc_start: 0.8023 (tmtt) cc_final: 0.7529 (tmtt) REVERT: D 73 ASP cc_start: 0.7356 (t0) cc_final: 0.6930 (t0) REVERT: D 99 ASP cc_start: 0.9166 (t70) cc_final: 0.8812 (t0) REVERT: D 126 MET cc_start: 0.8045 (tpt) cc_final: 0.7568 (tpt) REVERT: E 5 THR cc_start: 0.8794 (m) cc_final: 0.8467 (p) REVERT: E 51 ASP cc_start: 0.6730 (m-30) cc_final: 0.6474 (m-30) REVERT: B 111 CYS cc_start: 0.3532 (p) cc_final: 0.3219 (p) REVERT: B 233 TRP cc_start: 0.7910 (p-90) cc_final: 0.7578 (p-90) REVERT: B 338 ASP cc_start: 0.7938 (t0) cc_final: 0.7528 (t0) REVERT: B 389 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8867 (pp) REVERT: B 607 ARG cc_start: 0.8049 (mmt90) cc_final: 0.7827 (mmt90) REVERT: F 30 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8726 (mttt) REVERT: F 73 ASP cc_start: 0.7853 (t0) cc_final: 0.7415 (t0) REVERT: F 86 LEU cc_start: 0.9086 (mt) cc_final: 0.8856 (mp) REVERT: G 32 ASN cc_start: 0.8721 (m110) cc_final: 0.8358 (m-40) REVERT: G 84 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7878 (mp0) REVERT: C 362 ASP cc_start: 0.7751 (t0) cc_final: 0.7505 (t0) REVERT: C 389 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8978 (pp) REVERT: C 560 LYS cc_start: 0.7738 (mttt) cc_final: 0.6486 (tptt) REVERT: C 562 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8346 (tt) REVERT: C 589 TYR cc_start: 0.4294 (OUTLIER) cc_final: 0.3571 (t80) REVERT: C 642 ILE cc_start: 0.7863 (mp) cc_final: 0.7644 (mp) REVERT: H 73 ASP cc_start: 0.7315 (t0) cc_final: 0.7012 (t0) REVERT: I 91 THR cc_start: 0.9219 (t) cc_final: 0.8999 (p) outliers start: 71 outliers final: 46 residues processed: 311 average time/residue: 0.1446 time to fit residues: 69.9295 Evaluate side-chains 297 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 89 CYS Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 15 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 103 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN I 1 GLN ** I 32 ASN ** 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 = 0.3505 r_free = 0.3505 target = 0.118116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.081728 restraints weight = 32769.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.085055 restraints weight = 17179.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.087145 restraints weight = 11829.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.088436 restraints weight = 9503.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.089217 restraints weight = 8327.869| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20211 Z= 0.149 Angle : 0.594 13.993 27459 Z= 0.307 Chirality : 0.045 0.439 3105 Planarity : 0.004 0.046 3456 Dihedral : 4.792 43.807 3327 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.11 % Favored : 92.81 % Rotamer: Outliers : 3.55 % Allowed : 15.66 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.16), residues: 2406 helix: 0.85 (0.30), residues: 294 sheet: -0.75 (0.19), residues: 750 loop : -1.96 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 354 TYR 0.021 0.001 TYR A 408 PHE 0.012 0.001 PHE A 266 TRP 0.009 0.001 TRP C 233 HIS 0.005 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00350 (20163) covalent geometry : angle 0.58037 (27333) SS BOND : bond 0.00248 ( 18) SS BOND : angle 0.76379 ( 36) hydrogen bonds : bond 0.04850 ( 614) hydrogen bonds : angle 4.54203 ( 2643) link_NAG-ASN : bond 0.00392 ( 30) link_NAG-ASN : angle 2.25888 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 250 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8815 (ttm) cc_final: 0.8609 (ttm) REVERT: A 155 TYR cc_start: 0.7137 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: A 362 ASP cc_start: 0.7918 (t0) cc_final: 0.7494 (t0) REVERT: A 420 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8624 (p) REVERT: A 589 TYR cc_start: 0.4056 (OUTLIER) cc_final: 0.3002 (t80) REVERT: A 612 GLN cc_start: 0.8039 (tp-100) cc_final: 0.7546 (tp-100) REVERT: A 636 MET cc_start: 0.8636 (mmm) cc_final: 0.8126 (mmm) REVERT: D 23 LYS cc_start: 0.8029 (tmtt) cc_final: 0.7587 (tmtt) REVERT: D 73 ASP cc_start: 0.7312 (t0) cc_final: 0.6973 (t0) REVERT: D 99 ASP cc_start: 0.9179 (t70) cc_final: 0.8788 (t0) REVERT: D 126 MET cc_start: 0.7995 (tpt) cc_final: 0.7511 (tpt) REVERT: E 5 THR cc_start: 0.8817 (m) cc_final: 0.8503 (p) REVERT: E 16 GLN cc_start: 0.8586 (mt0) cc_final: 0.8144 (mt0) REVERT: E 51 ASP cc_start: 0.6715 (m-30) cc_final: 0.6455 (m-30) REVERT: B 338 ASP cc_start: 0.7947 (t0) cc_final: 0.7516 (t0) REVERT: B 389 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8854 (pp) REVERT: B 607 ARG cc_start: 0.8219 (mmt90) cc_final: 0.7960 (mmt90) REVERT: B 682 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7618 (mt-10) REVERT: F 23 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7810 (tptt) REVERT: F 73 ASP cc_start: 0.7583 (t0) cc_final: 0.7204 (t0) REVERT: G 32 ASN cc_start: 0.8753 (m110) cc_final: 0.8344 (m-40) REVERT: G 84 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7898 (mp0) REVERT: C 362 ASP cc_start: 0.7731 (t0) cc_final: 0.7488 (t70) REVERT: C 389 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8987 (pp) REVERT: C 560 LYS cc_start: 0.7612 (mttt) cc_final: 0.6544 (tptt) REVERT: C 562 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8328 (tt) REVERT: C 589 TYR cc_start: 0.4633 (OUTLIER) cc_final: 0.3866 (t80) REVERT: C 612 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7707 (tp-100) REVERT: C 642 ILE cc_start: 0.7915 (mp) cc_final: 0.7715 (mp) REVERT: H 23 LYS cc_start: 0.8265 (tptt) cc_final: 0.7725 (tmtt) REVERT: H 73 ASP cc_start: 0.7430 (t0) cc_final: 0.7149 (t0) REVERT: I 91 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8939 (p) outliers start: 76 outliers final: 53 residues processed: 305 average time/residue: 0.1490 time to fit residues: 70.0642 Evaluate side-chains 305 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 244 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 89 CYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 0.0970 chunk 101 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 169 optimal weight: 0.0010 chunk 50 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN G 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.119653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.083399 restraints weight = 32813.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.086787 restraints weight = 16989.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.088946 restraints weight = 11617.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.090242 restraints weight = 9261.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.091067 restraints weight = 8093.934| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20211 Z= 0.117 Angle : 0.568 13.181 27459 Z= 0.292 Chirality : 0.044 0.424 3105 Planarity : 0.003 0.046 3456 Dihedral : 4.502 36.403 3327 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.37 % Allowed : 16.27 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.17), residues: 2406 helix: 1.11 (0.30), residues: 294 sheet: -0.61 (0.19), residues: 792 loop : -1.89 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 354 TYR 0.018 0.001 TYR A 408 PHE 0.011 0.001 PHE A 266 TRP 0.011 0.001 TRP C 233 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00268 (20163) covalent geometry : angle 0.55516 (27333) SS BOND : bond 0.00259 ( 18) SS BOND : angle 0.70841 ( 36) hydrogen bonds : bond 0.04412 ( 614) hydrogen bonds : angle 4.33272 ( 2643) link_NAG-ASN : bond 0.00381 ( 30) link_NAG-ASN : angle 2.15899 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 260 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8594 (ttm) REVERT: A 133 ILE cc_start: 0.8735 (pt) cc_final: 0.8466 (pt) REVERT: A 155 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6305 (m-80) REVERT: A 239 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8467 (p) REVERT: A 244 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: A 362 ASP cc_start: 0.7872 (t0) cc_final: 0.7527 (t0) REVERT: A 420 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8577 (p) REVERT: A 589 TYR cc_start: 0.3980 (OUTLIER) cc_final: 0.2954 (t80) REVERT: A 636 MET cc_start: 0.8623 (mmm) cc_final: 0.8124 (mmm) REVERT: D 23 LYS cc_start: 0.8052 (tmtt) cc_final: 0.7519 (tmtt) REVERT: D 73 ASP cc_start: 0.7271 (t0) cc_final: 0.6859 (t0) REVERT: D 99 ASP cc_start: 0.9145 (t70) cc_final: 0.8803 (t0) REVERT: D 126 MET cc_start: 0.7942 (tpt) cc_final: 0.7474 (tpt) REVERT: E 5 THR cc_start: 0.8936 (m) cc_final: 0.8648 (p) REVERT: E 16 GLN cc_start: 0.8511 (mt0) cc_final: 0.8119 (mt0) REVERT: E 51 ASP cc_start: 0.6533 (m-30) cc_final: 0.6308 (m-30) REVERT: B 338 ASP cc_start: 0.7913 (t0) cc_final: 0.7662 (t0) REVERT: B 389 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8794 (pp) REVERT: B 408 TYR cc_start: 0.8510 (m-80) cc_final: 0.6989 (m-80) REVERT: B 682 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7504 (mt-10) REVERT: F 73 ASP cc_start: 0.7522 (t0) cc_final: 0.7056 (t0) REVERT: G 16 GLN cc_start: 0.8697 (mt0) cc_final: 0.8212 (mt0) REVERT: G 32 ASN cc_start: 0.8643 (m110) cc_final: 0.8365 (m-40) REVERT: G 84 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7945 (mp0) REVERT: G 98 VAL cc_start: 0.9229 (p) cc_final: 0.9023 (p) REVERT: C 362 ASP cc_start: 0.7706 (t0) cc_final: 0.7461 (t70) REVERT: C 389 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8961 (pp) REVERT: C 560 LYS cc_start: 0.7172 (mttt) cc_final: 0.6602 (tptt) REVERT: C 562 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8251 (tt) REVERT: C 589 TYR cc_start: 0.4938 (OUTLIER) cc_final: 0.4222 (t80) REVERT: H 23 LYS cc_start: 0.8273 (tptt) cc_final: 0.7764 (tmtt) REVERT: H 31 ASP cc_start: 0.8488 (m-30) cc_final: 0.8111 (m-30) REVERT: H 73 ASP cc_start: 0.7261 (t0) cc_final: 0.6948 (t0) REVERT: I 91 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8956 (p) outliers start: 72 outliers final: 52 residues processed: 310 average time/residue: 0.1411 time to fit residues: 68.0452 Evaluate side-chains 308 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 245 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 89 CYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 184 optimal weight: 0.0770 chunk 135 optimal weight: 0.7980 chunk 195 optimal weight: 0.5980 chunk 234 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS D 6 GLN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** 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 = 0.3533 r_free = 0.3533 target = 0.120079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.084112 restraints weight = 32431.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.087521 restraints weight = 16643.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.089685 restraints weight = 11281.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.090946 restraints weight = 8943.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.091799 restraints weight = 7846.121| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20211 Z= 0.107 Angle : 0.580 14.107 27459 Z= 0.294 Chirality : 0.045 0.486 3105 Planarity : 0.003 0.045 3456 Dihedral : 4.394 35.693 3327 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.41 % Allowed : 17.20 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.17), residues: 2406 helix: 1.29 (0.30), residues: 294 sheet: -0.50 (0.19), residues: 762 loop : -1.82 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 354 TYR 0.018 0.001 TYR A 408 PHE 0.011 0.001 PHE A 266 TRP 0.011 0.001 TRP C 233 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00239 (20163) covalent geometry : angle 0.55765 (27333) SS BOND : bond 0.00251 ( 18) SS BOND : angle 0.67765 ( 36) hydrogen bonds : bond 0.04270 ( 614) hydrogen bonds : angle 4.24055 ( 2643) link_NAG-ASN : bond 0.00504 ( 30) link_NAG-ASN : angle 2.81552 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 254 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 126 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8596 (ttm) REVERT: A 133 ILE cc_start: 0.8725 (pt) cc_final: 0.8452 (pt) REVERT: A 155 TYR cc_start: 0.7135 (OUTLIER) cc_final: 0.6255 (m-80) REVERT: A 239 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8445 (p) REVERT: A 244 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7354 (tt0) REVERT: A 362 ASP cc_start: 0.7808 (t0) cc_final: 0.7308 (t0) REVERT: A 420 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8641 (p) REVERT: A 565 MET cc_start: 0.7147 (mmt) cc_final: 0.6058 (mmt) REVERT: A 589 TYR cc_start: 0.3980 (OUTLIER) cc_final: 0.2962 (t80) REVERT: A 612 GLN cc_start: 0.7835 (tp-100) cc_final: 0.7322 (tp-100) REVERT: A 636 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8131 (mmm) REVERT: D 23 LYS cc_start: 0.8025 (tmtt) cc_final: 0.7597 (tmtt) REVERT: D 73 ASP cc_start: 0.7282 (t0) cc_final: 0.6856 (t0) REVERT: D 99 ASP cc_start: 0.9152 (t70) cc_final: 0.8839 (t0) REVERT: D 126 MET cc_start: 0.7794 (tpt) cc_final: 0.7355 (tpt) REVERT: E 5 THR cc_start: 0.8942 (m) cc_final: 0.8662 (p) REVERT: E 16 GLN cc_start: 0.8470 (mt0) cc_final: 0.8120 (mt0) REVERT: E 51 ASP cc_start: 0.6312 (m-30) cc_final: 0.6038 (m-30) REVERT: B 338 ASP cc_start: 0.7864 (t0) cc_final: 0.7510 (t0) REVERT: B 389 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8791 (pp) REVERT: B 408 TYR cc_start: 0.8227 (m-80) cc_final: 0.6868 (m-80) REVERT: F 73 ASP cc_start: 0.7549 (t0) cc_final: 0.7111 (t0) REVERT: G 32 ASN cc_start: 0.8617 (m110) cc_final: 0.8358 (m-40) REVERT: G 55 ARG cc_start: 0.8614 (ptp-170) cc_final: 0.8344 (ptp-170) REVERT: G 84 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7927 (mp0) REVERT: C 133 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8821 (pt) REVERT: C 389 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8933 (pp) REVERT: C 560 LYS cc_start: 0.7241 (mttt) cc_final: 0.6539 (tptt) REVERT: C 562 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8254 (tt) REVERT: C 589 TYR cc_start: 0.4934 (OUTLIER) cc_final: 0.4238 (t80) REVERT: H 23 LYS cc_start: 0.8235 (tptt) cc_final: 0.7712 (tmtt) REVERT: H 73 ASP cc_start: 0.7178 (t0) cc_final: 0.6827 (t0) REVERT: I 91 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8882 (p) outliers start: 73 outliers final: 50 residues processed: 302 average time/residue: 0.1508 time to fit residues: 70.0785 Evaluate side-chains 314 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 251 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 89 CYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 56 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.082696 restraints weight = 32622.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.086026 restraints weight = 17035.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.088152 restraints weight = 11716.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.089455 restraints weight = 9382.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.090255 restraints weight = 8208.575| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20211 Z= 0.137 Angle : 0.600 12.365 27459 Z= 0.305 Chirality : 0.046 0.682 3105 Planarity : 0.003 0.046 3456 Dihedral : 4.492 36.672 3327 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.32 % Allowed : 17.44 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.17), residues: 2406 helix: 1.30 (0.30), residues: 294 sheet: -0.55 (0.19), residues: 792 loop : -1.87 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 354 TYR 0.020 0.001 TYR A 408 PHE 0.012 0.001 PHE A 266 TRP 0.013 0.001 TRP C 233 HIS 0.005 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00322 (20163) covalent geometry : angle 0.58357 (27333) SS BOND : bond 0.00244 ( 18) SS BOND : angle 0.73806 ( 36) hydrogen bonds : bond 0.04620 ( 614) hydrogen bonds : angle 4.35122 ( 2643) link_NAG-ASN : bond 0.00571 ( 30) link_NAG-ASN : angle 2.47113 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 252 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.6282 (m-80) REVERT: A 239 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8491 (p) REVERT: A 244 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: A 362 ASP cc_start: 0.7809 (t0) cc_final: 0.7457 (t0) REVERT: A 420 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 560 LYS cc_start: 0.7619 (mttt) cc_final: 0.6709 (tptt) REVERT: A 565 MET cc_start: 0.7089 (mmt) cc_final: 0.5845 (mmt) REVERT: A 612 GLN cc_start: 0.7783 (tp-100) cc_final: 0.7291 (tp-100) REVERT: A 636 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8125 (mmm) REVERT: D 23 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7576 (tmtt) REVERT: D 73 ASP cc_start: 0.7361 (t0) cc_final: 0.6950 (t0) REVERT: D 99 ASP cc_start: 0.9172 (t70) cc_final: 0.8807 (t0) REVERT: E 5 THR cc_start: 0.8950 (m) cc_final: 0.8673 (p) REVERT: E 16 GLN cc_start: 0.8544 (mt0) cc_final: 0.8105 (mt0) REVERT: E 51 ASP cc_start: 0.6380 (m-30) cc_final: 0.6118 (m-30) REVERT: B 338 ASP cc_start: 0.7921 (t0) cc_final: 0.7611 (t0) REVERT: B 389 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8819 (pp) REVERT: B 408 TYR cc_start: 0.8553 (m-80) cc_final: 0.7013 (m-80) REVERT: F 73 ASP cc_start: 0.7474 (t0) cc_final: 0.7072 (t0) REVERT: G 32 ASN cc_start: 0.8675 (m110) cc_final: 0.8408 (m-40) REVERT: G 84 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8063 (mt-10) REVERT: C 389 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8968 (pp) REVERT: C 560 LYS cc_start: 0.7213 (mttt) cc_final: 0.6648 (tptt) REVERT: C 562 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8234 (tt) REVERT: C 589 TYR cc_start: 0.4801 (OUTLIER) cc_final: 0.4195 (t80) REVERT: H 10 GLU cc_start: 0.6685 (mm-30) cc_final: 0.6391 (mm-30) REVERT: H 23 LYS cc_start: 0.8216 (tptt) cc_final: 0.7696 (tmtt) REVERT: H 31 ASP cc_start: 0.8499 (m-30) cc_final: 0.8151 (m-30) REVERT: H 73 ASP cc_start: 0.7297 (t0) cc_final: 0.6842 (t0) REVERT: H 81 MET cc_start: 0.7845 (ttm) cc_final: 0.7597 (ttm) outliers start: 71 outliers final: 56 residues processed: 299 average time/residue: 0.1496 time to fit residues: 69.2954 Evaluate side-chains 314 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 249 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 89 CYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 112 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 207 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 209 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 219 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 ASN ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.081564 restraints weight = 32745.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.084888 restraints weight = 17157.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.087007 restraints weight = 11820.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.088257 restraints weight = 9467.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.089052 restraints weight = 8313.842| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20211 Z= 0.161 Angle : 0.612 11.919 27459 Z= 0.314 Chirality : 0.045 0.397 3105 Planarity : 0.004 0.046 3456 Dihedral : 4.681 52.717 3327 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.18 % Allowed : 17.63 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.16), residues: 2406 helix: 1.18 (0.30), residues: 294 sheet: -0.61 (0.19), residues: 780 loop : -1.90 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 354 TYR 0.021 0.001 TYR A 408 PHE 0.014 0.001 PHE B 541 TRP 0.016 0.001 TRP C 233 HIS 0.005 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00383 (20163) covalent geometry : angle 0.60124 (27333) SS BOND : bond 0.00252 ( 18) SS BOND : angle 0.78292 ( 36) hydrogen bonds : bond 0.04845 ( 614) hydrogen bonds : angle 4.45290 ( 2643) link_NAG-ASN : bond 0.00385 ( 30) link_NAG-ASN : angle 2.10270 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 255 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6114 (m-80) REVERT: A 244 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: A 362 ASP cc_start: 0.7859 (t0) cc_final: 0.7496 (t0) REVERT: A 420 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8620 (p) REVERT: A 560 LYS cc_start: 0.7653 (mttt) cc_final: 0.6821 (tptt) REVERT: A 565 MET cc_start: 0.7040 (mmt) cc_final: 0.5829 (mmt) REVERT: A 612 GLN cc_start: 0.7818 (tp-100) cc_final: 0.7366 (tp-100) REVERT: A 636 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8096 (mmm) REVERT: D 19 LYS cc_start: 0.8396 (mmmm) cc_final: 0.8170 (mmmm) REVERT: D 23 LYS cc_start: 0.8015 (tmtt) cc_final: 0.7581 (tmtt) REVERT: D 73 ASP cc_start: 0.7267 (t0) cc_final: 0.6869 (t0) REVERT: D 99 ASP cc_start: 0.9186 (t70) cc_final: 0.8758 (t0) REVERT: D 126 MET cc_start: 0.7981 (tpp) cc_final: 0.7600 (tpt) REVERT: E 5 THR cc_start: 0.8905 (m) cc_final: 0.8622 (p) REVERT: E 51 ASP cc_start: 0.6609 (m-30) cc_final: 0.6320 (m-30) REVERT: B 338 ASP cc_start: 0.7955 (t0) cc_final: 0.7679 (t0) REVERT: B 389 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8829 (pp) REVERT: F 73 ASP cc_start: 0.7426 (t0) cc_final: 0.7056 (t0) REVERT: G 32 ASN cc_start: 0.8701 (m110) cc_final: 0.8429 (m-40) REVERT: C 214 MET cc_start: 0.7344 (ptp) cc_final: 0.7139 (ptp) REVERT: C 295 ASP cc_start: 0.7923 (t0) cc_final: 0.7706 (t0) REVERT: C 389 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9007 (pp) REVERT: C 560 LYS cc_start: 0.7359 (mttt) cc_final: 0.6579 (tptt) REVERT: C 562 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8153 (tt) REVERT: C 589 TYR cc_start: 0.4806 (OUTLIER) cc_final: 0.4210 (t80) REVERT: H 10 GLU cc_start: 0.6650 (mm-30) cc_final: 0.6374 (mm-30) REVERT: H 23 LYS cc_start: 0.8297 (tptt) cc_final: 0.7766 (tmtt) REVERT: H 31 ASP cc_start: 0.8592 (m-30) cc_final: 0.8166 (m-30) REVERT: H 73 ASP cc_start: 0.7107 (t0) cc_final: 0.6658 (t0) outliers start: 68 outliers final: 59 residues processed: 300 average time/residue: 0.1524 time to fit residues: 70.2714 Evaluate side-chains 320 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 253 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 89 CYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 57 optimal weight: 0.2980 chunk 115 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 241 optimal weight: 0.0770 chunk 82 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 193 optimal weight: 0.1980 chunk 161 optimal weight: 0.8980 chunk 76 optimal weight: 0.0770 chunk 182 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 overall best weight: 0.1494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN A 583 ASN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN G 1 GLN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.087411 restraints weight = 32351.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.090908 restraints weight = 16497.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.093119 restraints weight = 11148.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.094476 restraints weight = 8822.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.095253 restraints weight = 7672.573| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 20211 Z= 0.094 Angle : 0.563 11.425 27459 Z= 0.286 Chirality : 0.044 0.381 3105 Planarity : 0.003 0.046 3456 Dihedral : 4.156 37.980 3327 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.57 % Allowed : 18.42 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.17), residues: 2406 helix: 1.72 (0.30), residues: 294 sheet: -0.47 (0.19), residues: 798 loop : -1.77 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 354 TYR 0.017 0.001 TYR A 408 PHE 0.016 0.001 PHE B 541 TRP 0.012 0.001 TRP C 349 HIS 0.003 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00197 (20163) covalent geometry : angle 0.55147 (27333) SS BOND : bond 0.00218 ( 18) SS BOND : angle 0.67173 ( 36) hydrogen bonds : bond 0.03808 ( 614) hydrogen bonds : angle 4.05566 ( 2643) link_NAG-ASN : bond 0.00415 ( 30) link_NAG-ASN : angle 2.00318 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3599.84 seconds wall clock time: 62 minutes 58.62 seconds (3778.62 seconds total)