Starting phenix.real_space_refine on Fri Jun 20 22:31:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kdd_22819/06_2025/7kdd_22819.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kdd_22819/06_2025/7kdd_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_22819/06_2025/7kdd_22819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kdd_22819/06_2025/7kdd_22819.map" model { file = "/net/cci-nas-00/data/ceres_data/7kdd_22819/06_2025/7kdd_22819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kdd_22819/06_2025/7kdd_22819.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.49, per 1000 atoms: 0.58 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: 4.86 Conformation dependent library (CDL) restraints added in 2.6 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: 4.77 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: 9.93 Time building geometry restraints manager: 5.47 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 697 or resid 1001 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 50.450 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.860 ------------------------------------------------------------------------------- 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 : 6.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (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 TRP 0.018 0.001 TRP A 233 HIS 0.008 0.001 HIS B 264 PHE 0.008 0.001 PHE E 100 TYR 0.018 0.001 TYR A 155 ARG 0.004 0.000 ARG C 311 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 30) link_NAG-ASN : angle 2.50279 ( 90) hydrogen bonds : bond 0.22533 ( 614) hydrogen bonds : angle 9.11000 ( 2643) SS BOND : bond 0.00225 ( 18) SS BOND : angle 1.20970 ( 36) covalent geometry : bond 0.00852 (20163) covalent geometry : angle 0.75330 (27333) *********************** 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 : 2.602 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: 0.3254 (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: 0.3930 time to fit residues: 171.2700 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 : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 4.9990 chunk 184 optimal weight: 0.0570 chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 220 optimal weight: 0.0170 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.120107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.084413 restraints weight = 32699.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.087763 restraints weight = 16719.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.089907 restraints weight = 11368.905| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20211 Z= 0.117 Angle : 0.599 16.843 27459 Z= 0.308 Chirality : 0.045 0.487 3105 Planarity : 0.004 0.043 3456 Dihedral : 5.238 39.233 3327 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.48 % Favored : 93.39 % Rotamer: Outliers : 0.61 % Allowed : 9.35 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.17), residues: 2406 helix: 0.57 (0.31), residues: 294 sheet: -0.96 (0.19), residues: 798 loop : -1.99 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 334 HIS 0.005 0.001 HIS C 202 PHE 0.016 0.001 PHE C 633 TYR 0.020 0.001 TYR A 408 ARG 0.003 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 30) link_NAG-ASN : angle 2.49560 ( 90) hydrogen bonds : bond 0.05083 ( 614) hydrogen bonds : angle 5.05968 ( 2643) SS BOND : bond 0.00264 ( 18) SS BOND : angle 0.90702 ( 36) covalent geometry : bond 0.00252 (20163) covalent geometry : angle 0.58216 (27333) *********************** 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 281 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 268 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.7888 (t0) cc_final: 0.7673 (t0) REVERT: A 589 TYR cc_start: 0.4018 (OUTLIER) cc_final: 0.2602 (t80) REVERT: D 6 GLN cc_start: 0.8412 (tt0) cc_final: 0.8201 (tt0) REVERT: D 23 LYS cc_start: 0.7995 (tmtt) cc_final: 0.7489 (tmtt) REVERT: D 73 ASP cc_start: 0.7439 (t0) cc_final: 0.6911 (t0) REVERT: D 76 THR cc_start: 0.8445 (p) cc_final: 0.8088 (p) REVERT: D 126 MET cc_start: 0.7937 (tpt) cc_final: 0.7479 (tpt) REVERT: E 5 THR cc_start: 0.8857 (m) cc_final: 0.8504 (p) REVERT: B 338 ASP cc_start: 0.7878 (t0) cc_final: 0.7508 (t0) REVERT: B 390 ASP cc_start: 0.8604 (t0) cc_final: 0.8381 (m-30) REVERT: F 73 ASP cc_start: 0.7638 (t0) cc_final: 0.7248 (t0) REVERT: G 84 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7582 (mp0) REVERT: C 233 TRP cc_start: 0.7283 (p-90) cc_final: 0.6893 (p-90) REVERT: C 560 LYS cc_start: 0.7525 (mttt) cc_final: 0.6136 (tptt) REVERT: H 73 ASP cc_start: 0.7930 (t70) cc_final: 0.7727 (t0) REVERT: H 123 GLN cc_start: 0.8662 (pm20) cc_final: 0.8313 (pm20) outliers start: 13 outliers final: 7 residues processed: 271 average time/residue: 0.3100 time to fit residues: 130.6607 Evaluate side-chains 245 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 237 time to evaluate : 2.187 ------------------------------------------------------------------------------- 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 8 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 206 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.119257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.083162 restraints weight = 32728.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.086478 restraints weight = 17066.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.088583 restraints weight = 11743.858| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20211 Z= 0.139 Angle : 0.602 16.062 27459 Z= 0.306 Chirality : 0.046 0.464 3105 Planarity : 0.004 0.041 3456 Dihedral : 4.946 36.549 3327 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.73 % Favored : 93.14 % Rotamer: Outliers : 1.50 % Allowed : 12.62 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.17), residues: 2406 helix: 0.51 (0.30), residues: 312 sheet: -0.93 (0.18), residues: 792 loop : -1.93 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 233 HIS 0.005 0.001 HIS B 264 PHE 0.011 0.001 PHE A 266 TYR 0.020 0.001 TYR A 408 ARG 0.005 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 30) link_NAG-ASN : angle 3.02369 ( 90) hydrogen bonds : bond 0.04980 ( 614) hydrogen bonds : angle 4.76266 ( 2643) SS BOND : bond 0.00264 ( 18) SS BOND : angle 0.87724 ( 36) covalent geometry : bond 0.00322 (20163) covalent geometry : angle 0.57658 (27333) *********************** 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 286 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.7990 (t0) cc_final: 0.7721 (t0) REVERT: A 589 TYR cc_start: 0.3870 (OUTLIER) cc_final: 0.2732 (t80) REVERT: A 612 GLN cc_start: 0.8214 (tp40) cc_final: 0.7745 (tp-100) REVERT: D 23 LYS cc_start: 0.8015 (tmtt) cc_final: 0.7506 (tmtt) REVERT: D 73 ASP cc_start: 0.7354 (t0) cc_final: 0.6872 (t0) REVERT: D 126 MET cc_start: 0.7856 (tpt) cc_final: 0.7451 (tpt) REVERT: E 5 THR cc_start: 0.8883 (m) cc_final: 0.8538 (p) REVERT: B 338 ASP cc_start: 0.7893 (t0) cc_final: 0.7458 (t0) REVERT: F 19 LYS cc_start: 0.8228 (tptm) cc_final: 0.7833 (tppt) REVERT: F 23 LYS cc_start: 0.7938 (tmtt) cc_final: 0.7654 (tptt) REVERT: F 30 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8768 (mttt) REVERT: F 73 ASP cc_start: 0.7694 (t0) cc_final: 0.7118 (t0) REVERT: G 84 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7975 (mp0) REVERT: G 91 THR cc_start: 0.9124 (t) cc_final: 0.8885 (p) REVERT: C 560 LYS cc_start: 0.7614 (mttt) cc_final: 0.6186 (tptt) REVERT: C 589 TYR cc_start: 0.4308 (OUTLIER) cc_final: 0.3482 (t80) REVERT: H 123 GLN cc_start: 0.8644 (pm20) cc_final: 0.8336 (pm20) outliers start: 32 outliers final: 21 residues processed: 271 average time/residue: 0.3179 time to fit residues: 133.1581 Evaluate side-chains 255 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL 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 107 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 146 VAL 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 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 75 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain H residue 69 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 227 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 205 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 G 16 GLN C 599 ASN I 1 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.083520 restraints weight = 32659.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.086863 restraints weight = 16892.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.088992 restraints weight = 11539.407| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20211 Z= 0.132 Angle : 0.588 15.470 27459 Z= 0.300 Chirality : 0.044 0.450 3105 Planarity : 0.003 0.042 3456 Dihedral : 4.698 36.575 3327 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.48 % Favored : 93.47 % Rotamer: Outliers : 2.66 % Allowed : 13.70 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.17), residues: 2406 helix: 0.91 (0.30), residues: 294 sheet: -0.68 (0.19), residues: 774 loop : -1.88 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 233 HIS 0.005 0.001 HIS B 264 PHE 0.011 0.001 PHE A 266 TYR 0.018 0.001 TYR A 408 ARG 0.005 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 30) link_NAG-ASN : angle 2.83042 ( 90) hydrogen bonds : bond 0.04693 ( 614) hydrogen bonds : angle 4.56230 ( 2643) SS BOND : bond 0.00263 ( 18) SS BOND : angle 0.79492 ( 36) covalent geometry : bond 0.00306 (20163) covalent geometry : angle 0.56587 (27333) *********************** 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 309 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 252 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.8017 (t0) cc_final: 0.7699 (t0) REVERT: A 420 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8660 (p) REVERT: A 589 TYR cc_start: 0.3871 (OUTLIER) cc_final: 0.2754 (t80) REVERT: D 23 LYS cc_start: 0.8013 (tmtt) cc_final: 0.7524 (tmtt) REVERT: D 73 ASP cc_start: 0.7285 (t0) cc_final: 0.6844 (t0) REVERT: D 126 MET cc_start: 0.7817 (tpt) cc_final: 0.7402 (tpt) REVERT: E 5 THR cc_start: 0.8931 (m) cc_final: 0.8611 (p) REVERT: B 338 ASP cc_start: 0.7895 (t0) cc_final: 0.7430 (t0) REVERT: B 389 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8794 (pp) REVERT: B 408 TYR cc_start: 0.8265 (m-80) cc_final: 0.6772 (m-80) REVERT: F 19 LYS cc_start: 0.8255 (tptm) cc_final: 0.7856 (tppt) REVERT: F 30 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8772 (mttt) REVERT: F 73 ASP cc_start: 0.7588 (t0) cc_final: 0.7136 (t0) REVERT: G 32 ASN cc_start: 0.8708 (m110) cc_final: 0.8352 (m-40) REVERT: G 84 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7968 (mp0) REVERT: G 91 THR cc_start: 0.9090 (t) cc_final: 0.8813 (p) REVERT: C 560 LYS cc_start: 0.7587 (mttt) cc_final: 0.6236 (tptt) REVERT: C 589 TYR cc_start: 0.4467 (OUTLIER) cc_final: 0.3689 (t80) REVERT: H 73 ASP cc_start: 0.7247 (t0) cc_final: 0.6999 (t0) REVERT: I 91 THR cc_start: 0.9212 (t) cc_final: 0.8890 (p) outliers start: 57 outliers final: 34 residues processed: 292 average time/residue: 0.3046 time to fit residues: 137.6593 Evaluate side-chains 272 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 2.318 ------------------------------------------------------------------------------- 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 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 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 75 VAL 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 214 MET 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 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 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 197 VAL Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 603 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 75 optimal weight: 0.0060 chunk 168 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 225 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN G 16 GLN C 583 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.082567 restraints weight = 32782.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.085903 restraints weight = 16989.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.088028 restraints weight = 11630.494| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 20211 Z= 0.150 Angle : 0.594 14.740 27459 Z= 0.304 Chirality : 0.045 0.445 3105 Planarity : 0.004 0.043 3456 Dihedral : 4.634 36.610 3327 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 3.18 % Allowed : 13.93 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2406 helix: 0.93 (0.30), residues: 294 sheet: -0.67 (0.19), residues: 747 loop : -1.88 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.006 0.001 HIS B 264 PHE 0.011 0.001 PHE A 266 TYR 0.018 0.001 TYR A 408 ARG 0.005 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 30) link_NAG-ASN : angle 2.49407 ( 90) hydrogen bonds : bond 0.04825 ( 614) hydrogen bonds : angle 4.54436 ( 2643) SS BOND : bond 0.00269 ( 18) SS BOND : angle 0.94048 ( 36) covalent geometry : bond 0.00353 (20163) covalent geometry : angle 0.57655 (27333) *********************** 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 316 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 248 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.7863 (t0) cc_final: 0.7400 (t0) REVERT: A 420 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8658 (p) REVERT: A 589 TYR cc_start: 0.3853 (OUTLIER) cc_final: 0.2752 (t80) REVERT: A 612 GLN cc_start: 0.7978 (tp-100) cc_final: 0.7447 (tp-100) REVERT: A 636 MET cc_start: 0.8584 (mmm) cc_final: 0.8162 (mmm) REVERT: D 23 LYS cc_start: 0.8004 (tmtt) cc_final: 0.7502 (tmtt) REVERT: D 73 ASP cc_start: 0.7342 (t0) cc_final: 0.6922 (t0) REVERT: D 126 MET cc_start: 0.7932 (tpt) cc_final: 0.7468 (tpt) REVERT: E 5 THR cc_start: 0.8931 (m) cc_final: 0.8619 (p) REVERT: E 51 ASP cc_start: 0.6460 (m-30) cc_final: 0.6188 (m-30) REVERT: B 338 ASP cc_start: 0.7934 (t0) cc_final: 0.7518 (t0) REVERT: B 389 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8800 (pp) REVERT: B 408 TYR cc_start: 0.8432 (m-80) cc_final: 0.7099 (m-80) REVERT: F 23 LYS cc_start: 0.8015 (tmtt) cc_final: 0.7786 (tptt) REVERT: F 30 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8768 (mttt) REVERT: F 73 ASP cc_start: 0.7661 (t0) cc_final: 0.7188 (t0) REVERT: G 5 THR cc_start: 0.8922 (m) cc_final: 0.8469 (p) REVERT: G 16 GLN cc_start: 0.8754 (mt0) cc_final: 0.7908 (mt0) REVERT: G 17 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8253 (ttp) REVERT: G 32 ASN cc_start: 0.8722 (m110) cc_final: 0.8366 (m-40) REVERT: G 91 THR cc_start: 0.9109 (t) cc_final: 0.8833 (p) REVERT: C 389 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8955 (pp) REVERT: C 560 LYS cc_start: 0.7496 (mttt) cc_final: 0.6315 (tptt) REVERT: C 589 TYR cc_start: 0.4464 (OUTLIER) cc_final: 0.3704 (t80) REVERT: H 23 LYS cc_start: 0.8252 (tptt) cc_final: 0.7689 (tmtt) REVERT: H 31 ASP cc_start: 0.8512 (m-30) cc_final: 0.8143 (m-30) REVERT: H 73 ASP cc_start: 0.7229 (t0) cc_final: 0.6888 (t0) outliers start: 68 outliers final: 44 residues processed: 297 average time/residue: 0.2931 time to fit residues: 135.4452 Evaluate side-chains 283 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 2.065 ------------------------------------------------------------------------------- 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 196 THR Chi-restraints excluded: chain A residue 343 THR 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 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 75 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 146 VAL 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 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 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 C residue 101 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 389 LEU 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 81 MET Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 74 LEU 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 159 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 226 optimal weight: 0.0000 chunk 11 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 612 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.082063 restraints weight = 32851.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.085401 restraints weight = 17160.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.087521 restraints weight = 11780.611| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20211 Z= 0.158 Angle : 0.600 13.946 27459 Z= 0.308 Chirality : 0.045 0.436 3105 Planarity : 0.004 0.045 3456 Dihedral : 4.613 36.890 3327 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.94 % Favored : 93.02 % Rotamer: Outliers : 3.65 % Allowed : 14.73 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.16), residues: 2406 helix: 0.99 (0.30), residues: 294 sheet: -0.67 (0.19), residues: 762 loop : -1.88 (0.15), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 334 HIS 0.006 0.001 HIS B 264 PHE 0.012 0.001 PHE A 266 TYR 0.018 0.001 TYR A 408 ARG 0.006 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 30) link_NAG-ASN : angle 2.35399 ( 90) hydrogen bonds : bond 0.04862 ( 614) hydrogen bonds : angle 4.51370 ( 2643) SS BOND : bond 0.00296 ( 18) SS BOND : angle 0.77569 ( 36) covalent geometry : bond 0.00374 (20163) covalent geometry : angle 0.58578 (27333) *********************** 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 322 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 244 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6254 (m-80) REVERT: A 362 ASP cc_start: 0.7877 (t0) cc_final: 0.7402 (t0) REVERT: A 420 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8643 (p) REVERT: A 565 MET cc_start: 0.7108 (mmt) cc_final: 0.6162 (mmt) REVERT: A 589 TYR cc_start: 0.3825 (OUTLIER) cc_final: 0.2723 (t80) REVERT: A 636 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8128 (mmm) REVERT: D 19 LYS cc_start: 0.8454 (mmmm) cc_final: 0.8104 (mmmm) REVERT: D 23 LYS cc_start: 0.7967 (tmtt) cc_final: 0.7560 (tmtt) REVERT: D 73 ASP cc_start: 0.7314 (t0) cc_final: 0.6862 (t0) REVERT: D 126 MET cc_start: 0.7902 (tpt) cc_final: 0.7459 (tpt) REVERT: E 5 THR cc_start: 0.8945 (m) cc_final: 0.8645 (p) REVERT: E 51 ASP cc_start: 0.6594 (m-30) cc_final: 0.6325 (m-30) REVERT: B 94 CYS cc_start: 0.7978 (m) cc_final: 0.7689 (p) REVERT: B 338 ASP cc_start: 0.7903 (t0) cc_final: 0.7679 (t0) REVERT: B 389 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8815 (pp) REVERT: F 73 ASP cc_start: 0.7674 (t0) cc_final: 0.7242 (t0) REVERT: G 5 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8487 (p) REVERT: G 32 ASN cc_start: 0.8736 (m110) cc_final: 0.8372 (m-40) REVERT: G 84 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7647 (mp0) REVERT: G 91 THR cc_start: 0.9089 (t) cc_final: 0.8796 (p) REVERT: C 133 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8841 (pt) REVERT: C 211 MET cc_start: 0.8489 (mpp) cc_final: 0.8269 (mpp) REVERT: C 389 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8989 (pp) REVERT: C 560 LYS cc_start: 0.7550 (mttt) cc_final: 0.6417 (tptt) REVERT: C 562 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8339 (tt) REVERT: C 589 TYR cc_start: 0.4498 (OUTLIER) cc_final: 0.3745 (t80) REVERT: C 612 GLN cc_start: 0.7887 (tp-100) cc_final: 0.7682 (tp-100) REVERT: H 23 LYS cc_start: 0.8266 (tptt) cc_final: 0.7728 (tmtt) REVERT: H 73 ASP cc_start: 0.7328 (t0) cc_final: 0.7009 (t0) outliers start: 78 outliers final: 53 residues processed: 296 average time/residue: 0.3080 time to fit residues: 141.2639 Evaluate side-chains 301 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 238 time to evaluate : 2.263 ------------------------------------------------------------------------------- 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 343 THR 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 A residue 682 GLU Chi-restraints excluded: chain D residue 51 ILE 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 75 VAL 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 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 612 GLN 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 5 THR 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 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 197 VAL 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 603 LEU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 81 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 114 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 233 optimal weight: 0.4980 chunk 240 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 612 GLN F 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.119988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.083712 restraints weight = 32505.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.087100 restraints weight = 16870.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.089253 restraints weight = 11546.982| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2059 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= 0.115 Angle : 0.571 13.329 27459 Z= 0.291 Chirality : 0.044 0.420 3105 Planarity : 0.003 0.045 3456 Dihedral : 4.390 36.492 3327 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.09 % Allowed : 15.15 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.17), residues: 2406 helix: 1.22 (0.30), residues: 294 sheet: -0.56 (0.19), residues: 762 loop : -1.83 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 233 HIS 0.004 0.001 HIS B 264 PHE 0.011 0.001 PHE A 266 TYR 0.016 0.001 TYR A 408 ARG 0.006 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 30) link_NAG-ASN : angle 2.23495 ( 90) hydrogen bonds : bond 0.04436 ( 614) hydrogen bonds : angle 4.32118 ( 2643) SS BOND : bond 0.00248 ( 18) SS BOND : angle 0.69647 ( 36) covalent geometry : bond 0.00262 (20163) covalent geometry : angle 0.55674 (27333) *********************** 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 320 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 254 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.7144 (OUTLIER) cc_final: 0.6198 (m-80) REVERT: A 362 ASP cc_start: 0.7892 (t0) cc_final: 0.7343 (t0) REVERT: A 420 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8590 (p) REVERT: A 524 ASN cc_start: 0.8826 (t0) cc_final: 0.8616 (t0) REVERT: A 565 MET cc_start: 0.7128 (mmt) cc_final: 0.5943 (mmt) REVERT: A 589 TYR cc_start: 0.3937 (OUTLIER) cc_final: 0.2929 (t80) REVERT: A 612 GLN cc_start: 0.7815 (tp-100) cc_final: 0.7312 (tp-100) REVERT: A 636 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8139 (mmm) REVERT: D 19 LYS cc_start: 0.8405 (mmmm) cc_final: 0.8068 (mmmm) REVERT: D 23 LYS cc_start: 0.7947 (tmtt) cc_final: 0.7522 (tmtt) REVERT: D 73 ASP cc_start: 0.7187 (t0) cc_final: 0.6744 (t0) REVERT: D 126 MET cc_start: 0.7864 (tpt) cc_final: 0.7469 (tpt) REVERT: E 5 THR cc_start: 0.8936 (m) cc_final: 0.8634 (p) REVERT: E 16 GLN cc_start: 0.8563 (mt0) cc_final: 0.8138 (mt0) REVERT: E 51 ASP cc_start: 0.6411 (m-30) cc_final: 0.6173 (m-30) REVERT: B 94 CYS cc_start: 0.7905 (m) cc_final: 0.7666 (p) REVERT: B 338 ASP cc_start: 0.7873 (t0) cc_final: 0.7642 (t0) REVERT: B 389 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8745 (pp) REVERT: B 408 TYR cc_start: 0.8297 (m-80) cc_final: 0.7185 (m-80) REVERT: B 606 HIS cc_start: 0.7987 (m90) cc_final: 0.7281 (m-70) REVERT: F 73 ASP cc_start: 0.7570 (t0) cc_final: 0.7125 (t0) REVERT: G 5 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8441 (p) REVERT: G 16 GLN cc_start: 0.8800 (mt0) cc_final: 0.7918 (mt0) REVERT: G 17 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8255 (ttp) REVERT: G 32 ASN cc_start: 0.8677 (m110) cc_final: 0.8317 (m-40) REVERT: G 84 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7877 (mp0) REVERT: G 91 THR cc_start: 0.9086 (t) cc_final: 0.8810 (p) REVERT: C 133 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8837 (pt) REVERT: C 389 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8969 (pp) REVERT: C 560 LYS cc_start: 0.7169 (mttt) cc_final: 0.6554 (tptt) REVERT: C 562 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8340 (tt) REVERT: C 589 TYR cc_start: 0.4560 (OUTLIER) cc_final: 0.3800 (t80) REVERT: H 23 LYS cc_start: 0.8226 (tptt) cc_final: 0.7705 (tmtt) REVERT: H 31 ASP cc_start: 0.8493 (m-30) cc_final: 0.8147 (m-30) REVERT: H 73 ASP cc_start: 0.7104 (t0) cc_final: 0.6658 (t0) outliers start: 66 outliers final: 47 residues processed: 298 average time/residue: 0.3173 time to fit residues: 145.3240 Evaluate side-chains 301 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL 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 420 VAL 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 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 75 VAL 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 612 GLN 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 3 VAL 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 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 197 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 10 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 205 optimal weight: 8.9990 chunk 191 optimal weight: 0.0060 chunk 134 optimal weight: 0.8980 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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 380 GLN B 612 GLN G 1 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.117908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.081603 restraints weight = 32800.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.084899 restraints weight = 17033.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.087001 restraints weight = 11677.592| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20211 Z= 0.166 Angle : 0.607 12.783 27459 Z= 0.312 Chirality : 0.045 0.410 3105 Planarity : 0.004 0.046 3456 Dihedral : 4.525 36.540 3327 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.55 % Allowed : 15.90 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.16), residues: 2406 helix: 1.16 (0.30), residues: 294 sheet: -0.54 (0.19), residues: 756 loop : -1.85 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 334 HIS 0.006 0.001 HIS B 264 PHE 0.012 0.001 PHE A 266 TYR 0.019 0.001 TYR A 408 ARG 0.006 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 30) link_NAG-ASN : angle 2.18584 ( 90) hydrogen bonds : bond 0.04892 ( 614) hydrogen bonds : angle 4.47189 ( 2643) SS BOND : bond 0.00263 ( 18) SS BOND : angle 0.77273 ( 36) covalent geometry : bond 0.00397 (20163) covalent geometry : angle 0.59474 (27333) *********************** 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 316 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 240 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: A 239 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8447 (p) REVERT: A 362 ASP cc_start: 0.7944 (t0) cc_final: 0.7369 (t0) REVERT: A 420 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8637 (p) REVERT: A 542 MET cc_start: 0.7711 (mtt) cc_final: 0.7490 (mtp) REVERT: A 565 MET cc_start: 0.7273 (mmt) cc_final: 0.6046 (mmt) REVERT: A 589 TYR cc_start: 0.4104 (OUTLIER) cc_final: 0.3089 (t80) REVERT: A 612 GLN cc_start: 0.7850 (tp-100) cc_final: 0.7357 (tp-100) REVERT: A 636 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8145 (mmm) REVERT: D 23 LYS cc_start: 0.7948 (tmtt) cc_final: 0.7513 (tmtt) REVERT: D 73 ASP cc_start: 0.7304 (t0) cc_final: 0.6826 (t0) REVERT: E 5 THR cc_start: 0.8959 (m) cc_final: 0.8666 (p) REVERT: E 16 GLN cc_start: 0.8600 (mt0) cc_final: 0.8137 (mt0) REVERT: E 51 ASP cc_start: 0.6640 (m-30) cc_final: 0.6366 (m-30) REVERT: B 94 CYS cc_start: 0.7933 (m) cc_final: 0.7695 (p) REVERT: B 338 ASP cc_start: 0.7918 (t0) cc_final: 0.7683 (t0) REVERT: B 389 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8808 (pp) REVERT: B 408 TYR cc_start: 0.8585 (m-80) cc_final: 0.7557 (m-80) REVERT: F 23 LYS cc_start: 0.8005 (tmtt) cc_final: 0.7770 (tptt) REVERT: F 73 ASP cc_start: 0.7536 (t0) cc_final: 0.7128 (t0) REVERT: G 5 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8520 (p) REVERT: G 16 GLN cc_start: 0.8848 (mt0) cc_final: 0.7973 (mt0) REVERT: G 32 ASN cc_start: 0.8742 (m110) cc_final: 0.8358 (m-40) REVERT: G 84 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7878 (mp0) REVERT: G 91 THR cc_start: 0.9079 (t) cc_final: 0.8788 (p) REVERT: C 133 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8816 (pt) REVERT: C 211 MET cc_start: 0.8466 (mpp) cc_final: 0.8246 (mpp) REVERT: C 214 MET cc_start: 0.7351 (ptp) cc_final: 0.7147 (ptp) REVERT: C 389 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8996 (pp) REVERT: C 560 LYS cc_start: 0.7141 (mttt) cc_final: 0.6491 (tptt) REVERT: C 562 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8260 (tt) REVERT: C 589 TYR cc_start: 0.4674 (OUTLIER) cc_final: 0.3896 (t80) REVERT: H 23 LYS cc_start: 0.8283 (tptt) cc_final: 0.7742 (tmtt) REVERT: H 73 ASP cc_start: 0.7282 (t0) cc_final: 0.6839 (t0) REVERT: H 81 MET cc_start: 0.7952 (ttm) cc_final: 0.7745 (ttm) outliers start: 76 outliers final: 56 residues processed: 293 average time/residue: 0.3530 time to fit residues: 162.9911 Evaluate side-chains 304 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 237 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL 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 250 CYS 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 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 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 108 ASN 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 427 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 612 GLN 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 3 VAL Chi-restraints excluded: chain G residue 5 THR 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 G residue 98 VAL 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 197 VAL 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 106 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 204 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 216 optimal weight: 0.4980 chunk 175 optimal weight: 2.9990 chunk 185 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 612 GLN F 62 GLN ** C 478 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 = 0.3522 r_free = 0.3522 target = 0.119248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.083288 restraints weight = 32277.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.086648 restraints weight = 16589.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.088753 restraints weight = 11270.745| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20211 Z= 0.118 Angle : 0.579 12.304 27459 Z= 0.295 Chirality : 0.044 0.396 3105 Planarity : 0.003 0.045 3456 Dihedral : 4.350 36.590 3327 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.41 % Allowed : 16.08 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.17), residues: 2406 helix: 1.38 (0.30), residues: 294 sheet: -0.50 (0.19), residues: 762 loop : -1.80 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 233 HIS 0.004 0.001 HIS B 264 PHE 0.011 0.001 PHE A 266 TYR 0.017 0.001 TYR A 408 ARG 0.006 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 30) link_NAG-ASN : angle 2.11522 ( 90) hydrogen bonds : bond 0.04429 ( 614) hydrogen bonds : angle 4.30132 ( 2643) SS BOND : bond 0.00245 ( 18) SS BOND : angle 0.66854 ( 36) covalent geometry : bond 0.00270 (20163) covalent geometry : angle 0.56708 (27333) *********************** 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 319 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 246 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.8669 (pt) cc_final: 0.8384 (pt) REVERT: A 155 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.6333 (m-80) REVERT: A 239 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8365 (p) REVERT: A 362 ASP cc_start: 0.7876 (t0) cc_final: 0.7316 (t0) REVERT: A 420 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8629 (p) REVERT: A 524 ASN cc_start: 0.8831 (t0) cc_final: 0.8623 (t0) REVERT: A 560 LYS cc_start: 0.7616 (mttt) cc_final: 0.6732 (tptt) REVERT: A 565 MET cc_start: 0.7257 (mmt) cc_final: 0.6027 (mmt) REVERT: A 612 GLN cc_start: 0.7838 (tp-100) cc_final: 0.7368 (tp-100) REVERT: A 636 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8166 (mmm) REVERT: D 23 LYS cc_start: 0.7931 (tmtt) cc_final: 0.7517 (tmtt) REVERT: D 73 ASP cc_start: 0.7354 (t0) cc_final: 0.6889 (t0) REVERT: D 126 MET cc_start: 0.7935 (tpp) cc_final: 0.7529 (tpt) REVERT: E 5 THR cc_start: 0.8946 (m) cc_final: 0.8648 (p) REVERT: E 16 GLN cc_start: 0.8500 (mt0) cc_final: 0.8095 (mt0) REVERT: E 51 ASP cc_start: 0.6450 (m-30) cc_final: 0.6207 (m-30) REVERT: B 94 CYS cc_start: 0.7923 (m) cc_final: 0.7704 (p) REVERT: B 389 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8746 (pp) REVERT: B 408 TYR cc_start: 0.8294 (m-80) cc_final: 0.7182 (m-80) REVERT: F 23 LYS cc_start: 0.8038 (tmtt) cc_final: 0.7792 (tptt) REVERT: F 73 ASP cc_start: 0.7441 (t0) cc_final: 0.7023 (t0) REVERT: G 5 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8416 (p) REVERT: G 32 ASN cc_start: 0.8689 (m110) cc_final: 0.8331 (m-40) REVERT: G 84 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7802 (mp0) REVERT: G 91 THR cc_start: 0.9031 (t) cc_final: 0.8777 (p) REVERT: C 133 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8841 (pt) REVERT: C 211 MET cc_start: 0.8499 (mpp) cc_final: 0.8243 (mpp) REVERT: C 389 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8954 (pp) REVERT: C 560 LYS cc_start: 0.7271 (mttt) cc_final: 0.6525 (tptt) REVERT: C 562 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8267 (tt) REVERT: C 589 TYR cc_start: 0.4828 (OUTLIER) cc_final: 0.4115 (t80) REVERT: H 10 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6461 (mm-30) REVERT: H 23 LYS cc_start: 0.8254 (tptt) cc_final: 0.7706 (tmtt) REVERT: H 31 ASP cc_start: 0.8508 (m-30) cc_final: 0.8148 (m-30) REVERT: H 73 ASP cc_start: 0.7112 (t0) cc_final: 0.6664 (t0) REVERT: H 81 MET cc_start: 0.7849 (ttm) cc_final: 0.7630 (ttm) outliers start: 73 outliers final: 56 residues processed: 295 average time/residue: 0.4433 time to fit residues: 208.5021 Evaluate side-chains 306 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 240 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL 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 250 CYS 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 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 63 LYS 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 75 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 108 ASN 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 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 3 VAL Chi-restraints excluded: chain G residue 5 THR 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 156 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 197 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 186 optimal weight: 0.6980 chunk 205 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.082702 restraints weight = 32652.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.086033 restraints weight = 17050.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.088175 restraints weight = 11708.680| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20211 Z= 0.137 Angle : 0.590 12.053 27459 Z= 0.302 Chirality : 0.044 0.396 3105 Planarity : 0.003 0.045 3456 Dihedral : 4.349 36.346 3327 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.32 % Allowed : 16.22 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.17), residues: 2406 helix: 1.40 (0.30), residues: 294 sheet: -0.52 (0.19), residues: 786 loop : -1.86 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 233 HIS 0.005 0.001 HIS B 264 PHE 0.012 0.001 PHE A 266 TYR 0.018 0.001 TYR A 408 ARG 0.007 0.000 ARG G 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 30) link_NAG-ASN : angle 2.06769 ( 90) hydrogen bonds : bond 0.04591 ( 614) hydrogen bonds : angle 4.34741 ( 2643) SS BOND : bond 0.00243 ( 18) SS BOND : angle 0.71435 ( 36) covalent geometry : bond 0.00324 (20163) covalent geometry : angle 0.57912 (27333) ********************** 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 315 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 244 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.8764 (pt) cc_final: 0.8487 (pt) REVERT: A 155 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6336 (m-80) REVERT: A 239 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8360 (p) REVERT: A 362 ASP cc_start: 0.7877 (t0) cc_final: 0.7311 (t0) REVERT: A 420 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8631 (p) REVERT: A 524 ASN cc_start: 0.8846 (t0) cc_final: 0.8610 (t0) REVERT: A 560 LYS cc_start: 0.7729 (mttt) cc_final: 0.6935 (tptt) REVERT: A 565 MET cc_start: 0.7250 (mmt) cc_final: 0.6011 (mmt) REVERT: A 612 GLN cc_start: 0.7838 (tp-100) cc_final: 0.7618 (tp-100) REVERT: A 636 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8165 (mmm) REVERT: D 23 LYS cc_start: 0.7933 (tmtt) cc_final: 0.7503 (tmtt) REVERT: D 73 ASP cc_start: 0.7372 (t0) cc_final: 0.6928 (t0) REVERT: D 126 MET cc_start: 0.7899 (tpp) cc_final: 0.7516 (tpt) REVERT: E 5 THR cc_start: 0.8956 (m) cc_final: 0.8664 (p) REVERT: E 16 GLN cc_start: 0.8556 (mt0) cc_final: 0.8075 (mt0) REVERT: E 51 ASP cc_start: 0.6538 (m-30) cc_final: 0.6290 (m-30) REVERT: B 389 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8696 (pp) REVERT: B 408 TYR cc_start: 0.8380 (m-80) cc_final: 0.7239 (m-80) REVERT: F 23 LYS cc_start: 0.8025 (tmtt) cc_final: 0.7771 (tptt) REVERT: F 73 ASP cc_start: 0.7474 (t0) cc_final: 0.7050 (t0) REVERT: G 5 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8442 (p) REVERT: G 16 GLN cc_start: 0.8873 (mt0) cc_final: 0.8238 (mt0) REVERT: G 32 ASN cc_start: 0.8726 (m110) cc_final: 0.8369 (m-40) REVERT: G 84 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7800 (mp0) REVERT: C 133 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8849 (pt) REVERT: C 211 MET cc_start: 0.8513 (mpp) cc_final: 0.8254 (mpp) REVERT: C 389 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8970 (pp) REVERT: C 560 LYS cc_start: 0.7323 (mttt) cc_final: 0.6575 (tptt) REVERT: C 562 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8245 (tt) REVERT: C 589 TYR cc_start: 0.4921 (OUTLIER) cc_final: 0.4226 (t80) REVERT: H 10 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6455 (mm-30) REVERT: H 23 LYS cc_start: 0.8282 (tptt) cc_final: 0.7718 (tmtt) REVERT: H 31 ASP cc_start: 0.8557 (m-30) cc_final: 0.8172 (m-30) REVERT: H 73 ASP cc_start: 0.7141 (t0) cc_final: 0.6727 (t0) outliers start: 71 outliers final: 58 residues processed: 290 average time/residue: 0.4804 time to fit residues: 220.1122 Evaluate side-chains 307 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 239 time to evaluate : 5.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL 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 250 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 420 VAL 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 63 LYS 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 75 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 108 ASN 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 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 3 VAL Chi-restraints excluded: chain G residue 5 THR 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 156 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 197 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 231 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 220 optimal weight: 0.0570 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 0.0030 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 overall best weight: 0.6112 ------------------------------------------------------------------------------- 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** F 62 GLN ** 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 = 0.3541 r_free = 0.3541 target = 0.120623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.084306 restraints weight = 32799.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.087708 restraints weight = 16958.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.089865 restraints weight = 11574.784| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20211 Z= 0.111 Angle : 0.568 11.723 27459 Z= 0.289 Chirality : 0.043 0.387 3105 Planarity : 0.003 0.045 3456 Dihedral : 4.164 35.779 3327 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.99 % Allowed : 16.74 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2406 helix: 1.64 (0.30), residues: 294 sheet: -0.51 (0.19), residues: 792 loop : -1.79 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 233 HIS 0.004 0.001 HIS B 264 PHE 0.011 0.001 PHE C 541 TYR 0.016 0.001 TYR A 408 ARG 0.006 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 30) link_NAG-ASN : angle 2.00299 ( 90) hydrogen bonds : bond 0.04236 ( 614) hydrogen bonds : angle 4.20446 ( 2643) SS BOND : bond 0.00234 ( 18) SS BOND : angle 0.66709 ( 36) covalent geometry : bond 0.00254 (20163) covalent geometry : angle 0.55688 (27333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7267.63 seconds wall clock time: 130 minutes 1.04 seconds (7801.04 seconds total)