Starting phenix.real_space_refine on Mon Feb 19 15:25:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdd_22819/02_2024/7kdd_22819.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdd_22819/02_2024/7kdd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdd_22819/02_2024/7kdd_22819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdd_22819/02_2024/7kdd_22819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdd_22819/02_2024/7kdd_22819.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdd_22819/02_2024/7kdd_22819.pdb" } 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 Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 338": "OD1" <-> "OD2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B GLU 474": "OE1" <-> "OE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B ASP 679": "OD1" <-> "OD2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F ASP 90": "OD1" <-> "OD2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 295": "OD1" <-> "OD2" Residue "C PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 338": "OD1" <-> "OD2" Residue "C TYR 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 665": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 10.99, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 7.72 Conformation dependent library (CDL) restraints added in 4.4 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: 3.50 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: 10.78 Time building geometry restraints manager: 8.16 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: 99.54 - 106.43: 425 106.43 - 113.32: 11047 113.32 - 120.22: 6753 120.22 - 127.11: 8914 127.11 - 134.00: 194 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 2.440 nonbonded pdb=" OD2 ASP H 73 " pdb=" OG1 THR H 76 " model vdw 2.120 2.440 nonbonded pdb=" OH TYR H 33 " pdb=" O LEU H 112 " model vdw 2.204 2.440 nonbonded pdb=" OH TYR A 667 " pdb=" O ARG C 131 " model vdw 2.205 2.440 nonbonded pdb=" NE2 GLN H 6 " pdb=" O TYR H 94 " model vdw 2.212 2.520 ... (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 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 6.300 Check model and map are aligned: 0.330 Set scattering table: 0.320 Process input model: 58.980 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.170 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.000 ------------------------------------------------------------------------------- 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 20163 Z= 0.546 Angle : 0.753 8.829 27333 Z= 0.365 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 2.398 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: 0.3077 time to fit residues: 130.9489 Evaluate side-chains 234 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 2.363 ------------------------------------------------------------------------------- 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: 5.9990 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 190 optimal weight: 0.0870 chunk 73 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 C 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20163 Z= 0.225 Angle : 0.585 6.853 27333 Z= 0.306 Chirality : 0.045 0.495 3105 Planarity : 0.004 0.042 3456 Dihedral : 5.655 55.167 3327 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.36 % Favored : 92.44 % Rotamer: Outliers : 0.89 % Allowed : 10.00 % Favored : 89.11 % 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: -2.04 (0.17), residues: 2406 helix: 0.47 (0.31), residues: 294 sheet: -1.01 (0.18), residues: 804 loop : -2.06 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 334 HIS 0.007 0.001 HIS B 264 PHE 0.016 0.001 PHE C 633 TYR 0.021 0.001 TYR A 408 ARG 0.003 0.000 ARG I 62 *********************** 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 274 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 255 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.7925 (t0) cc_final: 0.7688 (t0) REVERT: A 589 TYR cc_start: 0.4103 (OUTLIER) cc_final: 0.2648 (t80) REVERT: A 612 GLN cc_start: 0.8170 (tp40) cc_final: 0.7760 (tp-100) REVERT: D 23 LYS cc_start: 0.8083 (tmtt) cc_final: 0.7606 (tmtt) REVERT: D 73 ASP cc_start: 0.7567 (t0) cc_final: 0.7159 (t0) REVERT: D 76 THR cc_start: 0.8537 (p) cc_final: 0.8180 (p) REVERT: D 126 MET cc_start: 0.7980 (tpt) cc_final: 0.7577 (tpt) REVERT: E 5 THR cc_start: 0.8758 (m) cc_final: 0.8466 (p) REVERT: B 338 ASP cc_start: 0.7896 (t0) cc_final: 0.7545 (t0) REVERT: F 73 ASP cc_start: 0.7605 (t0) cc_final: 0.7251 (t0) REVERT: G 84 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7630 (mp0) REVERT: C 233 TRP cc_start: 0.7263 (p-90) cc_final: 0.7009 (p-90) REVERT: H 54 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8600 (tm-30) REVERT: H 73 ASP cc_start: 0.7422 (t70) cc_final: 0.7063 (t0) REVERT: H 81 MET cc_start: 0.8224 (ptm) cc_final: 0.7892 (ptm) REVERT: H 123 GLN cc_start: 0.8606 (pm20) cc_final: 0.8356 (pm20) REVERT: I 32 ASN cc_start: 0.8540 (m-40) cc_final: 0.8321 (m-40) outliers start: 19 outliers final: 13 residues processed: 262 average time/residue: 0.3409 time to fit residues: 138.6101 Evaluate side-chains 249 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 235 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 221 optimal weight: 4.9990 chunk 238 optimal weight: 0.8980 chunk 196 optimal weight: 0.4980 chunk 219 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20163 Z= 0.213 Angle : 0.561 6.871 27333 Z= 0.293 Chirality : 0.045 0.467 3105 Planarity : 0.003 0.042 3456 Dihedral : 5.266 45.424 3327 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.19 % Favored : 92.60 % Rotamer: Outliers : 2.01 % Allowed : 13.28 % Favored : 84.71 % 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: -1.97 (0.16), residues: 2406 helix: 0.42 (0.30), residues: 312 sheet: -0.94 (0.19), residues: 774 loop : -2.01 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.005 0.000 ARG C 354 *********************** 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 281 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 238 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8801 (ttm) cc_final: 0.8561 (ttm) REVERT: A 165 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8068 (p0) REVERT: A 362 ASP cc_start: 0.7951 (t0) cc_final: 0.7678 (t0) REVERT: A 589 TYR cc_start: 0.3972 (OUTLIER) cc_final: 0.2788 (t80) REVERT: A 612 GLN cc_start: 0.8166 (tp40) cc_final: 0.7747 (tp-100) REVERT: D 23 LYS cc_start: 0.8108 (tmtt) cc_final: 0.7609 (tmtt) REVERT: D 73 ASP cc_start: 0.7382 (t0) cc_final: 0.6926 (t0) REVERT: D 76 THR cc_start: 0.8477 (p) cc_final: 0.8090 (p) REVERT: D 126 MET cc_start: 0.7886 (tpt) cc_final: 0.7573 (tpt) REVERT: E 5 THR cc_start: 0.8735 (m) cc_final: 0.8426 (p) REVERT: B 338 ASP cc_start: 0.7898 (t0) cc_final: 0.7527 (t0) REVERT: F 19 LYS cc_start: 0.8132 (tptm) cc_final: 0.7813 (tppt) REVERT: F 73 ASP cc_start: 0.7546 (t0) cc_final: 0.7233 (t0) REVERT: F 87 ARG cc_start: 0.6645 (ttm110) cc_final: 0.6215 (ttm110) REVERT: C 589 TYR cc_start: 0.4530 (OUTLIER) cc_final: 0.3723 (t80) REVERT: H 123 GLN cc_start: 0.8579 (pm20) cc_final: 0.8342 (pm20) outliers start: 43 outliers final: 30 residues processed: 265 average time/residue: 0.3144 time to fit residues: 128.9437 Evaluate side-chains 261 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 228 time to evaluate : 2.159 ------------------------------------------------------------------------------- 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 165 ASN Chi-restraints excluded: chain A residue 176 ILE 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 70 THR 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 165 ASN 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 654 ASP 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 G residue 98 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 16 GLN G 16 GLN C 583 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20163 Z= 0.347 Angle : 0.615 7.219 27333 Z= 0.323 Chirality : 0.047 0.467 3105 Planarity : 0.004 0.042 3456 Dihedral : 5.360 42.551 3327 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.69 % Favored : 91.11 % Rotamer: Outliers : 3.69 % Allowed : 14.54 % Favored : 81.77 % 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: -2.14 (0.16), residues: 2406 helix: 0.34 (0.29), residues: 312 sheet: -1.06 (0.18), residues: 822 loop : -2.16 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 334 HIS 0.008 0.001 HIS B 264 PHE 0.015 0.001 PHE B 309 TYR 0.023 0.001 TYR A 408 ARG 0.005 0.000 ARG C 354 *********************** 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 318 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 239 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8106 (p0) REVERT: A 362 ASP cc_start: 0.8034 (t0) cc_final: 0.7702 (t0) REVERT: A 420 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8711 (p) REVERT: A 589 TYR cc_start: 0.4031 (OUTLIER) cc_final: 0.2851 (t80) REVERT: A 612 GLN cc_start: 0.8073 (tp40) cc_final: 0.7682 (tp-100) REVERT: D 19 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8169 (mmmm) REVERT: D 23 LYS cc_start: 0.8094 (tmtt) cc_final: 0.7671 (tmtt) REVERT: D 73 ASP cc_start: 0.7627 (t0) cc_final: 0.7195 (t0) REVERT: D 126 MET cc_start: 0.7913 (tpt) cc_final: 0.7601 (tpt) REVERT: E 5 THR cc_start: 0.8743 (m) cc_final: 0.8450 (p) REVERT: B 210 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8579 (m) REVERT: B 338 ASP cc_start: 0.7941 (t0) cc_final: 0.7536 (t0) REVERT: B 389 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8903 (pp) REVERT: F 23 LYS cc_start: 0.8073 (tmtt) cc_final: 0.7864 (tptt) REVERT: F 73 ASP cc_start: 0.7881 (t0) cc_final: 0.7534 (t0) REVERT: C 589 TYR cc_start: 0.4604 (OUTLIER) cc_final: 0.3860 (t80) REVERT: H 73 ASP cc_start: 0.7230 (t0) cc_final: 0.6998 (t0) REVERT: H 123 GLN cc_start: 0.8619 (pm20) cc_final: 0.8351 (pm20) REVERT: I 32 ASN cc_start: 0.8670 (m-40) cc_final: 0.8464 (m-40) outliers start: 79 outliers final: 49 residues processed: 297 average time/residue: 0.3151 time to fit residues: 146.2220 Evaluate side-chains 285 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 230 time to evaluate : 2.410 ------------------------------------------------------------------------------- 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 165 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 70 THR 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 165 ASN Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 THR 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 G residue 86 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 654 ASP 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 99 ILE 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 195 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 20163 Z= 0.233 Angle : 0.565 7.222 27333 Z= 0.296 Chirality : 0.045 0.448 3105 Planarity : 0.003 0.046 3456 Dihedral : 5.014 41.137 3327 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.94 % Favored : 92.89 % Rotamer: Outliers : 3.69 % Allowed : 15.61 % Favored : 80.69 % 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: -2.03 (0.16), residues: 2406 helix: 0.57 (0.29), residues: 312 sheet: -0.95 (0.18), residues: 810 loop : -2.15 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.006 0.001 HIS B 264 PHE 0.013 0.001 PHE A 266 TYR 0.020 0.001 TYR A 408 ARG 0.005 0.000 ARG C 354 *********************** 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 320 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 241 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8157 (p0) REVERT: A 244 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: A 362 ASP cc_start: 0.7986 (t0) cc_final: 0.7656 (t0) REVERT: A 420 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8661 (p) REVERT: A 565 MET cc_start: 0.8603 (mtm) cc_final: 0.8354 (mtm) REVERT: A 589 TYR cc_start: 0.4165 (OUTLIER) cc_final: 0.3064 (t80) REVERT: A 636 MET cc_start: 0.8590 (mmm) cc_final: 0.8152 (mmm) REVERT: D 19 LYS cc_start: 0.8425 (mmmm) cc_final: 0.8150 (mmmm) REVERT: D 23 LYS cc_start: 0.8098 (tmtt) cc_final: 0.7668 (tmtt) REVERT: D 63 LYS cc_start: 0.8779 (ptmm) cc_final: 0.8505 (ptmm) REVERT: D 73 ASP cc_start: 0.7597 (t0) cc_final: 0.7173 (t0) REVERT: D 126 MET cc_start: 0.7910 (tpt) cc_final: 0.7655 (tpt) REVERT: E 5 THR cc_start: 0.8731 (m) cc_final: 0.8439 (p) REVERT: B 111 CYS cc_start: 0.3403 (p) cc_final: 0.3089 (p) REVERT: B 210 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8541 (m) REVERT: B 233 TRP cc_start: 0.7926 (p-90) cc_final: 0.7690 (p-90) REVERT: B 338 ASP cc_start: 0.7900 (t0) cc_final: 0.7466 (t0) REVERT: B 389 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8902 (pp) REVERT: F 30 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8700 (mttt) REVERT: F 73 ASP cc_start: 0.7810 (t0) cc_final: 0.7473 (t0) REVERT: G 16 GLN cc_start: 0.8804 (mt0) cc_final: 0.8027 (mt0) REVERT: C 389 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9021 (pp) REVERT: C 560 LYS cc_start: 0.7645 (mttt) cc_final: 0.6222 (tptt) REVERT: C 562 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8363 (tt) REVERT: C 589 TYR cc_start: 0.4324 (OUTLIER) cc_final: 0.3538 (t80) REVERT: H 31 ASP cc_start: 0.8473 (m-30) cc_final: 0.8058 (m-30) REVERT: H 73 ASP cc_start: 0.7270 (t0) cc_final: 0.6875 (t0) REVERT: H 123 GLN cc_start: 0.8606 (pm20) cc_final: 0.8345 (pm20) outliers start: 79 outliers final: 54 residues processed: 298 average time/residue: 0.3094 time to fit residues: 143.0663 Evaluate side-chains 298 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 234 time to evaluate : 2.419 ------------------------------------------------------------------------------- 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 165 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 434 ILE 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 648 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 81 MET 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 98 VAL Chi-restraints excluded: chain I residue 99 ILE 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 79 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 ASN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 20163 Z= 0.434 Angle : 0.658 7.335 27333 Z= 0.346 Chirality : 0.048 0.450 3105 Planarity : 0.004 0.047 3456 Dihedral : 5.440 42.134 3327 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.56 % Favored : 90.23 % Rotamer: Outliers : 4.44 % Allowed : 15.94 % Favored : 79.62 % 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: -2.23 (0.16), residues: 2406 helix: 0.31 (0.29), residues: 312 sheet: -1.07 (0.18), residues: 780 loop : -2.24 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 334 HIS 0.008 0.001 HIS B 365 PHE 0.013 0.002 PHE A 266 TYR 0.026 0.002 TYR A 408 ARG 0.005 0.000 ARG C 354 *********************** 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 338 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 243 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6228 (m-80) REVERT: A 165 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8073 (p0) REVERT: A 362 ASP cc_start: 0.8130 (t0) cc_final: 0.7756 (t0) REVERT: A 589 TYR cc_start: 0.4563 (OUTLIER) cc_final: 0.3373 (t80) REVERT: A 636 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8012 (mmm) REVERT: D 19 LYS cc_start: 0.8610 (mmmm) cc_final: 0.8194 (mmmm) REVERT: D 23 LYS cc_start: 0.8157 (tmtt) cc_final: 0.7726 (tmtt) REVERT: D 63 LYS cc_start: 0.8812 (ptmm) cc_final: 0.8543 (ptmm) REVERT: D 73 ASP cc_start: 0.7946 (t0) cc_final: 0.7528 (t0) REVERT: D 126 MET cc_start: 0.7931 (tpt) cc_final: 0.7614 (tpt) REVERT: E 5 THR cc_start: 0.8738 (m) cc_final: 0.8456 (p) REVERT: B 338 ASP cc_start: 0.8012 (t0) cc_final: 0.7618 (t0) REVERT: B 389 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8936 (pp) REVERT: F 23 LYS cc_start: 0.8142 (tmtt) cc_final: 0.7910 (tptt) REVERT: F 73 ASP cc_start: 0.8043 (t0) cc_final: 0.7707 (t0) REVERT: C 295 ASP cc_start: 0.8105 (t0) cc_final: 0.7786 (t0) REVERT: C 389 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9058 (pp) REVERT: C 562 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8231 (tt) REVERT: C 589 TYR cc_start: 0.4396 (OUTLIER) cc_final: 0.3655 (t80) REVERT: C 612 GLN cc_start: 0.7878 (tp-100) cc_final: 0.7669 (tp-100) REVERT: H 73 ASP cc_start: 0.7633 (t0) cc_final: 0.7206 (t0) outliers start: 95 outliers final: 70 residues processed: 309 average time/residue: 0.3068 time to fit residues: 145.6031 Evaluate side-chains 320 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 242 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 137 THR 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 165 ASN 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 371 MET Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 86 ASP 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 122 ASP Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 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 17 MET Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 434 ILE 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 C residue 648 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 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 52 ASN Chi-restraints excluded: chain I residue 99 ILE 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 226 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 171 optimal weight: 0.4980 chunk 197 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 234 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20163 Z= 0.176 Angle : 0.550 7.453 27333 Z= 0.287 Chirality : 0.044 0.419 3105 Planarity : 0.003 0.046 3456 Dihedral : 4.748 39.174 3327 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.65 % Favored : 93.18 % Rotamer: Outliers : 4.07 % Allowed : 16.41 % Favored : 79.52 % 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: -1.86 (0.17), residues: 2406 helix: 1.01 (0.31), residues: 294 sheet: -0.87 (0.18), residues: 822 loop : -2.07 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 349 HIS 0.005 0.001 HIS B 264 PHE 0.013 0.001 PHE A 266 TYR 0.019 0.001 TYR A 408 ARG 0.006 0.000 ARG C 354 *********************** 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 343 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 256 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: A 362 ASP cc_start: 0.7895 (t0) cc_final: 0.7486 (t0) REVERT: A 420 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8616 (p) REVERT: A 589 TYR cc_start: 0.4095 (OUTLIER) cc_final: 0.3046 (t80) REVERT: A 612 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7386 (tp-100) REVERT: A 636 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8179 (mmm) REVERT: D 19 LYS cc_start: 0.8441 (mmmm) cc_final: 0.8071 (mmmm) REVERT: D 23 LYS cc_start: 0.8098 (tmtt) cc_final: 0.7639 (tmtt) REVERT: D 63 LYS cc_start: 0.8789 (ptmm) cc_final: 0.8540 (ptmm) REVERT: D 73 ASP cc_start: 0.7474 (t0) cc_final: 0.7026 (t0) REVERT: D 126 MET cc_start: 0.7773 (tpt) cc_final: 0.7471 (tpt) REVERT: E 5 THR cc_start: 0.8728 (m) cc_final: 0.8447 (p) REVERT: E 52 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7365 (p0) REVERT: B 94 CYS cc_start: 0.7885 (m) cc_final: 0.7619 (p) REVERT: B 133 ILE cc_start: 0.8870 (pt) cc_final: 0.8670 (pt) REVERT: B 338 ASP cc_start: 0.7885 (t0) cc_final: 0.7419 (t0) REVERT: B 389 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8942 (pp) REVERT: B 648 MET cc_start: 0.8680 (tpp) cc_final: 0.8375 (tpt) REVERT: F 23 LYS cc_start: 0.8137 (tmtt) cc_final: 0.7917 (tptt) REVERT: F 30 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8623 (mttt) REVERT: F 73 ASP cc_start: 0.7725 (t0) cc_final: 0.7395 (t0) REVERT: G 16 GLN cc_start: 0.8803 (mt0) cc_final: 0.8270 (mt0) REVERT: G 32 ASN cc_start: 0.8740 (m110) cc_final: 0.8343 (m-40) REVERT: C 133 ILE cc_start: 0.9060 (pt) cc_final: 0.8844 (pt) REVERT: C 389 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9037 (pp) REVERT: C 560 LYS cc_start: 0.7011 (mttt) cc_final: 0.6258 (tptt) REVERT: C 562 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8277 (tt) REVERT: C 589 TYR cc_start: 0.4645 (OUTLIER) cc_final: 0.3841 (t80) REVERT: H 31 ASP cc_start: 0.8442 (m-30) cc_final: 0.8066 (m-30) REVERT: H 73 ASP cc_start: 0.7194 (t0) cc_final: 0.6726 (t0) outliers start: 87 outliers final: 57 residues processed: 319 average time/residue: 0.3087 time to fit residues: 151.6627 Evaluate side-chains 307 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 240 time to evaluate : 2.523 ------------------------------------------------------------------------------- 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 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 250 CYS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 89 CYS 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 93 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 184 optimal weight: 0.1980 chunk 213 optimal weight: 5.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS D 62 GLN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20163 Z= 0.161 Angle : 0.549 7.740 27333 Z= 0.284 Chirality : 0.044 0.414 3105 Planarity : 0.003 0.045 3456 Dihedral : 4.442 36.005 3327 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.07 % Favored : 92.81 % Rotamer: Outliers : 3.55 % Allowed : 17.67 % Favored : 78.78 % 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: -1.69 (0.17), residues: 2406 helix: 1.23 (0.31), residues: 294 sheet: -0.71 (0.19), residues: 792 loop : -2.00 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 233 HIS 0.004 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 *********************** 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 331 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 255 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.8714 (pt) cc_final: 0.8460 (pt) REVERT: A 155 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: A 165 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8138 (p0) REVERT: A 362 ASP cc_start: 0.7894 (t0) cc_final: 0.7490 (t0) REVERT: A 420 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8680 (p) REVERT: A 589 TYR cc_start: 0.4042 (OUTLIER) cc_final: 0.3012 (t80) REVERT: A 612 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7460 (tp-100) REVERT: A 636 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8167 (mmm) REVERT: D 19 LYS cc_start: 0.8409 (mmmm) cc_final: 0.8109 (mmmm) REVERT: D 23 LYS cc_start: 0.8102 (tmtt) cc_final: 0.7631 (tmtt) REVERT: D 63 LYS cc_start: 0.8751 (ptmm) cc_final: 0.8511 (ptmm) REVERT: D 73 ASP cc_start: 0.7288 (t0) cc_final: 0.7053 (t0) REVERT: D 123 GLN cc_start: 0.8681 (pm20) cc_final: 0.8480 (pm20) REVERT: D 126 MET cc_start: 0.8012 (tpt) cc_final: 0.7653 (tpt) REVERT: E 5 THR cc_start: 0.8724 (m) cc_final: 0.8440 (p) REVERT: B 94 CYS cc_start: 0.7869 (m) cc_final: 0.7638 (p) REVERT: B 338 ASP cc_start: 0.7870 (t0) cc_final: 0.7559 (t0) REVERT: B 389 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8931 (pp) REVERT: F 30 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8679 (mttt) REVERT: F 73 ASP cc_start: 0.7612 (t0) cc_final: 0.7272 (t0) REVERT: G 32 ASN cc_start: 0.8692 (m110) cc_final: 0.8214 (m-40) REVERT: C 133 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8812 (pt) REVERT: C 389 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9011 (pp) REVERT: C 560 LYS cc_start: 0.7076 (mttt) cc_final: 0.6365 (tptt) REVERT: C 562 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8258 (tt) REVERT: C 589 TYR cc_start: 0.4310 (OUTLIER) cc_final: 0.3571 (t80) REVERT: H 31 ASP cc_start: 0.8353 (m-30) cc_final: 0.8027 (m-30) REVERT: H 73 ASP cc_start: 0.7061 (t0) cc_final: 0.6632 (t0) REVERT: H 81 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7473 (ttm) REVERT: I 91 THR cc_start: 0.9268 (t) cc_final: 0.8978 (p) outliers start: 76 outliers final: 57 residues processed: 308 average time/residue: 0.3194 time to fit residues: 150.3443 Evaluate side-chains 316 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 247 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP 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 165 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 589 TYR 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 70 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain F residue 4 LEU 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 3 VAL 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 104 THR 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 161 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 52 ASN 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 224 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 218 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 217 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20163 Z= 0.341 Angle : 0.622 8.605 27333 Z= 0.325 Chirality : 0.046 0.411 3105 Planarity : 0.004 0.047 3456 Dihedral : 4.849 36.758 3327 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.10 % Favored : 91.69 % Rotamer: Outliers : 3.69 % Allowed : 17.91 % Favored : 78.40 % 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: -1.90 (0.16), residues: 2406 helix: 0.90 (0.30), residues: 294 sheet: -0.83 (0.19), residues: 780 loop : -2.10 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 233 HIS 0.006 0.001 HIS B 264 PHE 0.013 0.001 PHE A 266 TYR 0.023 0.001 TYR A 408 ARG 0.006 0.000 ARG C 354 *********************** 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 324 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 245 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6243 (m-80) REVERT: A 165 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8141 (p0) REVERT: A 362 ASP cc_start: 0.7941 (t0) cc_final: 0.7514 (t0) REVERT: A 420 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8694 (p) REVERT: A 565 MET cc_start: 0.7134 (mmt) cc_final: 0.5925 (mmt) REVERT: A 589 TYR cc_start: 0.4060 (OUTLIER) cc_final: 0.3014 (t80) REVERT: A 636 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8025 (mmm) REVERT: D 19 LYS cc_start: 0.8543 (mmmm) cc_final: 0.8169 (mmmm) REVERT: D 23 LYS cc_start: 0.8053 (tmtt) cc_final: 0.7601 (tmtt) REVERT: D 63 LYS cc_start: 0.8819 (ptmm) cc_final: 0.8562 (ptmm) REVERT: D 73 ASP cc_start: 0.7665 (t0) cc_final: 0.7348 (t0) REVERT: D 126 MET cc_start: 0.7773 (tpt) cc_final: 0.7451 (tpt) REVERT: E 5 THR cc_start: 0.8768 (m) cc_final: 0.8498 (p) REVERT: E 51 ASP cc_start: 0.6557 (m-30) cc_final: 0.6356 (m-30) REVERT: B 94 CYS cc_start: 0.7895 (m) cc_final: 0.7671 (p) REVERT: B 111 CYS cc_start: 0.3752 (p) cc_final: 0.3436 (p) REVERT: B 338 ASP cc_start: 0.7975 (t0) cc_final: 0.7749 (t0) REVERT: B 389 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8913 (pp) REVERT: F 30 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8704 (mttt) REVERT: F 73 ASP cc_start: 0.7867 (t0) cc_final: 0.7541 (t0) REVERT: G 5 THR cc_start: 0.8896 (m) cc_final: 0.8495 (p) REVERT: G 32 ASN cc_start: 0.8821 (m110) cc_final: 0.8327 (m-40) REVERT: C 295 ASP cc_start: 0.7927 (t0) cc_final: 0.7684 (t0) REVERT: C 389 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9045 (pp) REVERT: C 560 LYS cc_start: 0.7116 (mttt) cc_final: 0.6220 (tptt) REVERT: C 562 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8168 (tt) REVERT: C 589 TYR cc_start: 0.4381 (OUTLIER) cc_final: 0.3631 (t80) REVERT: H 31 ASP cc_start: 0.8482 (m-30) cc_final: 0.8013 (m-30) REVERT: H 73 ASP cc_start: 0.7525 (t0) cc_final: 0.7091 (t0) outliers start: 79 outliers final: 64 residues processed: 297 average time/residue: 0.3296 time to fit residues: 149.5507 Evaluate side-chains 314 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 240 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP 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 165 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 589 TYR 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 17 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain F residue 4 LEU 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 3 VAL Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 220 ASN 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 C residue 648 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 89 CYS Chi-restraints excluded: chain I residue 99 ILE 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 230 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 242 optimal weight: 0.9980 chunk 222 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20163 Z= 0.196 Angle : 0.567 7.912 27333 Z= 0.294 Chirality : 0.044 0.400 3105 Planarity : 0.003 0.047 3456 Dihedral : 4.544 36.570 3327 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.65 % Favored : 93.23 % Rotamer: Outliers : 3.37 % Allowed : 18.28 % Favored : 78.35 % 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: -1.74 (0.17), residues: 2406 helix: 1.15 (0.31), residues: 294 sheet: -0.72 (0.19), residues: 792 loop : -2.04 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 233 HIS 0.004 0.001 HIS B 264 PHE 0.014 0.001 PHE B 541 TYR 0.021 0.001 TYR A 408 ARG 0.006 0.000 ARG C 354 ********************** 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 319 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 247 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6258 (m-80) REVERT: A 165 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8137 (p0) REVERT: A 362 ASP cc_start: 0.7919 (t0) cc_final: 0.7498 (t0) REVERT: A 420 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8647 (p) REVERT: A 565 MET cc_start: 0.7046 (mmt) cc_final: 0.5867 (mmt) REVERT: A 612 GLN cc_start: 0.7702 (tp-100) cc_final: 0.7224 (tp-100) REVERT: A 636 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8187 (mmm) REVERT: D 19 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8125 (mmmm) REVERT: D 23 LYS cc_start: 0.8092 (tmtt) cc_final: 0.7649 (tmtt) REVERT: D 63 LYS cc_start: 0.8810 (ptmm) cc_final: 0.8583 (ptmm) REVERT: D 73 ASP cc_start: 0.7433 (t0) cc_final: 0.7085 (t0) REVERT: D 123 GLN cc_start: 0.8688 (pm20) cc_final: 0.8476 (pm20) REVERT: D 126 MET cc_start: 0.7980 (tpt) cc_final: 0.7612 (tpt) REVERT: E 5 THR cc_start: 0.8732 (m) cc_final: 0.8452 (p) REVERT: B 94 CYS cc_start: 0.7882 (m) cc_final: 0.7674 (p) REVERT: B 338 ASP cc_start: 0.7881 (t0) cc_final: 0.7563 (t0) REVERT: B 389 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8906 (pp) REVERT: F 30 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8684 (mttt) REVERT: F 73 ASP cc_start: 0.7670 (t0) cc_final: 0.7318 (t0) REVERT: G 5 THR cc_start: 0.8910 (m) cc_final: 0.8524 (p) REVERT: G 16 GLN cc_start: 0.8510 (mt0) cc_final: 0.8237 (mt0) REVERT: G 32 ASN cc_start: 0.8697 (m110) cc_final: 0.8189 (m-40) REVERT: G 94 ARG cc_start: 0.7874 (ppt170) cc_final: 0.7506 (ppt170) REVERT: C 295 ASP cc_start: 0.7916 (t0) cc_final: 0.7663 (t0) REVERT: C 389 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9045 (pp) REVERT: C 560 LYS cc_start: 0.7294 (mttt) cc_final: 0.6460 (tptt) REVERT: C 562 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8164 (tt) REVERT: C 589 TYR cc_start: 0.4561 (OUTLIER) cc_final: 0.3765 (t80) REVERT: H 31 ASP cc_start: 0.8427 (m-30) cc_final: 0.8082 (m-30) REVERT: H 73 ASP cc_start: 0.7211 (t0) cc_final: 0.6804 (t0) REVERT: I 91 THR cc_start: 0.9265 (t) cc_final: 0.8934 (p) outliers start: 72 outliers final: 60 residues processed: 297 average time/residue: 0.3238 time to fit residues: 147.4160 Evaluate side-chains 313 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 244 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP 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 165 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 589 TYR 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 17 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain F residue 4 LEU 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 3 VAL Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 89 CYS 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 205 optimal weight: 10.0000 chunk 59 optimal weight: 0.1980 chunk 177 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 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 = 0.3516 r_free = 0.3516 target = 0.118922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.082860 restraints weight = 32548.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.086211 restraints weight = 16984.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.088317 restraints weight = 11643.731| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20163 Z= 0.192 Angle : 0.564 7.332 27333 Z= 0.292 Chirality : 0.044 0.400 3105 Planarity : 0.003 0.047 3456 Dihedral : 4.383 34.091 3327 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.07 % Favored : 92.81 % Rotamer: Outliers : 3.37 % Allowed : 18.33 % Favored : 78.31 % 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 (0.17), residues: 2406 helix: 1.22 (0.31), residues: 294 sheet: -0.66 (0.19), residues: 792 loop : -2.00 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 233 HIS 0.004 0.001 HIS B 264 PHE 0.016 0.001 PHE B 541 TYR 0.020 0.001 TYR A 408 ARG 0.006 0.000 ARG C 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3877.14 seconds wall clock time: 72 minutes 15.97 seconds (4335.97 seconds total)