Starting phenix.real_space_refine on Fri Feb 23 05:22:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzb_20955/02_2024/6uzb_20955.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzb_20955/02_2024/6uzb_20955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzb_20955/02_2024/6uzb_20955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzb_20955/02_2024/6uzb_20955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzb_20955/02_2024/6uzb_20955.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzb_20955/02_2024/6uzb_20955.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 48 5.16 5 C 23153 2.51 5 N 6330 2.21 5 O 7406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 265": "OD1" <-> "OD2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 712": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C ARG 449": "NH1" <-> "NH2" Residue "C GLU 614": "OE1" <-> "OE2" Residue "C GLU 625": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 733": "OE1" <-> "OE2" Residue "D TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 449": "NH1" <-> "NH2" Residue "D GLU 525": "OE1" <-> "OE2" Residue "D GLU 609": "OE1" <-> "OE2" Residue "D GLU 625": "OE1" <-> "OE2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D GLU 733": "OE1" <-> "OE2" Residue "E GLU 398": "OE1" <-> "OE2" Residue "E ARG 449": "NH1" <-> "NH2" Residue "E GLU 465": "OE1" <-> "OE2" Residue "E GLU 525": "OE1" <-> "OE2" Residue "E GLU 609": "OE1" <-> "OE2" Residue "E GLU 625": "OE1" <-> "OE2" Residue "E GLU 654": "OE1" <-> "OE2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F ARG 449": "NH1" <-> "NH2" Residue "F GLU 525": "OE1" <-> "OE2" Residue "F GLU 609": "OE1" <-> "OE2" Residue "F GLU 614": "OE1" <-> "OE2" Residue "F GLU 645": "OE1" <-> "OE2" Residue "F GLU 712": "OE1" <-> "OE2" Residue "F GLU 733": "OE1" <-> "OE2" Residue "G ARG 449": "NH1" <-> "NH2" Residue "G GLU 645": "OE1" <-> "OE2" Residue "G GLU 650": "OE1" <-> "OE2" Residue "G GLU 712": "OE1" <-> "OE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 114": "NH1" <-> "NH2" Residue "H ASP 169": "OD1" <-> "OD2" Residue "H ARG 287": "NH1" <-> "NH2" Residue "H GLU 348": "OE1" <-> "OE2" Residue "H GLU 449": "OE1" <-> "OE2" Residue "H PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 654": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36951 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "B" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "C" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "D" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "E" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "F" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "G" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "H" Number of atoms: 5871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5871 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 699} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.83, per 1000 atoms: 0.51 Number of scatterers: 36951 At special positions: 0 Unit cell: (174.41, 175.48, 296.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 48 16.00 O 7406 8.00 N 6330 7.00 C 23153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.80 Conformation dependent library (CDL) restraints added in 6.7 seconds 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8838 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 80 sheets defined 23.0% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 209 through 214 removed outlier: 4.055A pdb=" N LYS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 214 " --> pdb=" O ILE A 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 209 through 214' Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.832A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.851A pdb=" N LEU A 401 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 480 through 487 removed outlier: 3.650A pdb=" N GLU A 486 " --> pdb=" O PRO A 482 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.601A pdb=" N THR A 576 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 614 removed outlier: 3.662A pdb=" N VAL A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 209 through 214 removed outlier: 4.403A pdb=" N LYS B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS B 214 " --> pdb=" O ILE B 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 209 through 214' Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 397 through 401 removed outlier: 3.574A pdb=" N LEU B 401 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 480 through 485 Processing helix chain 'B' and resid 522 through 531 Processing helix chain 'B' and resid 555 through 570 Processing helix chain 'B' and resid 573 through 581 removed outlier: 3.692A pdb=" N THR B 576 " --> pdb=" O ASN B 573 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LEU B 578 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP B 579 " --> pdb=" O THR B 576 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 581 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 615 through 617 No H-bonds generated for 'chain 'B' and resid 615 through 617' Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 659 through 663 removed outlier: 4.088A pdb=" N LEU B 663 " --> pdb=" O TYR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 706 No H-bonds generated for 'chain 'B' and resid 704 through 706' Processing helix chain 'B' and resid 730 through 734 removed outlier: 3.606A pdb=" N ILE B 734 " --> pdb=" O GLY B 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 397 through 401 removed outlier: 3.633A pdb=" N LEU C 401 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 Processing helix chain 'C' and resid 480 through 487 removed outlier: 3.816A pdb=" N THR C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 517 Processing helix chain 'C' and resid 522 through 531 removed outlier: 3.500A pdb=" N PHE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 570 Processing helix chain 'C' and resid 608 through 614 Processing helix chain 'C' and resid 717 through 721 removed outlier: 4.101A pdb=" N GLY C 720 " --> pdb=" O SER C 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 234 through 241 Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 397 through 401 removed outlier: 3.685A pdb=" N LEU D 401 " --> pdb=" O GLU D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 446 Processing helix chain 'D' and resid 480 through 486 Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.778A pdb=" N LYS D 518 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 531 removed outlier: 3.513A pdb=" N PHE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 548 No H-bonds generated for 'chain 'D' and resid 546 through 548' Processing helix chain 'D' and resid 555 through 569 Processing helix chain 'D' and resid 573 through 577 removed outlier: 3.836A pdb=" N THR D 576 " --> pdb=" O ASN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 614 removed outlier: 3.586A pdb=" N VAL D 612 " --> pdb=" O ASP D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 617 No H-bonds generated for 'chain 'D' and resid 615 through 617' Processing helix chain 'D' and resid 634 through 638 Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 207 through 215 removed outlier: 4.165A pdb=" N LYS E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS E 214 " --> pdb=" O ILE E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 397 through 401 removed outlier: 3.763A pdb=" N LEU E 401 " --> pdb=" O GLU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 480 through 486 Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.622A pdb=" N THR E 517 " --> pdb=" O LEU E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 532 removed outlier: 3.575A pdb=" N PHE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY E 532 " --> pdb=" O LYS E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 548 No H-bonds generated for 'chain 'E' and resid 546 through 548' Processing helix chain 'E' and resid 555 through 570 Processing helix chain 'E' and resid 573 through 581 removed outlier: 3.776A pdb=" N THR E 576 " --> pdb=" O ASN E 573 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL E 577 " --> pdb=" O ILE E 574 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU E 578 " --> pdb=" O TYR E 575 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP E 579 " --> pdb=" O THR E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 615 removed outlier: 4.073A pdb=" N VAL E 612 " --> pdb=" O ASP E 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'F' and resid 207 through 215 removed outlier: 3.773A pdb=" N HIS F 211 " --> pdb=" O ILE F 207 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS F 213 " --> pdb=" O ASN F 209 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS F 214 " --> pdb=" O ILE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'F' and resid 248 through 252 Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 480 through 485 Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.657A pdb=" N THR F 517 " --> pdb=" O LEU F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 531 removed outlier: 3.618A pdb=" N PHE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 568 Processing helix chain 'F' and resid 577 through 581 removed outlier: 3.937A pdb=" N ILE F 581 " --> pdb=" O LEU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 614 removed outlier: 4.195A pdb=" N VAL F 612 " --> pdb=" O ASP F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 734 No H-bonds generated for 'chain 'F' and resid 732 through 734' Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.812A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 401 removed outlier: 3.684A pdb=" N LEU G 401 " --> pdb=" O GLU G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 480 through 485 Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.516A pdb=" N THR G 517 " --> pdb=" O LEU G 514 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS G 518 " --> pdb=" O GLU G 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 514 through 518' Processing helix chain 'G' and resid 522 through 530 Processing helix chain 'G' and resid 546 through 548 No H-bonds generated for 'chain 'G' and resid 546 through 548' Processing helix chain 'G' and resid 555 through 569 Processing helix chain 'G' and resid 608 through 614 Processing helix chain 'G' and resid 632 through 637 removed outlier: 4.181A pdb=" N LYS G 637 " --> pdb=" O LYS G 633 " (cutoff:3.500A) Processing helix chain 'G' and resid 660 through 664 removed outlier: 3.958A pdb=" N LEU G 663 " --> pdb=" O TYR G 660 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN G 664 " --> pdb=" O ASP G 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 660 through 664' Processing helix chain 'H' and resid 21 through 30 Processing helix chain 'H' and resid 43 through 54 Processing helix chain 'H' and resid 57 through 67 removed outlier: 3.697A pdb=" N LEU H 61 " --> pdb=" O PRO H 57 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU H 67 " --> pdb=" O ILE H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.532A pdb=" N LEU H 84 " --> pdb=" O HIS H 81 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN H 85 " --> pdb=" O LYS H 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 85' Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.522A pdb=" N ASN H 93 " --> pdb=" O GLU H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.846A pdb=" N GLU H 135 " --> pdb=" O GLU H 131 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL H 136 " --> pdb=" O GLN H 132 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR H 137 " --> pdb=" O SER H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 150 removed outlier: 3.736A pdb=" N ILE H 148 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 169 removed outlier: 3.899A pdb=" N ASP H 169 " --> pdb=" O SER H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 177 Processing helix chain 'H' and resid 178 through 188 removed outlier: 3.767A pdb=" N GLU H 186 " --> pdb=" O LYS H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 200 Processing helix chain 'H' and resid 200 through 217 removed outlier: 3.958A pdb=" N PHE H 204 " --> pdb=" O ASN H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 220 No H-bonds generated for 'chain 'H' and resid 218 through 220' Processing helix chain 'H' and resid 221 through 228 Processing helix chain 'H' and resid 230 through 240 Processing helix chain 'H' and resid 241 through 255 removed outlier: 4.093A pdb=" N GLU H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL H 255 " --> pdb=" O LYS H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 272 removed outlier: 3.594A pdb=" N LEU H 269 " --> pdb=" O GLY H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 290 Processing helix chain 'H' and resid 299 through 307 removed outlier: 4.007A pdb=" N LEU H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 338 removed outlier: 3.713A pdb=" N LEU H 337 " --> pdb=" O ASP H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 361 removed outlier: 3.916A pdb=" N HIS H 361 " --> pdb=" O SER H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 382 Processing helix chain 'H' and resid 467 through 473 removed outlier: 3.615A pdb=" N LYS H 473 " --> pdb=" O THR H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 479 through 484 Processing helix chain 'H' and resid 488 through 504 Processing helix chain 'H' and resid 517 through 530 Processing helix chain 'H' and resid 574 through 585 Processing helix chain 'H' and resid 626 through 637 removed outlier: 3.609A pdb=" N ILE H 637 " --> pdb=" O ASN H 633 " (cutoff:3.500A) Processing helix chain 'H' and resid 651 through 672 removed outlier: 3.526A pdb=" N PHE H 655 " --> pdb=" O ASP H 651 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER H 669 " --> pdb=" O ALA H 665 " (cutoff:3.500A) Processing helix chain 'H' and resid 680 through 703 removed outlier: 3.784A pdb=" N LYS H 684 " --> pdb=" O SER H 680 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU H 703 " --> pdb=" O ILE H 699 " (cutoff:3.500A) Processing helix chain 'H' and resid 709 through 733 Processing helix chain 'H' and resid 739 through 747 removed outlier: 3.552A pdb=" N LEU H 743 " --> pdb=" O GLU H 739 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU H 747 " --> pdb=" O LEU H 743 " (cutoff:3.500A) Processing helix chain 'H' and resid 755 through 766 removed outlier: 3.940A pdb=" N ILE H 763 " --> pdb=" O VAL H 759 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE H 764 " --> pdb=" O PHE H 760 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 196 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 273 removed outlier: 6.674A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE A 269 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN A 361 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU A 271 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 359 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 410 through 411 removed outlier: 3.552A pdb=" N ALA A 358 " --> pdb=" O MET A 434 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE A 432 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 276 through 304 removed outlier: 3.546A pdb=" N ASN B 306 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 302 " --> pdb=" O SER B 325 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 298 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN B 292 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 288 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 280 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 311 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 318 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 318 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 311 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 279 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 340 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 338 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 334 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG B 297 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 332 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU G 340 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASN G 292 " --> pdb=" O ASP G 335 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER G 290 " --> pdb=" O SER G 337 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR G 282 " --> pdb=" O THR G 345 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR G 298 " --> pdb=" O SER G 329 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY G 323 " --> pdb=" O HIS G 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 323 through 324 removed outlier: 3.528A pdb=" N ASP C 276 " --> pdb=" O GLY C 351 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER C 290 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR D 293 " --> pdb=" O HIS C 336 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 340 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 342 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 329 through 332 removed outlier: 3.703A pdb=" N ASP D 276 " --> pdb=" O GLY D 351 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 284 " --> pdb=" O GLU D 343 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR D 286 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP F 276 " --> pdb=" O GLY F 351 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL F 320 " --> pdb=" O VAL G 309 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 309 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA F 322 " --> pdb=" O ALA G 307 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA G 307 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL G 320 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 305 " --> pdb=" O PHE G 324 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN G 326 " --> pdb=" O VAL A 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 334 through 353 removed outlier: 3.758A pdb=" N LYS F 291 " --> pdb=" O LEU E 338 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR F 298 " --> pdb=" O SER F 329 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU F 302 " --> pdb=" O SER F 325 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE F 324 " --> pdb=" O GLY G 305 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY G 305 " --> pdb=" O PHE F 324 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL F 332 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG G 297 " --> pdb=" O VAL F 332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 291 through 311 removed outlier: 4.630A pdb=" N VAL F 303 " --> pdb=" O ASN E 326 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN E 326 " --> pdb=" O VAL F 303 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY F 305 " --> pdb=" O PHE E 324 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA F 307 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA E 322 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER E 319 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU E 308 " --> pdb=" O SER E 319 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER E 321 " --> pdb=" O ASN E 306 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN E 306 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY E 323 " --> pdb=" O HIS E 304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS E 304 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER E 325 " --> pdb=" O GLU E 302 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU E 302 " --> pdb=" O SER E 325 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL E 309 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL D 320 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA E 311 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 318 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 389 through 395 removed outlier: 3.624A pdb=" N GLN A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR A 375 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 404 " --> pdb=" O TYR A 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 389 through 395 removed outlier: 3.624A pdb=" N GLN A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A 377 " --> pdb=" O TYR A 456 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR A 456 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN A 454 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR A 381 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR A 452 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU A 383 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU A 450 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU A 385 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 448 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N VAL A 455 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ASN A 476 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N GLY A 457 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N GLY A 474 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE A 459 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.770A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB4, first strand: chain 'A' and resid 596 through 598 removed outlier: 6.825A pdb=" N HIS A 597 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 628 through 629 Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.561A pdb=" N GLY A 641 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 645 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN A 697 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 192 through 196 Processing sheet with id=AB8, first strand: chain 'B' and resid 262 through 269 removed outlier: 6.495A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 409 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 262 through 269 removed outlier: 6.495A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 272 through 273 removed outlier: 4.724A pdb=" N ILE B 432 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.852A pdb=" N LEU B 383 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR B 393 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR B 381 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LYS B 395 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR B 375 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 404 " --> pdb=" O TYR B 375 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.852A pdb=" N LEU B 383 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR B 393 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR B 381 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LYS B 395 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL B 377 " --> pdb=" O TYR B 456 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR B 456 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN B 454 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR B 381 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR B 452 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B 383 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU B 450 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU B 385 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU B 448 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 10.895A pdb=" N VAL B 455 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N ASN B 476 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N GLY B 457 " --> pdb=" O GLY B 474 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N GLY B 474 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 459 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 501 through 506 removed outlier: 8.838A pdb=" N ILE B 589 " --> pdb=" O THR B 488 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 490 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE B 591 " --> pdb=" O ARG B 490 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 492 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ASP B 593 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 541 through 542 removed outlier: 3.754A pdb=" N LYS B 545 " --> pdb=" O TYR B 542 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 597 through 598 removed outlier: 6.885A pdb=" N HIS B 597 " --> pdb=" O VAL B 605 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 628 through 629 removed outlier: 3.601A pdb=" N THR B 674 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER B 667 " --> pdb=" O PHE B 675 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 639 through 643 removed outlier: 7.116A pdb=" N VAL B 696 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER B 728 " --> pdb=" O VAL B 696 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 698 " --> pdb=" O ILE B 726 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 645 through 646 removed outlier: 3.622A pdb=" N GLU B 654 " --> pdb=" O ILE B 646 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 192 through 196 Processing sheet with id=AD2, first strand: chain 'C' and resid 262 through 269 removed outlier: 6.587A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 262 through 269 removed outlier: 6.587A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 272 through 273 removed outlier: 3.566A pdb=" N ALA C 358 " --> pdb=" O MET C 434 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE C 432 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 310 through 311 Processing sheet with id=AD6, first strand: chain 'C' and resid 389 through 395 removed outlier: 3.605A pdb=" N GLN C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS C 395 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR C 375 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE C 404 " --> pdb=" O TYR C 375 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 389 through 395 removed outlier: 3.605A pdb=" N GLN C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS C 395 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL C 377 " --> pdb=" O TYR C 456 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR C 456 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLN C 454 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C 381 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 452 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU C 383 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU C 450 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU C 385 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU C 448 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N VAL C 455 " --> pdb=" O ASN C 476 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N ASN C 476 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N GLY C 457 " --> pdb=" O GLY C 474 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N GLY C 474 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE C 459 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.658A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AE1, first strand: chain 'C' and resid 596 through 598 removed outlier: 6.532A pdb=" N HIS C 597 " --> pdb=" O VAL C 605 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 619 through 622 removed outlier: 7.173A pdb=" N LEU C 628 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER C 622 " --> pdb=" O GLY C 626 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLY C 626 " --> pdb=" O SER C 622 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU C 629 " --> pdb=" O THR C 674 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR C 674 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 652 through 655 removed outlier: 3.803A pdb=" N LEU C 652 " --> pdb=" O ASP C 648 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C 701 " --> pdb=" O SER C 640 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR C 642 " --> pdb=" O TYR C 699 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR C 699 " --> pdb=" O TYR C 642 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL C 644 " --> pdb=" O ASN C 697 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASN C 697 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE C 646 " --> pdb=" O LYS C 695 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS C 695 " --> pdb=" O ILE C 646 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 192 through 196 Processing sheet with id=AE5, first strand: chain 'D' and resid 262 through 273 removed outlier: 6.733A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 409 through 411 removed outlier: 3.789A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE D 432 " --> pdb=" O LEU D 360 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.956A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS D 395 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR D 375 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 404 " --> pdb=" O TYR D 375 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.956A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS D 395 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL D 377 " --> pdb=" O TYR D 456 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR D 456 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLN D 454 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR D 381 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR D 452 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 383 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU D 450 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU D 385 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU D 448 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N VAL D 455 " --> pdb=" O ASN D 476 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ASN D 476 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N GLY D 457 " --> pdb=" O GLY D 474 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLY D 474 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.819A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 596 through 598 removed outlier: 5.945A pdb=" N HIS D 597 " --> pdb=" O VAL D 605 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 618 through 621 removed outlier: 4.418A pdb=" N GLU D 618 " --> pdb=" O ASN D 630 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU D 628 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 627 " --> pdb=" O ILE D 676 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 643 through 646 removed outlier: 3.970A pdb=" N ILE D 643 " --> pdb=" O TYR D 699 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 192 through 196 Processing sheet with id=AF5, first strand: chain 'E' and resid 262 through 273 removed outlier: 6.691A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE E 269 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN E 361 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU E 271 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG E 359 " --> pdb=" O LEU E 271 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 409 through 411 removed outlier: 3.660A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 358 " --> pdb=" O MET E 434 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE E 432 " --> pdb=" O LEU E 360 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 389 through 395 removed outlier: 6.945A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS E 395 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR E 375 " --> pdb=" O ILE E 404 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE E 404 " --> pdb=" O TYR E 375 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 389 through 395 removed outlier: 6.945A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS E 395 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL E 377 " --> pdb=" O TYR E 456 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TYR E 456 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLN E 454 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR E 381 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR E 452 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU E 383 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU E 450 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU E 385 " --> pdb=" O LEU E 448 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU E 448 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE E 459 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 501 through 506 removed outlier: 7.474A pdb=" N THR E 488 " --> pdb=" O MET E 587 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 597 through 598 Processing sheet with id=AG2, first strand: chain 'E' and resid 628 through 629 Processing sheet with id=AG3, first strand: chain 'E' and resid 643 through 645 removed outlier: 3.809A pdb=" N ASN E 697 " --> pdb=" O GLU E 645 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 192 through 196 Processing sheet with id=AG5, first strand: chain 'F' and resid 262 through 269 removed outlier: 6.608A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 262 through 269 removed outlier: 6.608A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 272 through 273 removed outlier: 4.753A pdb=" N ILE F 432 " --> pdb=" O LEU F 360 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 389 through 395 removed outlier: 6.938A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS F 395 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN F 403 " --> pdb=" O ASN F 376 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 389 through 395 removed outlier: 6.938A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS F 395 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL F 377 " --> pdb=" O TYR F 456 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR F 456 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN F 454 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR F 381 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR F 452 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU F 383 " --> pdb=" O LEU F 450 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU F 450 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU F 385 " --> pdb=" O LEU F 448 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU F 448 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N VAL F 455 " --> pdb=" O ASN F 476 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N ASN F 476 " --> pdb=" O VAL F 455 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N GLY F 457 " --> pdb=" O GLY F 474 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N GLY F 474 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE F 459 " --> pdb=" O ASP F 472 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 501 through 506 removed outlier: 8.940A pdb=" N ILE F 589 " --> pdb=" O THR F 488 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ASP F 593 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AH3, first strand: chain 'F' and resid 596 through 598 removed outlier: 6.939A pdb=" N HIS F 597 " --> pdb=" O VAL F 605 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 627 through 629 removed outlier: 3.659A pdb=" N LEU F 629 " --> pdb=" O THR F 674 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR F 674 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 639 through 647 removed outlier: 3.516A pdb=" N ASN F 697 " --> pdb=" O GLU F 645 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=AH7, first strand: chain 'G' and resid 262 through 273 removed outlier: 5.612A pdb=" N VAL G 264 " --> pdb=" O VAL G 367 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL G 367 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N MET G 266 " --> pdb=" O ARG G 365 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG G 365 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN G 268 " --> pdb=" O ASN G 363 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 409 through 411 removed outlier: 3.634A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE G 432 " --> pdb=" O LEU G 360 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 389 through 395 removed outlier: 3.694A pdb=" N GLN G 389 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU G 383 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR G 393 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR G 381 " --> pdb=" O THR G 393 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS G 395 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR G 375 " --> pdb=" O ILE G 404 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE G 404 " --> pdb=" O TYR G 375 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 389 through 395 removed outlier: 3.694A pdb=" N GLN G 389 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU G 383 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR G 393 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR G 381 " --> pdb=" O THR G 393 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS G 395 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL G 377 " --> pdb=" O TYR G 456 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR G 456 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN G 454 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR G 381 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR G 452 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU G 383 " --> pdb=" O LEU G 450 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU G 450 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU G 385 " --> pdb=" O LEU G 448 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU G 448 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 10.909A pdb=" N VAL G 455 " --> pdb=" O ASN G 476 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N ASN G 476 " --> pdb=" O VAL G 455 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N GLY G 457 " --> pdb=" O GLY G 474 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N GLY G 474 " --> pdb=" O GLY G 457 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.824A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 596 through 598 removed outlier: 3.617A pdb=" N GLY G 606 " --> pdb=" O HIS G 597 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 639 through 647 removed outlier: 3.599A pdb=" N GLY G 641 " --> pdb=" O VAL G 701 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE G 727 " --> pdb=" O VAL G 698 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA G 700 " --> pdb=" O LEU G 725 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU G 725 " --> pdb=" O ALA G 700 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 70 through 74 removed outlier: 6.123A pdb=" N GLU H 70 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE H 121 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR H 72 " --> pdb=" O ILE H 121 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 291 through 295 removed outlier: 3.702A pdb=" N LEU H 294 " --> pdb=" O ALA H 463 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA H 463 " --> pdb=" O LEU H 294 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'H' and resid 393 through 394 Processing sheet with id=AI8, first strand: chain 'H' and resid 562 through 563 1280 hydrogen bonds defined for protein. 3495 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: 17.92 Time building geometry restraints manager: 15.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7843 1.32 - 1.44: 8217 1.44 - 1.57: 21423 1.57 - 1.69: 2 1.69 - 1.81: 96 Bond restraints: 37581 Sorted by residual: bond pdb=" N SER C 711 " pdb=" CA SER C 711 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N ILE H 192 " pdb=" CA ILE H 192 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N SER B 711 " pdb=" CA SER B 711 " ideal model delta sigma weight residual 1.453 1.493 -0.039 1.27e-02 6.20e+03 9.66e+00 bond pdb=" N ASP B 599 " pdb=" CA ASP B 599 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.37e+00 bond pdb=" N GLU B 712 " pdb=" CA GLU B 712 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.17e-02 7.31e+03 8.90e+00 ... (remaining 37576 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.00: 682 106.00 - 113.02: 20354 113.02 - 120.04: 13298 120.04 - 127.06: 16271 127.06 - 134.09: 308 Bond angle restraints: 50913 Sorted by residual: angle pdb=" N ASP C 683 " pdb=" CA ASP C 683 " pdb=" C ASP C 683 " ideal model delta sigma weight residual 111.90 103.16 8.74 1.32e+00 5.74e-01 4.39e+01 angle pdb=" O PHE H 38 " pdb=" C PHE H 38 " pdb=" N THR H 39 " ideal model delta sigma weight residual 120.83 124.86 -4.03 7.40e-01 1.83e+00 2.97e+01 angle pdb=" C SER C 711 " pdb=" CA SER C 711 " pdb=" CB SER C 711 " ideal model delta sigma weight residual 111.78 100.61 11.17 2.20e+00 2.07e-01 2.58e+01 angle pdb=" C LYS A 496 " pdb=" N ASP A 497 " pdb=" CA ASP A 497 " ideal model delta sigma weight residual 122.08 129.48 -7.40 1.47e+00 4.63e-01 2.54e+01 angle pdb=" C SER D 711 " pdb=" N GLU D 712 " pdb=" CA GLU D 712 " ideal model delta sigma weight residual 121.19 128.85 -7.66 1.59e+00 3.96e-01 2.32e+01 ... (remaining 50908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 20329 17.77 - 35.54: 2167 35.54 - 53.30: 389 53.30 - 71.07: 77 71.07 - 88.84: 30 Dihedral angle restraints: 22992 sinusoidal: 9332 harmonic: 13660 Sorted by residual: dihedral pdb=" CA ASP G 608 " pdb=" C ASP G 608 " pdb=" N GLU G 609 " pdb=" CA GLU G 609 " ideal model delta harmonic sigma weight residual -180.00 -150.61 -29.39 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP D 608 " pdb=" C ASP D 608 " pdb=" N GLU D 609 " pdb=" CA GLU D 609 " ideal model delta harmonic sigma weight residual -180.00 -153.37 -26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" C ILE H 192 " pdb=" N ILE H 192 " pdb=" CA ILE H 192 " pdb=" CB ILE H 192 " ideal model delta harmonic sigma weight residual -122.00 -134.47 12.47 0 2.50e+00 1.60e-01 2.49e+01 ... (remaining 22989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5063 0.095 - 0.190: 677 0.190 - 0.286: 30 0.286 - 0.381: 5 0.381 - 0.476: 1 Chirality restraints: 5776 Sorted by residual: chirality pdb=" CB ILE C 689 " pdb=" CA ILE C 689 " pdb=" CG1 ILE C 689 " pdb=" CG2 ILE C 689 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CB ILE D 183 " pdb=" CA ILE D 183 " pdb=" CG1 ILE D 183 " pdb=" CG2 ILE D 183 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB ILE E 269 " pdb=" CA ILE E 269 " pdb=" CG1 ILE E 269 " pdb=" CG2 ILE E 269 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 5773 not shown) Planarity restraints: 6668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 607 " -0.024 2.00e-02 2.50e+03 4.89e-02 2.39e+01 pdb=" C ALA F 607 " 0.085 2.00e-02 2.50e+03 pdb=" O ALA F 607 " -0.032 2.00e-02 2.50e+03 pdb=" N ASP F 608 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 712 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C GLU G 712 " 0.066 2.00e-02 2.50e+03 pdb=" O GLU G 712 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN G 713 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE H 624 " -0.054 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO H 625 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO H 625 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO H 625 " -0.045 5.00e-02 4.00e+02 ... (remaining 6665 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7031 2.77 - 3.30: 31997 3.30 - 3.83: 60096 3.83 - 4.37: 70620 4.37 - 4.90: 124921 Nonbonded interactions: 294665 Sorted by model distance: nonbonded pdb=" CD1 LEU H 294 " pdb=" CD1 ILE H 562 " model vdw 2.236 3.880 nonbonded pdb=" O ILE B 484 " pdb=" OG1 THR B 488 " model vdw 2.248 2.440 nonbonded pdb=" O ILE C 484 " pdb=" OG1 THR C 488 " model vdw 2.249 2.440 nonbonded pdb=" O PHE D 236 " pdb=" OG1 THR D 240 " model vdw 2.251 2.440 nonbonded pdb=" OE2 GLU H 479 " pdb=" OH TYR H 503 " model vdw 2.253 2.440 ... (remaining 294660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.220 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 98.300 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 : 0.010 0.101 37581 Z= 0.672 Angle : 0.919 11.172 50913 Z= 0.519 Chirality : 0.063 0.476 5776 Planarity : 0.007 0.082 6668 Dihedral : 15.212 88.841 14154 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.34 % Favored : 93.61 % Rotamer: Outliers : 0.84 % Allowed : 8.56 % Favored : 90.60 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.10), residues: 4634 helix: -2.81 (0.13), residues: 858 sheet: -1.94 (0.14), residues: 1107 loop : -2.73 (0.10), residues: 2669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 226 HIS 0.013 0.002 HIS H 544 PHE 0.034 0.003 PHE B 727 TYR 0.045 0.002 TYR A 366 ARG 0.007 0.001 ARG E 600 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 209 time to evaluate : 3.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 MET cc_start: 0.5314 (ptp) cc_final: 0.4459 (pmm) REVERT: A 680 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5900 (pttm) REVERT: C 597 HIS cc_start: 0.7083 (m90) cc_final: 0.6737 (m90) REVERT: C 681 TYR cc_start: -0.0123 (OUTLIER) cc_final: -0.0420 (t80) REVERT: D 356 ASP cc_start: 0.7905 (t0) cc_final: 0.7299 (t0) REVERT: D 541 GLN cc_start: 0.7816 (mt0) cc_final: 0.7578 (mt0) REVERT: D 561 ASN cc_start: 0.8359 (t0) cc_final: 0.7833 (t0) REVERT: F 591 ILE cc_start: 0.8592 (mt) cc_final: 0.8297 (tt) REVERT: G 285 GLN cc_start: 0.7670 (mt0) cc_final: 0.7452 (pt0) REVERT: G 662 MET cc_start: 0.1249 (ptt) cc_final: 0.0318 (tpt) REVERT: H 77 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7827 (p0) REVERT: H 196 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7220 (t80) REVERT: H 713 LYS cc_start: 0.8966 (tttm) cc_final: 0.8391 (mttm) REVERT: H 765 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7909 (t0) outliers start: 35 outliers final: 10 residues processed: 241 average time/residue: 0.5882 time to fit residues: 220.0617 Evaluate side-chains 159 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain C residue 681 TYR Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 760 PHE Chi-restraints excluded: chain H residue 764 ILE Chi-restraints excluded: chain H residue 765 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 391 optimal weight: 7.9990 chunk 351 optimal weight: 20.0000 chunk 195 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 237 optimal weight: 50.0000 chunk 187 optimal weight: 2.9990 chunk 363 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 270 optimal weight: 0.0980 chunk 421 optimal weight: 40.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 389 GLN A 437 ASN A 630 ASN B 277 GLN B 281 ASN B 304 HIS B 328 ASN B 363 ASN B 389 GLN B 399 ASN B 435 ASN B 437 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN C 363 ASN C 389 GLN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN C 601 ASN C 657 ASN C 697 ASN C 713 ASN D 292 ASN D 353 ASN ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 553 ASN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN E 424 GLN E 494 ASN E 584 ASN E 602 ASN E 682 ASN E 691 ASN E 693 ASN E 719 ASN F 304 HIS F 363 ASN F 389 GLN F 543 GLN F 560 GLN F 564 ASN F 719 ASN G 389 GLN G 437 ASN G 499 ASN G 584 ASN H 188 ASN H 200 ASN ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 ASN H 343 GLN H 354 ASN H 406 ASN H 493 GLN H 528 ASN H 642 ASN H 677 HIS ** H 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37581 Z= 0.194 Angle : 0.549 7.984 50913 Z= 0.299 Chirality : 0.046 0.190 5776 Planarity : 0.004 0.064 6668 Dihedral : 6.126 55.481 5041 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.73 % Favored : 95.23 % Rotamer: Outliers : 1.03 % Allowed : 11.83 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.11), residues: 4634 helix: -1.07 (0.17), residues: 873 sheet: -1.40 (0.14), residues: 1176 loop : -2.18 (0.11), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 519 HIS 0.006 0.001 HIS H 544 PHE 0.015 0.001 PHE B 727 TYR 0.018 0.001 TYR A 366 ARG 0.003 0.000 ARG G 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 4.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 MET cc_start: 0.5316 (ptp) cc_final: 0.4488 (pmm) REVERT: A 680 LYS cc_start: 0.6611 (OUTLIER) cc_final: 0.6057 (pttm) REVERT: A 694 TYR cc_start: 0.1997 (OUTLIER) cc_final: 0.1375 (m-80) REVERT: B 435 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8701 (p0) REVERT: B 515 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8394 (mm-30) REVERT: B 600 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7167 (mmm160) REVERT: C 597 HIS cc_start: 0.7063 (m90) cc_final: 0.6732 (m90) REVERT: D 541 GLN cc_start: 0.7540 (mt0) cc_final: 0.7297 (mt0) REVERT: D 561 ASN cc_start: 0.8353 (t0) cc_final: 0.7829 (t0) REVERT: E 702 THR cc_start: 0.1419 (OUTLIER) cc_final: 0.1193 (p) REVERT: F 287 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7908 (mtp85) REVERT: F 591 ILE cc_start: 0.8677 (mt) cc_final: 0.8436 (tt) REVERT: G 662 MET cc_start: 0.0526 (ptt) cc_final: -0.0424 (tpt) REVERT: H 77 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7781 (p0) REVERT: H 196 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7761 (t80) REVERT: H 582 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7870 (tp) REVERT: H 713 LYS cc_start: 0.8907 (tttm) cc_final: 0.8323 (mttt) REVERT: H 765 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7701 (m-30) outliers start: 43 outliers final: 15 residues processed: 194 average time/residue: 0.5170 time to fit residues: 165.8389 Evaluate side-chains 166 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 4.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 702 THR Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 447 ASN Chi-restraints excluded: chain H residue 582 ILE Chi-restraints excluded: chain H residue 765 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 422 optimal weight: 50.0000 chunk 456 optimal weight: 10.0000 chunk 375 optimal weight: 6.9990 chunk 418 optimal weight: 50.0000 chunk 143 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 389 GLN A 697 ASN B 198 ASN B 336 HIS B 435 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 ASN C 570 ASN D 268 ASN D 353 ASN D 363 ASN ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN E 424 GLN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 682 ASN F 657 ASN G 285 GLN G 363 ASN G 584 ASN ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 676 ASN ** H 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.109 37581 Z= 0.535 Angle : 0.638 10.221 50913 Z= 0.343 Chirality : 0.050 0.236 5776 Planarity : 0.005 0.064 6668 Dihedral : 5.952 55.481 5025 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.13 % Favored : 93.85 % Rotamer: Outliers : 2.16 % Allowed : 14.62 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.11), residues: 4634 helix: -0.52 (0.18), residues: 882 sheet: -1.20 (0.14), residues: 1211 loop : -2.11 (0.11), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 226 HIS 0.007 0.001 HIS B 263 PHE 0.021 0.002 PHE B 727 TYR 0.027 0.002 TYR A 366 ARG 0.006 0.000 ARG C 595 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 139 time to evaluate : 4.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 694 TYR cc_start: 0.1995 (OUTLIER) cc_final: 0.1393 (m-80) REVERT: B 515 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8549 (mm-30) REVERT: C 597 HIS cc_start: 0.7009 (m90) cc_final: 0.6625 (m90) REVERT: D 541 GLN cc_start: 0.7737 (mt0) cc_final: 0.7459 (mt0) REVERT: D 561 ASN cc_start: 0.8413 (t0) cc_final: 0.7871 (t0) REVERT: E 263 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.6993 (p-80) REVERT: E 702 THR cc_start: 0.1758 (OUTLIER) cc_final: 0.1412 (p) REVERT: F 276 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7594 (p0) REVERT: F 591 ILE cc_start: 0.8788 (mt) cc_final: 0.8497 (tt) REVERT: G 662 MET cc_start: 0.0451 (ptt) cc_final: -0.0621 (tpt) REVERT: H 77 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7614 (p0) REVERT: H 196 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7782 (t80) REVERT: H 322 SER cc_start: -0.0060 (OUTLIER) cc_final: -0.0432 (m) REVERT: H 713 LYS cc_start: 0.8876 (tttm) cc_final: 0.8291 (mttt) REVERT: H 752 ASN cc_start: 0.4960 (OUTLIER) cc_final: 0.4718 (p0) REVERT: H 765 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8096 (t70) outliers start: 90 outliers final: 44 residues processed: 220 average time/residue: 0.4658 time to fit residues: 172.9553 Evaluate side-chains 188 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 134 time to evaluate : 4.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 539 ASN Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain E residue 702 THR Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 125 ASP Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 447 ASN Chi-restraints excluded: chain H residue 537 THR Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 752 ASN Chi-restraints excluded: chain H residue 765 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 20.0000 chunk 317 optimal weight: 5.9990 chunk 219 optimal weight: 0.0470 chunk 46 optimal weight: 20.0000 chunk 201 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 423 optimal weight: 50.0000 chunk 448 optimal weight: 20.0000 chunk 221 optimal weight: 0.9990 chunk 401 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN D 353 ASN D 389 GLN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN E 299 HIS E 424 GLN E 682 ASN F 328 ASN ** G 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37581 Z= 0.193 Angle : 0.507 12.048 50913 Z= 0.271 Chirality : 0.045 0.257 5776 Planarity : 0.004 0.063 6668 Dihedral : 5.357 51.900 5017 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.45 % Favored : 95.53 % Rotamer: Outliers : 1.97 % Allowed : 16.31 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.12), residues: 4634 helix: -0.22 (0.18), residues: 919 sheet: -0.87 (0.14), residues: 1190 loop : -1.80 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 346 HIS 0.005 0.001 HIS H 544 PHE 0.014 0.001 PHE A 678 TYR 0.013 0.001 TYR A 366 ARG 0.010 0.000 ARG F 595 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 140 time to evaluate : 4.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.7534 (tmt170) cc_final: 0.7315 (ttp80) REVERT: A 662 MET cc_start: 0.5643 (ptp) cc_final: 0.4599 (pmm) REVERT: B 287 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7491 (ttp80) REVERT: D 541 GLN cc_start: 0.7420 (mt0) cc_final: 0.7028 (mt0) REVERT: D 561 ASN cc_start: 0.8433 (t0) cc_final: 0.7892 (t0) REVERT: E 263 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.6987 (p-80) REVERT: E 702 THR cc_start: 0.1607 (OUTLIER) cc_final: 0.1177 (p) REVERT: F 276 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7437 (p0) REVERT: F 591 ILE cc_start: 0.8722 (mt) cc_final: 0.8423 (tt) REVERT: F 595 ARG cc_start: 0.7599 (mtm110) cc_final: 0.7328 (mtm110) REVERT: F 702 THR cc_start: 0.1267 (OUTLIER) cc_final: 0.0707 (p) REVERT: G 662 MET cc_start: 0.0397 (ptt) cc_final: -0.0722 (tpt) REVERT: H 77 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7662 (p0) REVERT: H 196 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7710 (t80) REVERT: H 713 LYS cc_start: 0.8892 (tttm) cc_final: 0.8313 (mttt) REVERT: H 765 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8095 (t70) outliers start: 82 outliers final: 40 residues processed: 215 average time/residue: 0.4853 time to fit residues: 174.1554 Evaluate side-chains 179 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 132 time to evaluate : 4.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain E residue 702 THR Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 447 ASN Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 752 ASN Chi-restraints excluded: chain H residue 765 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 10.0000 chunk 254 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 333 optimal weight: 0.9990 chunk 185 optimal weight: 6.9990 chunk 382 optimal weight: 30.0000 chunk 310 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 402 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 HIS ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN E 424 GLN E 499 ASN E 682 ASN E 697 ASN ** H 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 761 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37581 Z= 0.166 Angle : 0.487 9.387 50913 Z= 0.259 Chirality : 0.045 0.222 5776 Planarity : 0.003 0.061 6668 Dihedral : 5.030 49.852 5017 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 2.31 % Allowed : 16.74 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.12), residues: 4634 helix: 0.06 (0.18), residues: 919 sheet: -0.70 (0.14), residues: 1197 loop : -1.61 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 519 HIS 0.006 0.001 HIS H 544 PHE 0.046 0.001 PHE B 727 TYR 0.015 0.001 TYR H 292 ARG 0.007 0.000 ARG F 595 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 142 time to evaluate : 4.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 MET cc_start: 0.5643 (ptp) cc_final: 0.4563 (pmm) REVERT: B 287 ARG cc_start: 0.7737 (mtm110) cc_final: 0.7466 (ttp80) REVERT: B 350 MET cc_start: 0.7432 (tmm) cc_final: 0.7203 (tmm) REVERT: C 595 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7787 (ttp-110) REVERT: D 541 GLN cc_start: 0.7392 (mt0) cc_final: 0.7018 (mt0) REVERT: D 561 ASN cc_start: 0.8479 (t0) cc_final: 0.7956 (t0) REVERT: E 263 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.6923 (p-80) REVERT: E 628 LEU cc_start: 0.3594 (OUTLIER) cc_final: 0.3327 (mp) REVERT: E 629 LEU cc_start: 0.2561 (OUTLIER) cc_final: 0.1905 (tp) REVERT: E 702 THR cc_start: 0.1273 (OUTLIER) cc_final: 0.0847 (p) REVERT: F 276 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7451 (p0) REVERT: F 591 ILE cc_start: 0.8670 (mt) cc_final: 0.8311 (tt) REVERT: F 595 ARG cc_start: 0.7604 (mtm110) cc_final: 0.7288 (mtm110) REVERT: F 679 LYS cc_start: 0.2556 (OUTLIER) cc_final: 0.2070 (mmtt) REVERT: F 702 THR cc_start: 0.1260 (OUTLIER) cc_final: 0.0666 (p) REVERT: H 77 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7689 (p0) REVERT: H 196 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7737 (t80) REVERT: H 372 LEU cc_start: 0.1587 (OUTLIER) cc_final: 0.1322 (pp) outliers start: 96 outliers final: 54 residues processed: 230 average time/residue: 0.4681 time to fit residues: 181.8019 Evaluate side-chains 200 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 135 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 539 ASN Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 669 ARG Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain E residue 702 THR Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 450 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 375 LEU Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 447 ASN Chi-restraints excluded: chain H residue 537 THR Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 752 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 4.9990 chunk 403 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 263 optimal weight: 6.9990 chunk 110 optimal weight: 40.0000 chunk 448 optimal weight: 20.0000 chunk 372 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 37 optimal weight: 0.0770 chunk 148 optimal weight: 8.9990 chunk 235 optimal weight: 20.0000 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN B 326 ASN B 336 HIS ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN E 682 ASN E 693 ASN ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 37581 Z= 0.375 Angle : 0.557 8.962 50913 Z= 0.298 Chirality : 0.048 0.289 5776 Planarity : 0.004 0.059 6668 Dihedral : 5.140 47.023 5015 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.18 % Favored : 94.80 % Rotamer: Outliers : 2.53 % Allowed : 17.08 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.12), residues: 4634 helix: 0.05 (0.18), residues: 931 sheet: -0.67 (0.14), residues: 1197 loop : -1.63 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 226 HIS 0.007 0.001 HIS B 263 PHE 0.024 0.002 PHE B 727 TYR 0.021 0.001 TYR H 292 ARG 0.005 0.000 ARG C 595 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 137 time to evaluate : 4.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 276 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8063 (p0) REVERT: B 287 ARG cc_start: 0.7808 (mtm110) cc_final: 0.7533 (ttp80) REVERT: C 496 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8025 (ptmm) REVERT: C 556 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: C 595 ARG cc_start: 0.8300 (ttm110) cc_final: 0.7767 (ttp-110) REVERT: D 541 GLN cc_start: 0.7520 (mt0) cc_final: 0.7126 (mt0) REVERT: D 561 ASN cc_start: 0.8472 (t0) cc_final: 0.7957 (t0) REVERT: E 263 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.7005 (p-80) REVERT: E 464 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7418 (t80) REVERT: E 629 LEU cc_start: 0.2564 (OUTLIER) cc_final: 0.1913 (tp) REVERT: E 669 ARG cc_start: 0.1865 (OUTLIER) cc_final: 0.1575 (ttp-110) REVERT: E 702 THR cc_start: 0.1396 (OUTLIER) cc_final: 0.0940 (p) REVERT: F 276 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7477 (p0) REVERT: F 591 ILE cc_start: 0.8674 (mt) cc_final: 0.8314 (tt) REVERT: F 595 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7318 (mtm110) REVERT: F 679 LYS cc_start: 0.2843 (OUTLIER) cc_final: 0.2309 (mmtt) REVERT: F 702 THR cc_start: 0.1105 (OUTLIER) cc_final: 0.0569 (p) REVERT: G 600 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.5744 (mtp-110) REVERT: G 662 MET cc_start: 0.0395 (ptt) cc_final: -0.0645 (tpt) REVERT: H 77 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7637 (p0) REVERT: H 196 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7753 (t80) REVERT: H 372 LEU cc_start: 0.1681 (OUTLIER) cc_final: 0.1401 (pp) REVERT: H 374 HIS cc_start: 0.3208 (OUTLIER) cc_final: 0.2658 (m-70) outliers start: 105 outliers final: 67 residues processed: 231 average time/residue: 0.4753 time to fit residues: 184.3036 Evaluate side-chains 217 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 134 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 539 ASN Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 464 PHE Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 669 ARG Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 702 THR Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 600 ARG Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 125 ASP Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 323 ASP Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 374 HIS Chi-restraints excluded: chain H residue 375 LEU Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 447 ASN Chi-restraints excluded: chain H residue 537 THR Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 752 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 255 optimal weight: 0.9990 chunk 327 optimal weight: 3.9990 chunk 254 optimal weight: 0.6980 chunk 377 optimal weight: 4.9990 chunk 250 optimal weight: 0.7980 chunk 447 optimal weight: 6.9990 chunk 279 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 206 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN B 326 ASN B 336 HIS ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN E 424 GLN E 682 ASN E 693 ASN ** H 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 37581 Z= 0.220 Angle : 0.506 9.371 50913 Z= 0.269 Chirality : 0.045 0.216 5776 Planarity : 0.003 0.061 6668 Dihedral : 4.930 46.954 5013 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.47 % Favored : 95.51 % Rotamer: Outliers : 2.28 % Allowed : 17.85 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.12), residues: 4634 helix: 0.19 (0.18), residues: 931 sheet: -0.44 (0.15), residues: 1162 loop : -1.59 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 519 HIS 0.006 0.001 HIS H 544 PHE 0.024 0.001 PHE B 727 TYR 0.020 0.001 TYR H 292 ARG 0.003 0.000 ARG C 595 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 134 time to evaluate : 4.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 MET cc_start: 0.5517 (ptp) cc_final: 0.4557 (pmm) REVERT: B 276 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8059 (p0) REVERT: B 287 ARG cc_start: 0.7804 (mtm110) cc_final: 0.7535 (ttp80) REVERT: C 556 GLN cc_start: 0.7859 (pp30) cc_final: 0.7591 (tm-30) REVERT: C 595 ARG cc_start: 0.8291 (ttm110) cc_final: 0.7748 (ttp-110) REVERT: D 356 ASP cc_start: 0.7761 (t0) cc_final: 0.7336 (t0) REVERT: D 541 GLN cc_start: 0.7421 (mt0) cc_final: 0.7040 (mt0) REVERT: D 561 ASN cc_start: 0.8468 (t0) cc_final: 0.7977 (t0) REVERT: E 263 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.6978 (p-80) REVERT: E 629 LEU cc_start: 0.2512 (OUTLIER) cc_final: 0.1868 (tp) REVERT: E 702 THR cc_start: 0.1398 (OUTLIER) cc_final: 0.0930 (p) REVERT: F 276 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7430 (p0) REVERT: F 591 ILE cc_start: 0.8683 (mt) cc_final: 0.8316 (tt) REVERT: F 595 ARG cc_start: 0.7701 (mtm110) cc_final: 0.7350 (mtm110) REVERT: F 679 LYS cc_start: 0.2733 (OUTLIER) cc_final: 0.2239 (mmtt) REVERT: F 702 THR cc_start: 0.0804 (OUTLIER) cc_final: 0.0196 (p) REVERT: G 600 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.5805 (mtp-110) REVERT: H 77 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7682 (p0) REVERT: H 196 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7737 (t80) REVERT: H 372 LEU cc_start: 0.1664 (OUTLIER) cc_final: 0.1389 (pp) outliers start: 95 outliers final: 68 residues processed: 221 average time/residue: 0.4721 time to fit residues: 176.3260 Evaluate side-chains 212 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 133 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 539 ASN Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 669 ARG Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain E residue 702 THR Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 600 ARG Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 323 ASP Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 375 LEU Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 447 ASN Chi-restraints excluded: chain H residue 537 THR Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 752 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 50.0000 chunk 178 optimal weight: 6.9990 chunk 267 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 284 optimal weight: 5.9990 chunk 304 optimal weight: 3.9990 chunk 221 optimal weight: 0.0060 chunk 41 optimal weight: 0.8980 chunk 351 optimal weight: 40.0000 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN B 326 ASN B 336 HIS ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN E 424 GLN E 682 ASN G 560 GLN ** H 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 37581 Z= 0.232 Angle : 0.500 7.963 50913 Z= 0.266 Chirality : 0.045 0.234 5776 Planarity : 0.003 0.059 6668 Dihedral : 4.793 46.899 5013 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.60 % Favored : 95.38 % Rotamer: Outliers : 2.26 % Allowed : 18.06 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.12), residues: 4634 helix: 0.29 (0.19), residues: 931 sheet: -0.32 (0.15), residues: 1162 loop : -1.52 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 519 HIS 0.006 0.001 HIS H 544 PHE 0.022 0.001 PHE B 727 TYR 0.014 0.001 TYR A 366 ARG 0.002 0.000 ARG F 595 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 144 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 276 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8065 (p0) REVERT: B 287 ARG cc_start: 0.7715 (mtm110) cc_final: 0.7450 (ttp80) REVERT: C 556 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: C 595 ARG cc_start: 0.8311 (ttm110) cc_final: 0.7788 (ttp-110) REVERT: D 207 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9011 (mp) REVERT: D 541 GLN cc_start: 0.7412 (mt0) cc_final: 0.7029 (mt0) REVERT: D 561 ASN cc_start: 0.8493 (t0) cc_final: 0.7987 (t0) REVERT: E 263 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.6955 (p-80) REVERT: E 629 LEU cc_start: 0.2320 (OUTLIER) cc_final: 0.1807 (tp) REVERT: E 702 THR cc_start: 0.1434 (OUTLIER) cc_final: 0.0966 (p) REVERT: F 276 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7353 (p0) REVERT: F 568 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: F 591 ILE cc_start: 0.8686 (mt) cc_final: 0.8305 (tt) REVERT: F 595 ARG cc_start: 0.7726 (mtm110) cc_final: 0.7326 (mtm110) REVERT: F 702 THR cc_start: 0.0573 (OUTLIER) cc_final: -0.0031 (p) REVERT: G 537 ASN cc_start: 0.8150 (p0) cc_final: 0.7854 (p0) REVERT: G 600 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.5787 (mtm110) REVERT: H 77 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7578 (p0) REVERT: H 95 MET cc_start: 0.8013 (ttt) cc_final: 0.7560 (tmt) REVERT: H 196 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7760 (t80) REVERT: H 372 LEU cc_start: 0.1644 (OUTLIER) cc_final: 0.1375 (pp) outliers start: 94 outliers final: 69 residues processed: 229 average time/residue: 0.4837 time to fit residues: 185.2772 Evaluate side-chains 218 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 136 time to evaluate : 4.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 539 ASN Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 669 ARG Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain E residue 702 THR Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 568 GLU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 600 ARG Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain G residue 725 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 323 ASP Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 375 LEU Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 447 ASN Chi-restraints excluded: chain H residue 537 THR Chi-restraints excluded: chain H residue 661 VAL Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 752 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 406 optimal weight: 0.0980 chunk 428 optimal weight: 50.0000 chunk 390 optimal weight: 50.0000 chunk 416 optimal weight: 9.9990 chunk 250 optimal weight: 0.6980 chunk 181 optimal weight: 20.0000 chunk 327 optimal weight: 50.0000 chunk 127 optimal weight: 30.0000 chunk 376 optimal weight: 6.9990 chunk 394 optimal weight: 7.9990 chunk 415 optimal weight: 5.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN B 336 HIS ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN D 389 GLN E 424 GLN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 682 ASN ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 HIS ** H 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 37581 Z= 0.468 Angle : 0.588 10.755 50913 Z= 0.313 Chirality : 0.049 0.178 5776 Planarity : 0.004 0.058 6668 Dihedral : 5.000 45.954 5009 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.57 % Favored : 94.41 % Rotamer: Outliers : 2.45 % Allowed : 17.94 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.12), residues: 4634 helix: 0.13 (0.18), residues: 932 sheet: -0.43 (0.15), residues: 1155 loop : -1.63 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 226 HIS 0.008 0.001 HIS B 263 PHE 0.021 0.002 PHE B 727 TYR 0.022 0.002 TYR A 366 ARG 0.004 0.000 ARG H 580 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 135 time to evaluate : 4.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 276 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8101 (p0) REVERT: B 287 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7540 (ttp80) REVERT: C 595 ARG cc_start: 0.8379 (ttm110) cc_final: 0.7833 (ttp-110) REVERT: D 207 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9033 (mp) REVERT: D 356 ASP cc_start: 0.7883 (t0) cc_final: 0.7494 (t0) REVERT: D 561 ASN cc_start: 0.8466 (t0) cc_final: 0.7966 (t0) REVERT: E 263 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.6997 (p-80) REVERT: E 629 LEU cc_start: 0.2370 (OUTLIER) cc_final: 0.1876 (tp) REVERT: E 702 THR cc_start: 0.1466 (OUTLIER) cc_final: 0.0995 (p) REVERT: F 276 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7443 (p0) REVERT: F 568 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: F 591 ILE cc_start: 0.8700 (mt) cc_final: 0.8331 (tt) REVERT: F 702 THR cc_start: 0.0535 (OUTLIER) cc_final: -0.0088 (p) REVERT: G 600 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.5992 (mmt180) REVERT: H 77 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7403 (p0) REVERT: H 95 MET cc_start: 0.8285 (ttt) cc_final: 0.7979 (tmt) REVERT: H 196 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7783 (t80) REVERT: H 372 LEU cc_start: 0.1496 (OUTLIER) cc_final: 0.1233 (pp) outliers start: 102 outliers final: 81 residues processed: 229 average time/residue: 0.5010 time to fit residues: 191.5886 Evaluate side-chains 226 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 133 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 539 ASN Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 587 MET Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 669 ARG Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain E residue 702 THR Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 568 GLU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 600 ARG Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 125 ASP Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 323 ASP Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 375 LEU Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 447 ASN Chi-restraints excluded: chain H residue 537 THR Chi-restraints excluded: chain H residue 661 VAL Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 752 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 0.0010 chunk 440 optimal weight: 6.9990 chunk 268 optimal weight: 40.0000 chunk 209 optimal weight: 0.7980 chunk 306 optimal weight: 0.5980 chunk 462 optimal weight: 9.9990 chunk 425 optimal weight: 1.9990 chunk 368 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 284 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN B 326 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN D 389 GLN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 682 ASN G 560 GLN H 697 ASN ** H 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 37581 Z= 0.144 Angle : 0.478 10.629 50913 Z= 0.252 Chirality : 0.044 0.192 5776 Planarity : 0.003 0.058 6668 Dihedral : 4.582 45.037 5009 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.10 % Favored : 95.88 % Rotamer: Outliers : 1.80 % Allowed : 18.73 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.12), residues: 4634 helix: 0.41 (0.19), residues: 932 sheet: -0.23 (0.15), residues: 1092 loop : -1.38 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 519 HIS 0.006 0.001 HIS H 544 PHE 0.018 0.001 PHE B 727 TYR 0.013 0.001 TYR F 411 ARG 0.016 0.000 ARG F 595 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 138 time to evaluate : 4.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 ARG cc_start: 0.7712 (mtm110) cc_final: 0.7452 (ttp80) REVERT: C 556 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: C 595 ARG cc_start: 0.8303 (ttm110) cc_final: 0.7853 (ttp-110) REVERT: D 207 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9041 (mp) REVERT: D 541 GLN cc_start: 0.7363 (mt0) cc_final: 0.7000 (mt0) REVERT: D 561 ASN cc_start: 0.8486 (t0) cc_final: 0.7989 (t0) REVERT: E 263 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.6941 (p-80) REVERT: E 702 THR cc_start: 0.1464 (OUTLIER) cc_final: 0.0989 (p) REVERT: F 276 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7337 (p0) REVERT: F 568 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: F 591 ILE cc_start: 0.8678 (mt) cc_final: 0.8282 (tt) REVERT: F 702 THR cc_start: 0.0589 (OUTLIER) cc_final: -0.0054 (p) REVERT: G 537 ASN cc_start: 0.8098 (p0) cc_final: 0.7797 (p0) REVERT: G 600 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6024 (mmt180) REVERT: G 662 MET cc_start: 0.0353 (ptt) cc_final: 0.0057 (ptm) REVERT: H 77 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7669 (p0) REVERT: H 95 MET cc_start: 0.8062 (ttt) cc_final: 0.7720 (tmt) REVERT: H 196 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7738 (t80) REVERT: H 372 LEU cc_start: 0.1899 (OUTLIER) cc_final: 0.1628 (pp) REVERT: H 751 GLU cc_start: 0.6928 (pp20) cc_final: 0.6518 (pp20) outliers start: 75 outliers final: 57 residues processed: 208 average time/residue: 0.4895 time to fit residues: 170.6862 Evaluate side-chains 203 residues out of total 4161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 135 time to evaluate : 4.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 539 ASN Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 587 MET Chi-restraints excluded: chain E residue 669 ARG Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain E residue 702 THR Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 568 GLU Chi-restraints excluded: chain F residue 679 LYS Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 600 ARG Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain G residue 725 LEU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 323 ASP Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 375 LEU Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 447 ASN Chi-restraints excluded: chain H residue 537 THR Chi-restraints excluded: chain H residue 661 VAL Chi-restraints excluded: chain H residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 20.0000 chunk 392 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 339 optimal weight: 5.9990 chunk 54 optimal weight: 0.0970 chunk 102 optimal weight: 8.9990 chunk 368 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 378 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 overall best weight: 3.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN B 326 ASN B 336 HIS ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN E 424 GLN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 682 ASN H 697 ASN ** H 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.156312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.092134 restraints weight = 69727.506| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.03 r_work: 0.2695 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 37581 Z= 0.385 Angle : 0.548 10.620 50913 Z= 0.290 Chirality : 0.047 0.176 5776 Planarity : 0.004 0.058 6668 Dihedral : 4.767 43.733 5009 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.31 % Favored : 94.67 % Rotamer: Outliers : 1.88 % Allowed : 18.73 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.12), residues: 4634 helix: 0.33 (0.19), residues: 933 sheet: -0.24 (0.15), residues: 1162 loop : -1.49 (0.12), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 226 HIS 0.007 0.001 HIS B 263 PHE 0.018 0.001 PHE B 727 TYR 0.018 0.001 TYR A 366 ARG 0.008 0.000 ARG F 595 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7978.53 seconds wall clock time: 146 minutes 42.46 seconds (8802.46 seconds total)