Starting phenix.real_space_refine on Mon Mar 25 05:51:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2w_11050/03_2024/6z2w_11050_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2w_11050/03_2024/6z2w_11050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2w_11050/03_2024/6z2w_11050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2w_11050/03_2024/6z2w_11050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2w_11050/03_2024/6z2w_11050_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2w_11050/03_2024/6z2w_11050_updated.pdb" } resolution = 2.82 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= 0.022 sd= 0.916 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 Mg 4 5.21 5 S 200 5.16 5 C 29974 2.51 5 N 7772 2.21 5 O 8630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ARG 228": "NH1" <-> "NH2" Residue "D ARG 228": "NH1" <-> "NH2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "D ARG 331": "NH1" <-> "NH2" Residue "D ARG 377": "NH1" <-> "NH2" Residue "D ARG 451": "NH1" <-> "NH2" Residue "D PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D ARG 664": "NH1" <-> "NH2" Residue "D ARG 704": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C ARG 377": "NH1" <-> "NH2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C ARG 664": "NH1" <-> "NH2" Residue "C ARG 704": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 352": "NH1" <-> "NH2" Residue "E ARG 353": "NH1" <-> "NH2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 416": "NH1" <-> "NH2" Residue "E ARG 464": "NH1" <-> "NH2" Residue "E PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 504": "NH1" <-> "NH2" Residue "E ARG 520": "NH1" <-> "NH2" Residue "E ARG 549": "NH1" <-> "NH2" Residue "E ARG 582": "NH1" <-> "NH2" Residue "E ARG 585": "NH1" <-> "NH2" Residue "E TYR 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 985": "NH1" <-> "NH2" Residue "E ARG 1135": "NH1" <-> "NH2" Residue "E ARG 1284": "NH1" <-> "NH2" Residue "E ARG 1403": "NH1" <-> "NH2" Residue "E ARG 1412": "NH1" <-> "NH2" Residue "E ARG 1456": "NH1" <-> "NH2" Residue "E PHE 1458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1498": "NH1" <-> "NH2" Residue "E ARG 1670": "NH1" <-> "NH2" Residue "E ARG 1760": "NH1" <-> "NH2" Residue "E ARG 1845": "NH1" <-> "NH2" Residue "E ARG 1949": "NH1" <-> "NH2" Residue "E ARG 1961": "NH1" <-> "NH2" Residue "E ARG 1983": "NH1" <-> "NH2" Residue "E PHE 2004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2048": "NH1" <-> "NH2" Residue "E ARG 2108": "NH1" <-> "NH2" Residue "E TYR 2117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2123": "NH1" <-> "NH2" Residue "E ARG 2161": "NH1" <-> "NH2" Residue "E ARG 2253": "NH1" <-> "NH2" Residue "E ARG 2263": "NH1" <-> "NH2" Residue "E ARG 2293": "NH1" <-> "NH2" Residue "E ARG 2310": "NH1" <-> "NH2" Residue "E ARG 2328": "NH1" <-> "NH2" Residue "E PHE 2367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "F PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F ARG 353": "NH1" <-> "NH2" Residue "F TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 416": "NH1" <-> "NH2" Residue "F ARG 464": "NH1" <-> "NH2" Residue "F PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 504": "NH1" <-> "NH2" Residue "F ARG 520": "NH1" <-> "NH2" Residue "F ARG 549": "NH1" <-> "NH2" Residue "F ARG 582": "NH1" <-> "NH2" Residue "F ARG 585": "NH1" <-> "NH2" Residue "F TYR 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 985": "NH1" <-> "NH2" Residue "F ARG 1135": "NH1" <-> "NH2" Residue "F ARG 1284": "NH1" <-> "NH2" Residue "F ARG 1403": "NH1" <-> "NH2" Residue "F ARG 1412": "NH1" <-> "NH2" Residue "F ARG 1456": "NH1" <-> "NH2" Residue "F PHE 1458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1498": "NH1" <-> "NH2" Residue "F ARG 1670": "NH1" <-> "NH2" Residue "F ARG 1760": "NH1" <-> "NH2" Residue "F ARG 1845": "NH1" <-> "NH2" Residue "F ARG 1949": "NH1" <-> "NH2" Residue "F ARG 1961": "NH1" <-> "NH2" Residue "F ARG 1983": "NH1" <-> "NH2" Residue "F PHE 2004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 2048": "NH1" <-> "NH2" Residue "F ARG 2108": "NH1" <-> "NH2" Residue "F TYR 2117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 2123": "NH1" <-> "NH2" Residue "F ARG 2161": "NH1" <-> "NH2" Residue "F ARG 2253": "NH1" <-> "NH2" Residue "F ARG 2263": "NH1" <-> "NH2" Residue "F ARG 2293": "NH1" <-> "NH2" Residue "F ARG 2310": "NH1" <-> "NH2" Residue "F ARG 2328": "NH1" <-> "NH2" Residue "F PHE 2367": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46588 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 4576 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 558, 4565 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 542} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Conformer: "B" Number of residues, atoms: 558, 4565 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 542} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 bond proxies already assigned to first conformer: 4641 Chain: "C" Number of atoms: 4576 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 558, 4565 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 542} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Conformer: "B" Number of residues, atoms: 558, 4565 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 542} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 bond proxies already assigned to first conformer: 4641 Chain: "E" Number of atoms: 18682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2325, 18682 Classifications: {'peptide': 2325} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 2255} Chain breaks: 6 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "F" Number of atoms: 18682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2325, 18682 Classifications: {'peptide': 2325} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 2255} Chain breaks: 6 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG D 228 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 228 " occ=0.50 residue: pdb=" N AARG C 228 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 228 " occ=0.50 Time building chain proxies: 26.75, per 1000 atoms: 0.57 Number of scatterers: 46588 At special positions: 0 Unit cell: (130.38, 227.9, 186.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 200 16.00 P 6 15.00 Mg 4 11.99 O 8630 8.00 N 7772 7.00 C 29974 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: 17.59 Conformation dependent library (CDL) restraints added in 10.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E2402 " pdb="ZN ZN E2402 " - pdb=" NE2 HIS E 553 " pdb=" ZN F2402 " pdb="ZN ZN F2402 " - pdb=" NE2 HIS F 553 " 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 284 helices and 6 sheets defined 57.1% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 17.54 Creating SS restraints... Processing helix chain 'D' and resid 202 through 211 Processing helix chain 'D' and resid 222 through 228 removed outlier: 4.160A pdb=" N AARG D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 264 removed outlier: 3.825A pdb=" N LYS D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 286 removed outlier: 3.900A pdb=" N ASP D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 307 removed outlier: 4.553A pdb=" N PHE D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 332 Processing helix chain 'D' and resid 356 through 380 Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 393 through 406 Processing helix chain 'D' and resid 415 through 433 removed outlier: 3.744A pdb=" N SER D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 447 through 461 removed outlier: 4.231A pdb=" N THR D 455 " --> pdb=" O ARG D 451 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG D 456 " --> pdb=" O ASP D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'D' and resid 501 through 507 removed outlier: 3.760A pdb=" N SER D 505 " --> pdb=" O GLY D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 562 removed outlier: 3.699A pdb=" N MET D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 592 removed outlier: 4.158A pdb=" N SER D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET D 589 " --> pdb=" O GLU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 621 removed outlier: 3.903A pdb=" N ILE D 608 " --> pdb=" O ARG D 604 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU D 609 " --> pdb=" O CYS D 605 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR D 613 " --> pdb=" O GLU D 609 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU D 618 " --> pdb=" O ILE D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 625 No H-bonds generated for 'chain 'D' and resid 623 through 625' Processing helix chain 'D' and resid 628 through 634 removed outlier: 3.593A pdb=" N LYS D 632 " --> pdb=" O GLU D 628 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 633 " --> pdb=" O GLU D 629 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 628 through 634' Processing helix chain 'D' and resid 636 through 649 removed outlier: 3.648A pdb=" N PHE D 645 " --> pdb=" O SER D 641 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N CYS D 648 " --> pdb=" O ARG D 644 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN D 649 " --> pdb=" O PHE D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 667 removed outlier: 3.893A pdb=" N ASP D 662 " --> pdb=" O ARG D 658 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 666 " --> pdb=" O ASP D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 697 through 709 removed outlier: 5.340A pdb=" N ASN D 702 " --> pdb=" O LYS D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 725 removed outlier: 3.717A pdb=" N ILE D 724 " --> pdb=" O MET D 720 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU D 725 " --> pdb=" O ALA D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 742 removed outlier: 3.843A pdb=" N ASP D 739 " --> pdb=" O LEU D 735 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 740 " --> pdb=" O GLU D 736 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 211 Processing helix chain 'C' and resid 222 through 228 removed outlier: 4.162A pdb=" N AARG C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 264 removed outlier: 3.835A pdb=" N LYS C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 286 removed outlier: 3.907A pdb=" N ASP C 272 " --> pdb=" O ASP C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 307 removed outlier: 4.552A pdb=" N PHE C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 332 Processing helix chain 'C' and resid 356 through 380 Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 415 through 433 removed outlier: 3.743A pdb=" N SER C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 444 Processing helix chain 'C' and resid 447 through 461 removed outlier: 4.233A pdb=" N THR C 455 " --> pdb=" O ARG C 451 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 469 No H-bonds generated for 'chain 'C' and resid 467 through 469' Processing helix chain 'C' and resid 501 through 507 removed outlier: 3.760A pdb=" N SER C 505 " --> pdb=" O GLY C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 562 removed outlier: 3.701A pdb=" N MET C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 592 removed outlier: 4.156A pdb=" N SER C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET C 589 " --> pdb=" O GLU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 621 removed outlier: 3.905A pdb=" N ILE C 608 " --> pdb=" O ARG C 604 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU C 609 " --> pdb=" O CYS C 605 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR C 613 " --> pdb=" O GLU C 609 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 618 " --> pdb=" O ILE C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 625 No H-bonds generated for 'chain 'C' and resid 623 through 625' Processing helix chain 'C' and resid 628 through 634 removed outlier: 3.596A pdb=" N LYS C 632 " --> pdb=" O GLU C 628 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 633 " --> pdb=" O GLU C 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 628 through 634' Processing helix chain 'C' and resid 636 through 649 removed outlier: 3.640A pdb=" N PHE C 645 " --> pdb=" O SER C 641 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N CYS C 648 " --> pdb=" O ARG C 644 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN C 649 " --> pdb=" O PHE C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 667 removed outlier: 3.895A pdb=" N ASP C 662 " --> pdb=" O ARG C 658 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 666 " --> pdb=" O ASP C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 680 Processing helix chain 'C' and resid 697 through 709 removed outlier: 5.338A pdb=" N ASN C 702 " --> pdb=" O LYS C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 725 removed outlier: 3.712A pdb=" N ILE C 724 " --> pdb=" O MET C 720 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 725 " --> pdb=" O ALA C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 742 removed outlier: 3.853A pdb=" N ASP C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER C 740 " --> pdb=" O GLU C 736 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 17 removed outlier: 3.829A pdb=" N LEU E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.913A pdb=" N ILE E 52 " --> pdb=" O ASN E 49 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU E 55 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS E 56 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 82 removed outlier: 4.248A pdb=" N THR E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 112 removed outlier: 3.607A pdb=" N ASP E 104 " --> pdb=" O GLN E 100 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP E 105 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE E 109 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER E 110 " --> pdb=" O PHE E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 129 removed outlier: 4.137A pdb=" N MET E 123 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.888A pdb=" N LYS E 143 " --> pdb=" O LYS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 160 removed outlier: 3.742A pdb=" N TYR E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 172 through 188 removed outlier: 3.731A pdb=" N PHE E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 228 removed outlier: 3.637A pdb=" N ASN E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG E 220 " --> pdb=" O GLN E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 252 removed outlier: 3.844A pdb=" N LYS E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE E 244 " --> pdb=" O GLN E 240 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 251 " --> pdb=" O VAL E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 283 Processing helix chain 'E' and resid 294 through 306 Processing helix chain 'E' and resid 312 through 318 removed outlier: 3.521A pdb=" N HIS E 318 " --> pdb=" O CYS E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 354 Processing helix chain 'E' and resid 391 through 402 removed outlier: 4.045A pdb=" N LYS E 395 " --> pdb=" O LYS E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 418 Processing helix chain 'E' and resid 432 through 444 removed outlier: 3.872A pdb=" N LEU E 436 " --> pdb=" O PHE E 432 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN E 437 " --> pdb=" O LYS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 470 removed outlier: 3.648A pdb=" N CYS E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 525 Processing helix chain 'E' and resid 532 through 534 No H-bonds generated for 'chain 'E' and resid 532 through 534' Processing helix chain 'E' and resid 537 through 553 Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'E' and resid 582 through 595 removed outlier: 4.308A pdb=" N ARG E 590 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE E 591 " --> pdb=" O LEU E 587 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE E 592 " --> pdb=" O SER E 588 " (cutoff:3.500A) Proline residue: E 593 - end of helix Processing helix chain 'E' and resid 607 through 617 removed outlier: 4.353A pdb=" N SER E 617 " --> pdb=" O LYS E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 635 removed outlier: 3.526A pdb=" N LYS E 624 " --> pdb=" O PRO E 621 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU E 625 " --> pdb=" O VAL E 622 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN E 626 " --> pdb=" O VAL E 623 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU E 627 " --> pdb=" O LYS E 624 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP E 631 " --> pdb=" O VAL E 628 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN E 633 " --> pdb=" O ALA E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 654 removed outlier: 3.741A pdb=" N ASP E 644 " --> pdb=" O ASN E 640 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 648 " --> pdb=" O ASP E 644 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE E 653 " --> pdb=" O LYS E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 659 through 675 Processing helix chain 'E' and resid 680 through 684 Processing helix chain 'E' and resid 688 through 691 No H-bonds generated for 'chain 'E' and resid 688 through 691' Processing helix chain 'E' and resid 694 through 696 No H-bonds generated for 'chain 'E' and resid 694 through 696' Processing helix chain 'E' and resid 703 through 713 Processing helix chain 'E' and resid 719 through 723 removed outlier: 3.914A pdb=" N ILE E 723 " --> pdb=" O THR E 719 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 719 through 723' Processing helix chain 'E' and resid 725 through 732 removed outlier: 3.594A pdb=" N ILE E 729 " --> pdb=" O GLN E 725 " (cutoff:3.500A) Proline residue: E 730 - end of helix No H-bonds generated for 'chain 'E' and resid 725 through 732' Processing helix chain 'E' and resid 741 through 748 Processing helix chain 'E' and resid 756 through 764 Processing helix chain 'E' and resid 768 through 777 Processing helix chain 'E' and resid 784 through 792 Processing helix chain 'E' and resid 810 through 819 removed outlier: 4.211A pdb=" N LEU E 819 " --> pdb=" O GLU E 815 " (cutoff:3.500A) Processing helix chain 'E' and resid 828 through 844 removed outlier: 3.723A pdb=" N ASN E 833 " --> pdb=" O SER E 829 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E 834 " --> pdb=" O ASP E 830 " (cutoff:3.500A) Processing helix chain 'E' and resid 856 through 859 removed outlier: 3.587A pdb=" N LYS E 859 " --> pdb=" O SER E 856 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 856 through 859' Processing helix chain 'E' and resid 869 through 877 removed outlier: 3.819A pdb=" N GLN E 877 " --> pdb=" O GLN E 873 " (cutoff:3.500A) Processing helix chain 'E' and resid 881 through 891 Processing helix chain 'E' and resid 900 through 915 Processing helix chain 'E' and resid 919 through 924 removed outlier: 3.977A pdb=" N ILE E 923 " --> pdb=" O LYS E 920 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER E 924 " --> pdb=" O SER E 921 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 938 removed outlier: 4.227A pdb=" N ILE E 931 " --> pdb=" O ALA E 927 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 943 through 955 removed outlier: 3.696A pdb=" N ARG E 955 " --> pdb=" O HIS E 951 " (cutoff:3.500A) Processing helix chain 'E' and resid 960 through 962 No H-bonds generated for 'chain 'E' and resid 960 through 962' Processing helix chain 'E' and resid 967 through 975 removed outlier: 3.778A pdb=" N PHE E 972 " --> pdb=" O SER E 968 " (cutoff:3.500A) Processing helix chain 'E' and resid 982 through 997 removed outlier: 3.754A pdb=" N THR E 994 " --> pdb=" O SER E 990 " (cutoff:3.500A) Processing helix chain 'E' and resid 1000 through 1004 Processing helix chain 'E' and resid 1009 through 1016 removed outlier: 3.859A pdb=" N LEU E1014 " --> pdb=" O THR E1010 " (cutoff:3.500A) Processing helix chain 'E' and resid 1023 through 1026 No H-bonds generated for 'chain 'E' and resid 1023 through 1026' Processing helix chain 'E' and resid 1028 through 1036 removed outlier: 3.792A pdb=" N MET E1032 " --> pdb=" O GLN E1028 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS E1035 " --> pdb=" O ARG E1031 " (cutoff:3.500A) Processing helix chain 'E' and resid 1043 through 1047 Processing helix chain 'E' and resid 1057 through 1075 removed outlier: 4.411A pdb=" N LEU E1062 " --> pdb=" O ILE E1058 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL E1067 " --> pdb=" O ASP E1063 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG E1070 " --> pdb=" O GLU E1066 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR E1074 " --> pdb=" O ARG E1070 " (cutoff:3.500A) Processing helix chain 'E' and resid 1091 through 1104 Processing helix chain 'E' and resid 1110 through 1123 Processing helix chain 'E' and resid 1149 through 1162 removed outlier: 3.773A pdb=" N LYS E1154 " --> pdb=" O VAL E1150 " (cutoff:3.500A) Processing helix chain 'E' and resid 1164 through 1169 removed outlier: 3.619A pdb=" N TRP E1169 " --> pdb=" O VAL E1165 " (cutoff:3.500A) Processing helix chain 'E' and resid 1174 through 1190 removed outlier: 3.703A pdb=" N LEU E1188 " --> pdb=" O ILE E1184 " (cutoff:3.500A) Processing helix chain 'E' and resid 1207 through 1215 removed outlier: 3.612A pdb=" N LEU E1212 " --> pdb=" O ASN E1208 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS E1215 " --> pdb=" O LYS E1211 " (cutoff:3.500A) Processing helix chain 'E' and resid 1218 through 1224 removed outlier: 4.749A pdb=" N THR E1223 " --> pdb=" O VAL E1219 " (cutoff:3.500A) Processing helix chain 'E' and resid 1226 through 1228 No H-bonds generated for 'chain 'E' and resid 1226 through 1228' Processing helix chain 'E' and resid 1254 through 1266 removed outlier: 3.643A pdb=" N LYS E1259 " --> pdb=" O LYS E1255 " (cutoff:3.500A) Processing helix chain 'E' and resid 1278 through 1282 Processing helix chain 'E' and resid 1289 through 1303 Proline residue: E1296 - end of helix Processing helix chain 'E' and resid 1314 through 1327 removed outlier: 3.595A pdb=" N ILE E1321 " --> pdb=" O ASN E1317 " (cutoff:3.500A) Processing helix chain 'E' and resid 1338 through 1369 removed outlier: 3.753A pdb=" N ILE E1349 " --> pdb=" O CYS E1345 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL E1352 " --> pdb=" O SER E1348 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE E1353 " --> pdb=" O ILE E1349 " (cutoff:3.500A) Processing helix chain 'E' and resid 1381 through 1391 removed outlier: 3.922A pdb=" N ARG E1387 " --> pdb=" O ASN E1383 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE E1388 " --> pdb=" O MET E1384 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP E1389 " --> pdb=" O LEU E1385 " (cutoff:3.500A) Processing helix chain 'E' and resid 1400 through 1405 Processing helix chain 'E' and resid 1410 through 1422 Processing helix chain 'E' and resid 1435 through 1438 No H-bonds generated for 'chain 'E' and resid 1435 through 1438' Processing helix chain 'E' and resid 1440 through 1443 No H-bonds generated for 'chain 'E' and resid 1440 through 1443' Processing helix chain 'E' and resid 1451 through 1455 Processing helix chain 'E' and resid 1463 through 1472 removed outlier: 3.506A pdb=" N GLU E1469 " --> pdb=" O SER E1465 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU E1470 " --> pdb=" O LYS E1466 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN E1471 " --> pdb=" O ILE E1467 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR E1472 " --> pdb=" O GLU E1468 " (cutoff:3.500A) Processing helix chain 'E' and resid 1476 through 1486 removed outlier: 3.505A pdb=" N ASP E1481 " --> pdb=" O LYS E1477 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS E1482 " --> pdb=" O LEU E1478 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL E1485 " --> pdb=" O ASP E1481 " (cutoff:3.500A) Processing helix chain 'E' and resid 1494 through 1505 removed outlier: 3.639A pdb=" N MET E1499 " --> pdb=" O THR E1495 " (cutoff:3.500A) Processing helix chain 'E' and resid 1509 through 1513 Processing helix chain 'E' and resid 1531 through 1544 removed outlier: 3.805A pdb=" N ILE E1537 " --> pdb=" O GLU E1533 " (cutoff:3.500A) Processing helix chain 'E' and resid 1548 through 1552 Processing helix chain 'E' and resid 1554 through 1558 Processing helix chain 'E' and resid 1567 through 1583 removed outlier: 4.205A pdb=" N LEU E1571 " --> pdb=" O ARG E1567 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN E1572 " --> pdb=" O GLU E1568 " (cutoff:3.500A) Processing helix chain 'E' and resid 1587 through 1603 Processing helix chain 'E' and resid 1618 through 1634 removed outlier: 3.958A pdb=" N LYS E1623 " --> pdb=" O ASN E1619 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP E1629 " --> pdb=" O HIS E1625 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU E1630 " --> pdb=" O SER E1626 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER E1631 " --> pdb=" O LEU E1627 " (cutoff:3.500A) Processing helix chain 'E' and resid 1639 through 1652 removed outlier: 3.897A pdb=" N SER E1644 " --> pdb=" O PHE E1640 " (cutoff:3.500A) Processing helix chain 'E' and resid 1660 through 1674 Processing helix chain 'E' and resid 1680 through 1699 removed outlier: 3.633A pdb=" N LYS E1688 " --> pdb=" O ALA E1684 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN E1699 " --> pdb=" O GLN E1695 " (cutoff:3.500A) Processing helix chain 'E' and resid 1703 through 1715 removed outlier: 3.587A pdb=" N SER E1707 " --> pdb=" O LEU E1703 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU E1708 " --> pdb=" O ASP E1704 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N HIS E1712 " --> pdb=" O GLU E1708 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS E1713 " --> pdb=" O SER E1709 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E1714 " --> pdb=" O LEU E1710 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU E1715 " --> pdb=" O MET E1711 " (cutoff:3.500A) Processing helix chain 'E' and resid 1721 through 1732 removed outlier: 3.786A pdb=" N ALA E1726 " --> pdb=" O GLU E1722 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU E1727 " --> pdb=" O LEU E1723 " (cutoff:3.500A) Processing helix chain 'E' and resid 1735 through 1750 removed outlier: 3.546A pdb=" N LYS E1748 " --> pdb=" O GLU E1744 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN E1750 " --> pdb=" O HIS E1746 " (cutoff:3.500A) Processing helix chain 'E' and resid 1761 through 1772 Processing helix chain 'E' and resid 1779 through 1792 removed outlier: 3.664A pdb=" N GLN E1785 " --> pdb=" O GLN E1781 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP E1788 " --> pdb=" O LYS E1784 " (cutoff:3.500A) Processing helix chain 'E' and resid 1798 through 1815 removed outlier: 5.187A pdb=" N GLU E1812 " --> pdb=" O SER E1808 " (cutoff:3.500A) Processing helix chain 'E' and resid 1824 through 1836 removed outlier: 3.815A pdb=" N ALA E1829 " --> pdb=" O PHE E1825 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E1835 " --> pdb=" O SER E1831 " (cutoff:3.500A) Processing helix chain 'E' and resid 1845 through 1864 Proline residue: E1849 - end of helix removed outlier: 3.950A pdb=" N ILE E1858 " --> pdb=" O PHE E1854 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA E1859 " --> pdb=" O TRP E1855 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA E1860 " --> pdb=" O LEU E1856 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E1863 " --> pdb=" O ALA E1859 " (cutoff:3.500A) Processing helix chain 'E' and resid 1873 through 1891 removed outlier: 4.073A pdb=" N SER E1883 " --> pdb=" O GLU E1879 " (cutoff:3.500A) Processing helix chain 'E' and resid 1895 through 1905 removed outlier: 3.871A pdb=" N PHE E1899 " --> pdb=" O ILE E1896 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N THR E1902 " --> pdb=" O PHE E1899 " (cutoff:3.500A) Processing helix chain 'E' and resid 1916 through 1928 removed outlier: 4.046A pdb=" N LEU E1923 " --> pdb=" O ILE E1919 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E1926 " --> pdb=" O ILE E1922 " (cutoff:3.500A) Processing helix chain 'E' and resid 1931 through 1941 removed outlier: 5.016A pdb=" N TRP E1936 " --> pdb=" O SER E1932 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR E1937 " --> pdb=" O HIS E1933 " (cutoff:3.500A) Processing helix chain 'E' and resid 1949 through 1962 removed outlier: 4.022A pdb=" N LYS E1959 " --> pdb=" O HIS E1955 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR E1960 " --> pdb=" O ILE E1956 " (cutoff:3.500A) Processing helix chain 'E' and resid 1970 through 1983 removed outlier: 3.648A pdb=" N ALA E1980 " --> pdb=" O ASP E1976 " (cutoff:3.500A) Processing helix chain 'E' and resid 2020 through 2023 No H-bonds generated for 'chain 'E' and resid 2020 through 2023' Processing helix chain 'E' and resid 2085 through 2101 removed outlier: 4.512A pdb=" N PHE E2099 " --> pdb=" O THR E2095 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU E2100 " --> pdb=" O THR E2096 " (cutoff:3.500A) Processing helix chain 'E' and resid 2105 through 2108 No H-bonds generated for 'chain 'E' and resid 2105 through 2108' Processing helix chain 'E' and resid 2138 through 2146 removed outlier: 3.700A pdb=" N THR E2144 " --> pdb=" O SER E2140 " (cutoff:3.500A) Processing helix chain 'E' and resid 2157 through 2164 removed outlier: 4.245A pdb=" N ARG E2161 " --> pdb=" O SER E2157 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP E2162 " --> pdb=" O LEU E2158 " (cutoff:3.500A) Processing helix chain 'E' and resid 2169 through 2180 removed outlier: 3.594A pdb=" N ASP E2179 " --> pdb=" O MET E2175 " (cutoff:3.500A) Processing helix chain 'E' and resid 2185 through 2191 removed outlier: 3.659A pdb=" N PHE E2189 " --> pdb=" O LEU E2185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU E2190 " --> pdb=" O TYR E2186 " (cutoff:3.500A) Processing helix chain 'E' and resid 2196 through 2219 removed outlier: 3.745A pdb=" N MET E2213 " --> pdb=" O SER E2209 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET E2215 " --> pdb=" O ALA E2211 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS E2218 " --> pdb=" O ALA E2214 " (cutoff:3.500A) Processing helix chain 'E' and resid 2250 through 2252 No H-bonds generated for 'chain 'E' and resid 2250 through 2252' Processing helix chain 'E' and resid 2266 through 2272 removed outlier: 4.169A pdb=" N ASP E2270 " --> pdb=" O PRO E2266 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E2271 " --> pdb=" O ASN E2267 " (cutoff:3.500A) Processing helix chain 'E' and resid 2280 through 2294 Processing helix chain 'E' and resid 2296 through 2309 removed outlier: 4.786A pdb=" N THR E2305 " --> pdb=" O ASN E2301 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE E2306 " --> pdb=" O VAL E2302 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N MET E2307 " --> pdb=" O ILE E2303 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR E2308 " --> pdb=" O GLU E2304 " (cutoff:3.500A) Processing helix chain 'E' and resid 2317 through 2328 Processing helix chain 'E' and resid 2340 through 2351 removed outlier: 3.532A pdb=" N GLU E2345 " --> pdb=" O ALA E2341 " (cutoff:3.500A) Processing helix chain 'E' and resid 2354 through 2357 No H-bonds generated for 'chain 'E' and resid 2354 through 2357' Processing helix chain 'F' and resid 5 through 17 removed outlier: 3.829A pdb=" N LEU F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 57 removed outlier: 3.913A pdb=" N ILE F 52 " --> pdb=" O ASN F 49 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU F 55 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS F 56 " --> pdb=" O ARG F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 82 removed outlier: 4.248A pdb=" N THR F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 112 removed outlier: 3.607A pdb=" N ASP F 104 " --> pdb=" O GLN F 100 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER F 110 " --> pdb=" O PHE F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 129 removed outlier: 4.136A pdb=" N MET F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS F 126 " --> pdb=" O PHE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 removed outlier: 3.888A pdb=" N LYS F 143 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 160 removed outlier: 3.741A pdb=" N TYR F 157 " --> pdb=" O THR F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 172 through 188 removed outlier: 3.731A pdb=" N PHE F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 228 removed outlier: 3.636A pdb=" N ASN F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG F 220 " --> pdb=" O GLN F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 252 removed outlier: 3.845A pdb=" N LYS F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR F 243 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE F 244 " --> pdb=" O GLN F 240 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL F 251 " --> pdb=" O VAL F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 283 Processing helix chain 'F' and resid 294 through 306 Processing helix chain 'F' and resid 312 through 318 removed outlier: 3.521A pdb=" N HIS F 318 " --> pdb=" O CYS F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 354 Processing helix chain 'F' and resid 391 through 402 removed outlier: 4.046A pdb=" N LYS F 395 " --> pdb=" O LYS F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 418 Processing helix chain 'F' and resid 432 through 444 removed outlier: 3.872A pdb=" N LEU F 436 " --> pdb=" O PHE F 432 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN F 437 " --> pdb=" O LYS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 470 removed outlier: 3.647A pdb=" N CYS F 467 " --> pdb=" O GLY F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 525 Processing helix chain 'F' and resid 532 through 534 No H-bonds generated for 'chain 'F' and resid 532 through 534' Processing helix chain 'F' and resid 537 through 553 Processing helix chain 'F' and resid 570 through 577 Processing helix chain 'F' and resid 582 through 595 removed outlier: 4.308A pdb=" N ARG F 590 " --> pdb=" O LEU F 586 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE F 591 " --> pdb=" O LEU F 587 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE F 592 " --> pdb=" O SER F 588 " (cutoff:3.500A) Proline residue: F 593 - end of helix Processing helix chain 'F' and resid 607 through 617 removed outlier: 4.354A pdb=" N SER F 617 " --> pdb=" O LYS F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 635 removed outlier: 3.526A pdb=" N LYS F 624 " --> pdb=" O PRO F 621 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU F 625 " --> pdb=" O VAL F 622 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN F 626 " --> pdb=" O VAL F 623 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU F 627 " --> pdb=" O LYS F 624 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP F 631 " --> pdb=" O VAL F 628 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN F 633 " --> pdb=" O ALA F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 654 removed outlier: 3.741A pdb=" N ASP F 644 " --> pdb=" O ASN F 640 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 648 " --> pdb=" O ASP F 644 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE F 653 " --> pdb=" O LYS F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 659 through 675 Processing helix chain 'F' and resid 680 through 684 Processing helix chain 'F' and resid 688 through 691 No H-bonds generated for 'chain 'F' and resid 688 through 691' Processing helix chain 'F' and resid 694 through 696 No H-bonds generated for 'chain 'F' and resid 694 through 696' Processing helix chain 'F' and resid 703 through 713 Processing helix chain 'F' and resid 719 through 723 removed outlier: 3.915A pdb=" N ILE F 723 " --> pdb=" O THR F 719 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 719 through 723' Processing helix chain 'F' and resid 725 through 732 removed outlier: 3.595A pdb=" N ILE F 729 " --> pdb=" O GLN F 725 " (cutoff:3.500A) Proline residue: F 730 - end of helix No H-bonds generated for 'chain 'F' and resid 725 through 732' Processing helix chain 'F' and resid 741 through 748 Processing helix chain 'F' and resid 756 through 764 Processing helix chain 'F' and resid 768 through 777 Processing helix chain 'F' and resid 784 through 792 Processing helix chain 'F' and resid 810 through 819 removed outlier: 4.212A pdb=" N LEU F 819 " --> pdb=" O GLU F 815 " (cutoff:3.500A) Processing helix chain 'F' and resid 828 through 845 removed outlier: 3.723A pdb=" N ASN F 833 " --> pdb=" O SER F 829 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 834 " --> pdb=" O ASP F 830 " (cutoff:3.500A) Processing helix chain 'F' and resid 856 through 859 removed outlier: 3.587A pdb=" N LYS F 859 " --> pdb=" O SER F 856 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 856 through 859' Processing helix chain 'F' and resid 869 through 877 removed outlier: 3.819A pdb=" N GLN F 877 " --> pdb=" O GLN F 873 " (cutoff:3.500A) Processing helix chain 'F' and resid 881 through 891 Processing helix chain 'F' and resid 900 through 915 Processing helix chain 'F' and resid 919 through 924 removed outlier: 3.977A pdb=" N ILE F 923 " --> pdb=" O LYS F 920 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER F 924 " --> pdb=" O SER F 921 " (cutoff:3.500A) Processing helix chain 'F' and resid 926 through 938 removed outlier: 4.227A pdb=" N ILE F 931 " --> pdb=" O ALA F 927 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR F 935 " --> pdb=" O ILE F 931 " (cutoff:3.500A) Processing helix chain 'F' and resid 943 through 955 removed outlier: 3.696A pdb=" N ARG F 955 " --> pdb=" O HIS F 951 " (cutoff:3.500A) Processing helix chain 'F' and resid 960 through 962 No H-bonds generated for 'chain 'F' and resid 960 through 962' Processing helix chain 'F' and resid 967 through 975 removed outlier: 3.778A pdb=" N PHE F 972 " --> pdb=" O SER F 968 " (cutoff:3.500A) Processing helix chain 'F' and resid 982 through 997 removed outlier: 3.754A pdb=" N THR F 994 " --> pdb=" O SER F 990 " (cutoff:3.500A) Processing helix chain 'F' and resid 1000 through 1004 Processing helix chain 'F' and resid 1009 through 1016 removed outlier: 3.859A pdb=" N LEU F1014 " --> pdb=" O THR F1010 " (cutoff:3.500A) Processing helix chain 'F' and resid 1023 through 1026 No H-bonds generated for 'chain 'F' and resid 1023 through 1026' Processing helix chain 'F' and resid 1028 through 1036 removed outlier: 3.793A pdb=" N MET F1032 " --> pdb=" O GLN F1028 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS F1035 " --> pdb=" O ARG F1031 " (cutoff:3.500A) Processing helix chain 'F' and resid 1043 through 1047 Processing helix chain 'F' and resid 1057 through 1075 removed outlier: 4.411A pdb=" N LEU F1062 " --> pdb=" O ILE F1058 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL F1067 " --> pdb=" O ASP F1063 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG F1070 " --> pdb=" O GLU F1066 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR F1074 " --> pdb=" O ARG F1070 " (cutoff:3.500A) Processing helix chain 'F' and resid 1091 through 1104 Processing helix chain 'F' and resid 1110 through 1123 Processing helix chain 'F' and resid 1149 through 1162 removed outlier: 3.773A pdb=" N LYS F1154 " --> pdb=" O VAL F1150 " (cutoff:3.500A) Processing helix chain 'F' and resid 1164 through 1169 removed outlier: 3.620A pdb=" N TRP F1169 " --> pdb=" O VAL F1165 " (cutoff:3.500A) Processing helix chain 'F' and resid 1174 through 1190 removed outlier: 3.703A pdb=" N LEU F1188 " --> pdb=" O ILE F1184 " (cutoff:3.500A) Processing helix chain 'F' and resid 1207 through 1215 removed outlier: 3.611A pdb=" N LEU F1212 " --> pdb=" O ASN F1208 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS F1215 " --> pdb=" O LYS F1211 " (cutoff:3.500A) Processing helix chain 'F' and resid 1218 through 1224 removed outlier: 4.750A pdb=" N THR F1223 " --> pdb=" O VAL F1219 " (cutoff:3.500A) Processing helix chain 'F' and resid 1226 through 1228 No H-bonds generated for 'chain 'F' and resid 1226 through 1228' Processing helix chain 'F' and resid 1254 through 1266 removed outlier: 3.642A pdb=" N LYS F1259 " --> pdb=" O LYS F1255 " (cutoff:3.500A) Processing helix chain 'F' and resid 1278 through 1282 Processing helix chain 'F' and resid 1289 through 1303 Proline residue: F1296 - end of helix Processing helix chain 'F' and resid 1314 through 1327 removed outlier: 3.595A pdb=" N ILE F1321 " --> pdb=" O ASN F1317 " (cutoff:3.500A) Processing helix chain 'F' and resid 1338 through 1369 removed outlier: 3.753A pdb=" N ILE F1349 " --> pdb=" O CYS F1345 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL F1352 " --> pdb=" O SER F1348 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE F1353 " --> pdb=" O ILE F1349 " (cutoff:3.500A) Processing helix chain 'F' and resid 1381 through 1391 removed outlier: 3.923A pdb=" N ARG F1387 " --> pdb=" O ASN F1383 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE F1388 " --> pdb=" O MET F1384 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP F1389 " --> pdb=" O LEU F1385 " (cutoff:3.500A) Processing helix chain 'F' and resid 1400 through 1405 Processing helix chain 'F' and resid 1410 through 1422 Processing helix chain 'F' and resid 1435 through 1438 No H-bonds generated for 'chain 'F' and resid 1435 through 1438' Processing helix chain 'F' and resid 1440 through 1443 No H-bonds generated for 'chain 'F' and resid 1440 through 1443' Processing helix chain 'F' and resid 1451 through 1455 Processing helix chain 'F' and resid 1463 through 1472 removed outlier: 3.506A pdb=" N GLU F1469 " --> pdb=" O SER F1465 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU F1470 " --> pdb=" O LYS F1466 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN F1471 " --> pdb=" O ILE F1467 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR F1472 " --> pdb=" O GLU F1468 " (cutoff:3.500A) Processing helix chain 'F' and resid 1476 through 1486 removed outlier: 3.505A pdb=" N ASP F1481 " --> pdb=" O LYS F1477 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS F1482 " --> pdb=" O LEU F1478 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL F1485 " --> pdb=" O ASP F1481 " (cutoff:3.500A) Processing helix chain 'F' and resid 1494 through 1505 removed outlier: 3.639A pdb=" N MET F1499 " --> pdb=" O THR F1495 " (cutoff:3.500A) Processing helix chain 'F' and resid 1509 through 1513 Processing helix chain 'F' and resid 1531 through 1544 removed outlier: 3.805A pdb=" N ILE F1537 " --> pdb=" O GLU F1533 " (cutoff:3.500A) Processing helix chain 'F' and resid 1548 through 1552 Processing helix chain 'F' and resid 1554 through 1558 Processing helix chain 'F' and resid 1567 through 1583 removed outlier: 4.205A pdb=" N LEU F1571 " --> pdb=" O ARG F1567 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN F1572 " --> pdb=" O GLU F1568 " (cutoff:3.500A) Processing helix chain 'F' and resid 1587 through 1603 Processing helix chain 'F' and resid 1618 through 1634 removed outlier: 3.958A pdb=" N LYS F1623 " --> pdb=" O ASN F1619 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP F1629 " --> pdb=" O HIS F1625 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU F1630 " --> pdb=" O SER F1626 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER F1631 " --> pdb=" O LEU F1627 " (cutoff:3.500A) Processing helix chain 'F' and resid 1639 through 1652 removed outlier: 3.897A pdb=" N SER F1644 " --> pdb=" O PHE F1640 " (cutoff:3.500A) Processing helix chain 'F' and resid 1660 through 1674 Processing helix chain 'F' and resid 1680 through 1699 removed outlier: 3.633A pdb=" N LYS F1688 " --> pdb=" O ALA F1684 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN F1699 " --> pdb=" O GLN F1695 " (cutoff:3.500A) Processing helix chain 'F' and resid 1703 through 1715 removed outlier: 3.588A pdb=" N SER F1707 " --> pdb=" O LEU F1703 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU F1708 " --> pdb=" O ASP F1704 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N HIS F1712 " --> pdb=" O GLU F1708 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS F1713 " --> pdb=" O SER F1709 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU F1714 " --> pdb=" O LEU F1710 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU F1715 " --> pdb=" O MET F1711 " (cutoff:3.500A) Processing helix chain 'F' and resid 1721 through 1732 removed outlier: 3.787A pdb=" N ALA F1726 " --> pdb=" O GLU F1722 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU F1727 " --> pdb=" O LEU F1723 " (cutoff:3.500A) Processing helix chain 'F' and resid 1735 through 1750 removed outlier: 3.546A pdb=" N LYS F1748 " --> pdb=" O GLU F1744 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN F1750 " --> pdb=" O HIS F1746 " (cutoff:3.500A) Processing helix chain 'F' and resid 1761 through 1772 Processing helix chain 'F' and resid 1779 through 1792 removed outlier: 3.664A pdb=" N GLN F1785 " --> pdb=" O GLN F1781 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP F1788 " --> pdb=" O LYS F1784 " (cutoff:3.500A) Processing helix chain 'F' and resid 1798 through 1815 removed outlier: 5.187A pdb=" N GLU F1812 " --> pdb=" O SER F1808 " (cutoff:3.500A) Processing helix chain 'F' and resid 1824 through 1836 removed outlier: 3.814A pdb=" N ALA F1829 " --> pdb=" O PHE F1825 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU F1835 " --> pdb=" O SER F1831 " (cutoff:3.500A) Processing helix chain 'F' and resid 1845 through 1864 Proline residue: F1849 - end of helix removed outlier: 3.950A pdb=" N ILE F1858 " --> pdb=" O PHE F1854 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA F1859 " --> pdb=" O TRP F1855 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA F1860 " --> pdb=" O LEU F1856 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE F1863 " --> pdb=" O ALA F1859 " (cutoff:3.500A) Processing helix chain 'F' and resid 1873 through 1891 removed outlier: 4.073A pdb=" N SER F1883 " --> pdb=" O GLU F1879 " (cutoff:3.500A) Processing helix chain 'F' and resid 1895 through 1905 removed outlier: 3.871A pdb=" N PHE F1899 " --> pdb=" O ILE F1896 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N THR F1902 " --> pdb=" O PHE F1899 " (cutoff:3.500A) Processing helix chain 'F' and resid 1916 through 1928 removed outlier: 4.046A pdb=" N LEU F1923 " --> pdb=" O ILE F1919 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU F1926 " --> pdb=" O ILE F1922 " (cutoff:3.500A) Processing helix chain 'F' and resid 1931 through 1941 removed outlier: 5.016A pdb=" N TRP F1936 " --> pdb=" O SER F1932 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR F1937 " --> pdb=" O HIS F1933 " (cutoff:3.500A) Processing helix chain 'F' and resid 1949 through 1962 removed outlier: 4.022A pdb=" N LYS F1959 " --> pdb=" O HIS F1955 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR F1960 " --> pdb=" O ILE F1956 " (cutoff:3.500A) Processing helix chain 'F' and resid 1970 through 1983 removed outlier: 3.647A pdb=" N ALA F1980 " --> pdb=" O ASP F1976 " (cutoff:3.500A) Processing helix chain 'F' and resid 2020 through 2023 No H-bonds generated for 'chain 'F' and resid 2020 through 2023' Processing helix chain 'F' and resid 2085 through 2101 removed outlier: 4.512A pdb=" N PHE F2099 " --> pdb=" O THR F2095 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU F2100 " --> pdb=" O THR F2096 " (cutoff:3.500A) Processing helix chain 'F' and resid 2105 through 2108 No H-bonds generated for 'chain 'F' and resid 2105 through 2108' Processing helix chain 'F' and resid 2138 through 2146 removed outlier: 3.700A pdb=" N THR F2144 " --> pdb=" O SER F2140 " (cutoff:3.500A) Processing helix chain 'F' and resid 2157 through 2164 removed outlier: 4.244A pdb=" N ARG F2161 " --> pdb=" O SER F2157 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP F2162 " --> pdb=" O LEU F2158 " (cutoff:3.500A) Processing helix chain 'F' and resid 2169 through 2180 removed outlier: 3.594A pdb=" N ASP F2179 " --> pdb=" O MET F2175 " (cutoff:3.500A) Processing helix chain 'F' and resid 2185 through 2191 removed outlier: 3.660A pdb=" N PHE F2189 " --> pdb=" O LEU F2185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU F2190 " --> pdb=" O TYR F2186 " (cutoff:3.500A) Processing helix chain 'F' and resid 2196 through 2219 removed outlier: 3.745A pdb=" N MET F2213 " --> pdb=" O SER F2209 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET F2215 " --> pdb=" O ALA F2211 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS F2218 " --> pdb=" O ALA F2214 " (cutoff:3.500A) Processing helix chain 'F' and resid 2250 through 2252 No H-bonds generated for 'chain 'F' and resid 2250 through 2252' Processing helix chain 'F' and resid 2266 through 2272 removed outlier: 4.169A pdb=" N ASP F2270 " --> pdb=" O PRO F2266 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F2271 " --> pdb=" O ASN F2267 " (cutoff:3.500A) Processing helix chain 'F' and resid 2280 through 2294 Processing helix chain 'F' and resid 2296 through 2309 removed outlier: 4.786A pdb=" N THR F2305 " --> pdb=" O ASN F2301 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE F2306 " --> pdb=" O VAL F2302 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N MET F2307 " --> pdb=" O ILE F2303 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR F2308 " --> pdb=" O GLU F2304 " (cutoff:3.500A) Processing helix chain 'F' and resid 2317 through 2328 Processing helix chain 'F' and resid 2340 through 2351 removed outlier: 3.532A pdb=" N GLU F2345 " --> pdb=" O ALA F2341 " (cutoff:3.500A) Processing helix chain 'F' and resid 2354 through 2357 No H-bonds generated for 'chain 'F' and resid 2354 through 2357' Processing sheet with id= A, first strand: chain 'E' and resid 360 through 362 Processing sheet with id= B, first strand: chain 'E' and resid 2063 through 2068 removed outlier: 4.178A pdb=" N LYS E2063 " --> pdb=" O CYS E2079 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE E2077 " --> pdb=" O LEU E2065 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY E2076 " --> pdb=" O MET E2131 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG E2123 " --> pdb=" O CYS E2126 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE E2128 " --> pdb=" O SER E2121 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N SER E2121 " --> pdb=" O ILE E2128 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLU E2130 " --> pdb=" O VAL E2119 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL E2119 " --> pdb=" O GLU E2130 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 2135 through 2137 Processing sheet with id= D, first strand: chain 'F' and resid 360 through 362 Processing sheet with id= E, first strand: chain 'F' and resid 2063 through 2068 removed outlier: 4.178A pdb=" N LYS F2063 " --> pdb=" O CYS F2079 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE F2077 " --> pdb=" O LEU F2065 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY F2076 " --> pdb=" O MET F2131 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG F2123 " --> pdb=" O CYS F2126 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE F2128 " --> pdb=" O SER F2121 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N SER F2121 " --> pdb=" O ILE F2128 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLU F2130 " --> pdb=" O VAL F2119 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL F2119 " --> pdb=" O GLU F2130 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 2135 through 2137 1854 hydrogen bonds defined for protein. 5424 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: 18.60 Time building geometry restraints manager: 18.94 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: 8410 1.32 - 1.45: 11906 1.45 - 1.57: 26880 1.57 - 1.69: 16 1.69 - 1.81: 320 Bond restraints: 47532 Sorted by residual: bond pdb=" O3A ANP F2401 " pdb=" PB ANP F2401 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.44e+01 bond pdb=" O3A ANP E2401 " pdb=" PB ANP E2401 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" CA LEU F2244 " pdb=" C LEU F2244 " ideal model delta sigma weight residual 1.523 1.434 0.089 1.34e-02 5.57e+03 4.41e+01 bond pdb=" CA LEU E2244 " pdb=" C LEU E2244 " ideal model delta sigma weight residual 1.523 1.435 0.088 1.34e-02 5.57e+03 4.35e+01 bond pdb=" N3B ANP E2401 " pdb=" PG ANP E2401 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.91e+01 ... (remaining 47527 not shown) Histogram of bond angle deviations from ideal: 96.12 - 104.82: 636 104.82 - 113.53: 26762 113.53 - 122.23: 29956 122.23 - 130.93: 6772 130.93 - 139.63: 236 Bond angle restraints: 64362 Sorted by residual: angle pdb=" N ASP E2245 " pdb=" CA ASP E2245 " pdb=" C ASP E2245 " ideal model delta sigma weight residual 111.14 102.88 8.26 1.08e+00 8.57e-01 5.85e+01 angle pdb=" N ASP F2245 " pdb=" CA ASP F2245 " pdb=" C ASP F2245 " ideal model delta sigma weight residual 111.14 102.93 8.21 1.08e+00 8.57e-01 5.79e+01 angle pdb=" C ALA C 295 " pdb=" N VAL C 296 " pdb=" CA VAL C 296 " ideal model delta sigma weight residual 120.24 124.56 -4.32 6.30e-01 2.52e+00 4.70e+01 angle pdb=" N ILE E1863 " pdb=" CA ILE E1863 " pdb=" C ILE E1863 " ideal model delta sigma weight residual 113.53 107.41 6.12 9.80e-01 1.04e+00 3.90e+01 angle pdb=" N ILE F1863 " pdb=" CA ILE F1863 " pdb=" C ILE F1863 " ideal model delta sigma weight residual 113.53 107.42 6.11 9.80e-01 1.04e+00 3.88e+01 ... (remaining 64357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 28502 35.96 - 71.93: 255 71.93 - 107.89: 7 107.89 - 143.85: 0 143.85 - 179.82: 2 Dihedral angle restraints: 28766 sinusoidal: 11636 harmonic: 17130 Sorted by residual: dihedral pdb=" CD BARG C 228 " pdb=" NE BARG C 228 " pdb=" CZ BARG C 228 " pdb=" NH1BARG C 228 " ideal model delta sinusoidal sigma weight residual 0.00 179.82 -179.82 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG D 228 " pdb=" NE BARG D 228 " pdb=" CZ BARG D 228 " pdb=" NH1BARG D 228 " ideal model delta sinusoidal sigma weight residual 0.00 179.72 -179.72 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA ASN E1752 " pdb=" C ASN E1752 " pdb=" N SER E1753 " pdb=" CA SER E1753 " ideal model delta harmonic sigma weight residual -180.00 -131.57 -48.43 0 5.00e+00 4.00e-02 9.38e+01 ... (remaining 28763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 6143 0.084 - 0.169: 1116 0.169 - 0.253: 97 0.253 - 0.337: 15 0.337 - 0.422: 5 Chirality restraints: 7376 Sorted by residual: chirality pdb=" CA LEU F2244 " pdb=" N LEU F2244 " pdb=" C LEU F2244 " pdb=" CB LEU F2244 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA LEU E2244 " pdb=" N LEU E2244 " pdb=" C LEU E2244 " pdb=" CB LEU E2244 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CG LEU F2244 " pdb=" CB LEU F2244 " pdb=" CD1 LEU F2244 " pdb=" CD2 LEU F2244 " both_signs ideal model delta sigma weight residual False -2.59 -2.94 0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 7373 not shown) Planarity restraints: 8094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E1770 " -0.043 2.00e-02 2.50e+03 2.98e-02 2.23e+01 pdb=" CG TRP E1770 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP E1770 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E1770 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E1770 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E1770 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E1770 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E1770 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP E1770 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E1770 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F1770 " 0.043 2.00e-02 2.50e+03 2.98e-02 2.22e+01 pdb=" CG TRP F1770 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP F1770 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP F1770 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F1770 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F1770 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP F1770 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F1770 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP F1770 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F1770 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 470 " -0.020 2.00e-02 2.50e+03 3.89e-02 1.52e+01 pdb=" C VAL C 470 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL C 470 " -0.025 2.00e-02 2.50e+03 pdb=" N TYR C 471 " -0.023 2.00e-02 2.50e+03 ... (remaining 8091 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 647 2.64 - 3.20: 43231 3.20 - 3.77: 75604 3.77 - 4.33: 104969 4.33 - 4.90: 164927 Nonbonded interactions: 389378 Sorted by model distance: nonbonded pdb=" O1G ANP F2401 " pdb="MG MG F2403 " model vdw 2.071 2.170 nonbonded pdb=" O1G ANP E2401 " pdb="MG MG E2403 " model vdw 2.075 2.170 nonbonded pdb=" O1B ANP E2401 " pdb="MG MG E2404 " model vdw 2.083 2.170 nonbonded pdb=" O1B ANP F2401 " pdb="MG MG F2404 " model vdw 2.084 2.170 nonbonded pdb=" OD2 ASP E2243 " pdb="MG MG E2403 " model vdw 2.134 2.170 ... (remaining 389373 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 'C' and (resid 186 through 227 or resid 229 through 747)) selection = (chain 'D' and (resid 186 through 227 or resid 229 through 747)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.920 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: 0.040 Extract box with map and model: 10.910 Check model and map are aligned: 0.780 Set scattering table: 0.470 Process input model: 133.760 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 : 0.008 0.147 47532 Z= 0.526 Angle : 1.177 14.692 64362 Z= 0.622 Chirality : 0.065 0.422 7376 Planarity : 0.007 0.078 8094 Dihedral : 11.986 179.815 17622 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.81 % Allowed : 5.71 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.67 (0.08), residues: 5736 helix: -2.96 (0.06), residues: 3548 sheet: -1.17 (0.63), residues: 40 loop : -3.12 (0.11), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.005 TRP F1770 HIS 0.019 0.003 HIS C 665 PHE 0.044 0.004 PHE F1833 TYR 0.043 0.003 TYR E1535 ARG 0.023 0.002 ARG F1562 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1256 time to evaluate : 6.095 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: D 308 GLN cc_start: 0.8259 (pp30) cc_final: 0.8028 (pp30) REVERT: D 452 ASP cc_start: 0.7394 (m-30) cc_final: 0.7173 (m-30) REVERT: D 624 LYS cc_start: 0.8587 (mppt) cc_final: 0.8224 (tppt) REVERT: D 708 ILE cc_start: 0.8646 (mt) cc_final: 0.8440 (mt) REVERT: D 735 LEU cc_start: 0.8803 (pt) cc_final: 0.8596 (pt) REVERT: C 346 MET cc_start: 0.8191 (mmm) cc_final: 0.7946 (mmm) REVERT: C 452 ASP cc_start: 0.7430 (m-30) cc_final: 0.7227 (m-30) REVERT: C 624 LYS cc_start: 0.8606 (mppt) cc_final: 0.8243 (tppt) REVERT: C 708 ILE cc_start: 0.8645 (mt) cc_final: 0.8434 (mt) REVERT: C 735 LEU cc_start: 0.8789 (pt) cc_final: 0.8583 (pt) REVERT: E 241 LEU cc_start: 0.8081 (mm) cc_final: 0.7719 (mt) REVERT: E 488 TYR cc_start: 0.7883 (m-80) cc_final: 0.7653 (m-80) REVERT: E 664 MET cc_start: 0.8704 (mtt) cc_final: 0.8496 (mtt) REVERT: E 750 ASP cc_start: 0.6874 (m-30) cc_final: 0.6584 (p0) REVERT: E 830 ASP cc_start: 0.8127 (m-30) cc_final: 0.7860 (m-30) REVERT: E 1284 ARG cc_start: 0.7489 (mtt180) cc_final: 0.6947 (mtp-110) REVERT: E 1321 ILE cc_start: 0.8159 (pt) cc_final: 0.7782 (pp) REVERT: E 1340 ASP cc_start: 0.8836 (t0) cc_final: 0.8290 (m-30) REVERT: E 1388 ILE cc_start: 0.8480 (pp) cc_final: 0.8255 (mt) REVERT: E 1389 ASP cc_start: 0.7757 (m-30) cc_final: 0.7494 (m-30) REVERT: E 1402 GLN cc_start: 0.7864 (tt0) cc_final: 0.7569 (tp-100) REVERT: E 1477 LYS cc_start: 0.8531 (pmmt) cc_final: 0.8297 (pttm) REVERT: E 1494 LYS cc_start: 0.8478 (pmtt) cc_final: 0.8173 (mmmt) REVERT: E 1695 GLN cc_start: 0.8239 (pt0) cc_final: 0.7798 (pt0) REVERT: E 1711 MET cc_start: 0.8578 (mmp) cc_final: 0.8238 (mmm) REVERT: E 1907 ARG cc_start: 0.7004 (mtt-85) cc_final: 0.6656 (mtt-85) REVERT: E 2071 ASP cc_start: 0.7423 (t70) cc_final: 0.6852 (t0) REVERT: E 2099 PHE cc_start: 0.7642 (m-80) cc_final: 0.7332 (m-80) REVERT: E 2174 TYR cc_start: 0.8652 (t80) cc_final: 0.8387 (t80) REVERT: E 2228 GLU cc_start: 0.7993 (mp0) cc_final: 0.7732 (mp0) REVERT: F 241 LEU cc_start: 0.8136 (mm) cc_final: 0.7831 (mt) REVERT: F 326 ASP cc_start: 0.6824 (t70) cc_final: 0.6586 (t0) REVERT: F 414 LYS cc_start: 0.8335 (mtpt) cc_final: 0.7945 (mtmm) REVERT: F 488 TYR cc_start: 0.7885 (m-80) cc_final: 0.7572 (m-80) REVERT: F 634 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8729 (tt) REVERT: F 664 MET cc_start: 0.8617 (mtt) cc_final: 0.8324 (mtt) REVERT: F 830 ASP cc_start: 0.8087 (m-30) cc_final: 0.7649 (m-30) REVERT: F 836 MET cc_start: 0.8396 (tpp) cc_final: 0.7963 (tpp) REVERT: F 877 GLN cc_start: 0.6817 (pt0) cc_final: 0.6567 (pt0) REVERT: F 1067 VAL cc_start: 0.8388 (t) cc_final: 0.8105 (m) REVERT: F 1284 ARG cc_start: 0.7412 (mtt180) cc_final: 0.6895 (mtp-110) REVERT: F 1321 ILE cc_start: 0.8260 (pt) cc_final: 0.7894 (pp) REVERT: F 1340 ASP cc_start: 0.8789 (t0) cc_final: 0.8264 (m-30) REVERT: F 1477 LYS cc_start: 0.8628 (pmmt) cc_final: 0.8381 (pttm) REVERT: F 1494 LYS cc_start: 0.8443 (pmtt) cc_final: 0.8161 (mmmt) REVERT: F 1695 GLN cc_start: 0.8529 (pt0) cc_final: 0.8288 (pt0) REVERT: F 1704 ASP cc_start: 0.7563 (m-30) cc_final: 0.7310 (m-30) REVERT: F 1838 GLU cc_start: 0.6981 (pt0) cc_final: 0.6537 (pt0) REVERT: F 1848 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8086 (tt) REVERT: F 1858 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7454 (pt) REVERT: F 1873 MET cc_start: 0.7400 (ttm) cc_final: 0.6869 (tmt) REVERT: F 1895 TYR cc_start: 0.8386 (p90) cc_final: 0.8157 (p90) REVERT: F 1907 ARG cc_start: 0.6882 (mtt-85) cc_final: 0.6403 (mtt-85) REVERT: F 2071 ASP cc_start: 0.7479 (t70) cc_final: 0.6970 (t0) REVERT: F 2099 PHE cc_start: 0.7635 (m-80) cc_final: 0.7376 (m-80) REVERT: F 2123 ARG cc_start: 0.7777 (ttp-110) cc_final: 0.7494 (ttp-110) REVERT: F 2228 GLU cc_start: 0.7905 (mp0) cc_final: 0.7688 (mp0) REVERT: F 2355 ASP cc_start: 0.7482 (t70) cc_final: 0.7264 (t0) outliers start: 40 outliers final: 5 residues processed: 1279 average time/residue: 1.4951 time to fit residues: 2402.1986 Evaluate side-chains 669 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 661 time to evaluate : 5.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1248 ASN Chi-restraints excluded: chain E residue 2244 LEU Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 1248 ASN Chi-restraints excluded: chain F residue 1848 LEU Chi-restraints excluded: chain F residue 1858 ILE Chi-restraints excluded: chain F residue 2244 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 484 optimal weight: 3.9990 chunk 435 optimal weight: 2.9990 chunk 241 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 293 optimal weight: 6.9990 chunk 232 optimal weight: 30.0000 chunk 449 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 273 optimal weight: 8.9990 chunk 334 optimal weight: 3.9990 chunk 521 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 ASN D 380 GLN D 630 GLN D 671 HIS D 702 ASN D 718 GLN C 189 ASN C 380 GLN C 630 GLN C 671 HIS C 702 ASN C 718 GLN E 113 ASN E 284 ASN E 291 ASN E 392 GLN E 506 ASN E 616 GLN E 682 GLN E 868 GLN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1048 ASN E1059 ASN E1847 ASN E1891 HIS E1968 HIS ** E2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2088 ASN ** E2092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2159 HIS ** E2267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2301 ASN E2349 GLN E2356 ASN F 284 ASN F 506 ASN F 616 GLN F 682 GLN F 868 GLN ** F 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1048 ASN F1059 ASN F1402 GLN ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1699 ASN F1781 GLN F1847 ASN ** F1891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2088 ASN ** F2092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2159 HIS ** F2267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2356 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 47532 Z= 0.259 Angle : 0.719 10.108 64362 Z= 0.372 Chirality : 0.045 0.335 7376 Planarity : 0.005 0.064 8094 Dihedral : 8.255 178.171 6312 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.95 % Allowed : 14.56 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.10), residues: 5736 helix: -1.62 (0.08), residues: 3564 sheet: -0.92 (0.65), residues: 42 loop : -2.69 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E1770 HIS 0.008 0.001 HIS E1891 PHE 0.033 0.002 PHE E 404 TYR 0.021 0.002 TYR F2361 ARG 0.006 0.001 ARG E1393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 756 time to evaluate : 5.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 308 GLN cc_start: 0.8240 (pp30) cc_final: 0.7981 (pp30) REVERT: D 624 LYS cc_start: 0.8646 (mppt) cc_final: 0.8173 (tppt) REVERT: D 708 ILE cc_start: 0.8670 (mt) cc_final: 0.8461 (mt) REVERT: C 308 GLN cc_start: 0.8263 (pp30) cc_final: 0.7981 (pp30) REVERT: C 624 LYS cc_start: 0.8649 (mppt) cc_final: 0.8172 (tppt) REVERT: C 708 ILE cc_start: 0.8647 (mt) cc_final: 0.8445 (mt) REVERT: E 102 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8344 (tm) REVERT: E 159 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7546 (tm-30) REVERT: E 454 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7173 (mtp85) REVERT: E 750 ASP cc_start: 0.6909 (m-30) cc_final: 0.6636 (p0) REVERT: E 779 HIS cc_start: 0.7930 (m90) cc_final: 0.7655 (m90) REVERT: E 830 ASP cc_start: 0.7954 (m-30) cc_final: 0.7734 (m-30) REVERT: E 877 GLN cc_start: 0.6391 (OUTLIER) cc_final: 0.6100 (pt0) REVERT: E 1144 TYR cc_start: 0.8339 (m-80) cc_final: 0.8046 (m-80) REVERT: E 1284 ARG cc_start: 0.7548 (mtt180) cc_final: 0.7065 (mtp-110) REVERT: E 1340 ASP cc_start: 0.8624 (t0) cc_final: 0.8307 (m-30) REVERT: E 1362 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7804 (tm-30) REVERT: E 1402 GLN cc_start: 0.8030 (tt0) cc_final: 0.7638 (tp-100) REVERT: E 1501 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7912 (tptp) REVERT: E 1708 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7380 (pt0) REVERT: E 1711 MET cc_start: 0.8714 (mmp) cc_final: 0.8300 (mmm) REVERT: E 1727 GLU cc_start: 0.8121 (mp0) cc_final: 0.7685 (mp0) REVERT: E 1744 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: E 1853 THR cc_start: 0.8762 (t) cc_final: 0.8416 (t) REVERT: E 1865 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6377 (pt0) REVERT: E 1879 GLU cc_start: 0.7622 (tt0) cc_final: 0.7160 (tp30) REVERT: E 1887 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: E 1895 TYR cc_start: 0.8581 (p90) cc_final: 0.8189 (p90) REVERT: E 1907 ARG cc_start: 0.7137 (mtt-85) cc_final: 0.6830 (mtt-85) REVERT: E 2071 ASP cc_start: 0.7212 (t70) cc_final: 0.6617 (t0) REVERT: E 2130 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7189 (tm-30) REVERT: E 2175 MET cc_start: 0.8130 (mmm) cc_final: 0.7911 (mmm) REVERT: E 2228 GLU cc_start: 0.8008 (mp0) cc_final: 0.7632 (mp0) REVERT: F 102 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8425 (tm) REVERT: F 414 LYS cc_start: 0.8299 (mtpt) cc_final: 0.7992 (mtmt) REVERT: F 454 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7184 (mtp85) REVERT: F 488 TYR cc_start: 0.7847 (m-80) cc_final: 0.7545 (m-80) REVERT: F 574 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: F 664 MET cc_start: 0.8363 (mtt) cc_final: 0.8058 (mtt) REVERT: F 830 ASP cc_start: 0.8053 (m-30) cc_final: 0.7801 (m-30) REVERT: F 874 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8372 (tmmm) REVERT: F 1067 VAL cc_start: 0.8610 (t) cc_final: 0.8346 (m) REVERT: F 1144 TYR cc_start: 0.8291 (m-80) cc_final: 0.7998 (m-80) REVERT: F 1340 ASP cc_start: 0.8555 (t0) cc_final: 0.8328 (m-30) REVERT: F 1494 LYS cc_start: 0.8496 (pmtt) cc_final: 0.8161 (mmmt) REVERT: F 1704 ASP cc_start: 0.7562 (m-30) cc_final: 0.7314 (m-30) REVERT: F 1727 GLU cc_start: 0.8095 (mp0) cc_final: 0.7703 (mp0) REVERT: F 1848 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8108 (tt) REVERT: F 1873 MET cc_start: 0.7242 (ttm) cc_final: 0.6850 (tmt) REVERT: F 1895 TYR cc_start: 0.8556 (p90) cc_final: 0.8232 (p90) REVERT: F 1907 ARG cc_start: 0.6996 (mtt-85) cc_final: 0.6748 (mtt-85) REVERT: F 2020 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8286 (ptm-80) REVERT: F 2071 ASP cc_start: 0.7310 (t70) cc_final: 0.6782 (t0) REVERT: F 2130 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7115 (tm-30) REVERT: F 2174 TYR cc_start: 0.8434 (t80) cc_final: 0.8216 (t80) REVERT: F 2228 GLU cc_start: 0.7825 (mp0) cc_final: 0.7533 (mp0) REVERT: F 2331 ASP cc_start: 0.8321 (t0) cc_final: 0.8098 (t0) outliers start: 202 outliers final: 55 residues processed: 898 average time/residue: 1.3837 time to fit residues: 1586.4463 Evaluate side-chains 655 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 588 time to evaluate : 5.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 342 HIS Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 342 HIS Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 454 ARG Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 854 HIS Chi-restraints excluded: chain E residue 877 GLN Chi-restraints excluded: chain E residue 969 LEU Chi-restraints excluded: chain E residue 1023 LEU Chi-restraints excluded: chain E residue 1090 ASP Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1249 ASN Chi-restraints excluded: chain E residue 1499 MET Chi-restraints excluded: chain E residue 1549 GLN Chi-restraints excluded: chain E residue 1626 SER Chi-restraints excluded: chain E residue 1708 GLU Chi-restraints excluded: chain E residue 1744 GLU Chi-restraints excluded: chain E residue 1887 GLU Chi-restraints excluded: chain E residue 1950 VAL Chi-restraints excluded: chain E residue 2016 VAL Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2275 ILE Chi-restraints excluded: chain E residue 2280 THR Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2320 LEU Chi-restraints excluded: chain E residue 2350 GLU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 454 ARG Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 552 SER Chi-restraints excluded: chain F residue 574 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain F residue 756 ILE Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 874 LYS Chi-restraints excluded: chain F residue 969 LEU Chi-restraints excluded: chain F residue 1249 ASN Chi-restraints excluded: chain F residue 1626 SER Chi-restraints excluded: chain F residue 1708 GLU Chi-restraints excluded: chain F residue 1734 GLU Chi-restraints excluded: chain F residue 1747 GLU Chi-restraints excluded: chain F residue 1848 LEU Chi-restraints excluded: chain F residue 1950 VAL Chi-restraints excluded: chain F residue 2020 ARG Chi-restraints excluded: chain F residue 2105 ILE Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2227 CYS Chi-restraints excluded: chain F residue 2275 ILE Chi-restraints excluded: chain F residue 2350 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 289 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 433 optimal weight: 0.9980 chunk 354 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 522 optimal weight: 9.9990 chunk 564 optimal weight: 0.0270 chunk 465 optimal weight: 10.0000 chunk 517 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 418 optimal weight: 10.0000 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 596 GLN ** D 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN E 868 GLN E1955 HIS ** E2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2349 GLN E2356 ASN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 668 GLN F 868 GLN F1402 GLN ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 47532 Z= 0.183 Angle : 0.652 8.841 64362 Z= 0.335 Chirality : 0.043 0.309 7376 Planarity : 0.004 0.058 8094 Dihedral : 7.638 179.114 6298 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.05 % Allowed : 16.83 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.25 (0.11), residues: 5736 helix: -0.88 (0.08), residues: 3538 sheet: -0.74 (0.62), residues: 62 loop : -2.47 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F1770 HIS 0.015 0.001 HIS F1891 PHE 0.019 0.002 PHE F 386 TYR 0.022 0.001 TYR F2361 ARG 0.006 0.000 ARG E1952 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 745 time to evaluate : 5.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 231 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7828 (pt) REVERT: D 308 GLN cc_start: 0.8162 (pp30) cc_final: 0.7878 (pp30) REVERT: D 385 GLN cc_start: 0.7857 (mp10) cc_final: 0.7550 (pm20) REVERT: D 584 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7851 (ttp80) REVERT: D 624 LYS cc_start: 0.8594 (mppt) cc_final: 0.8382 (tptt) REVERT: C 231 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7790 (pt) REVERT: C 308 GLN cc_start: 0.8158 (pp30) cc_final: 0.7892 (pp30) REVERT: C 385 GLN cc_start: 0.7845 (mp10) cc_final: 0.7605 (pm20) REVERT: C 542 GLU cc_start: 0.7478 (tt0) cc_final: 0.7180 (tt0) REVERT: C 624 LYS cc_start: 0.8588 (mppt) cc_final: 0.8382 (tptt) REVERT: C 661 ARG cc_start: 0.7691 (ppp80) cc_final: 0.7448 (ptt180) REVERT: E 11 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.6770 (mt) REVERT: E 96 ASN cc_start: 0.7120 (p0) cc_final: 0.6477 (m-40) REVERT: E 397 ARG cc_start: 0.7924 (mtt180) cc_final: 0.7254 (mtt90) REVERT: E 454 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7359 (mtp180) REVERT: E 574 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: E 674 LYS cc_start: 0.8380 (ttmm) cc_final: 0.7994 (tptp) REVERT: E 750 ASP cc_start: 0.6689 (m-30) cc_final: 0.6343 (p0) REVERT: E 830 ASP cc_start: 0.7889 (m-30) cc_final: 0.7685 (m-30) REVERT: E 1048 ASN cc_start: 0.7745 (m-40) cc_final: 0.7330 (t0) REVERT: E 1144 TYR cc_start: 0.8268 (m-80) cc_final: 0.7994 (m-80) REVERT: E 1301 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: E 1340 ASP cc_start: 0.8574 (t0) cc_final: 0.8372 (m-30) REVERT: E 1362 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7807 (tm-30) REVERT: E 1494 LYS cc_start: 0.8463 (pmtt) cc_final: 0.8210 (mmmt) REVERT: E 1708 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7378 (pt0) REVERT: E 1711 MET cc_start: 0.8675 (mmp) cc_final: 0.8267 (mmm) REVERT: E 1727 GLU cc_start: 0.8106 (mp0) cc_final: 0.7665 (mp0) REVERT: E 1853 THR cc_start: 0.8754 (t) cc_final: 0.8494 (t) REVERT: E 1895 TYR cc_start: 0.8511 (p90) cc_final: 0.8026 (p90) REVERT: E 1905 LEU cc_start: 0.7452 (mm) cc_final: 0.6820 (tt) REVERT: E 1907 ARG cc_start: 0.7142 (mtt-85) cc_final: 0.6780 (mtp-110) REVERT: E 2071 ASP cc_start: 0.7198 (t70) cc_final: 0.6597 (t0) REVERT: E 2130 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7343 (tm-30) REVERT: E 2131 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8045 (mmt) REVERT: E 2228 GLU cc_start: 0.7796 (mp0) cc_final: 0.7493 (mp0) REVERT: F 11 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.6766 (mt) REVERT: F 96 ASN cc_start: 0.7132 (p0) cc_final: 0.6585 (m-40) REVERT: F 132 LYS cc_start: 0.6337 (OUTLIER) cc_final: 0.5298 (ptmt) REVERT: F 414 LYS cc_start: 0.8300 (mtpt) cc_final: 0.8015 (mtmt) REVERT: F 454 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7089 (mtp85) REVERT: F 488 TYR cc_start: 0.7736 (m-80) cc_final: 0.7449 (m-80) REVERT: F 574 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: F 578 MET cc_start: 0.8064 (ptm) cc_final: 0.7843 (ptp) REVERT: F 830 ASP cc_start: 0.8011 (m-30) cc_final: 0.7788 (m-30) REVERT: F 1048 ASN cc_start: 0.7751 (m110) cc_final: 0.7468 (t0) REVERT: F 1067 VAL cc_start: 0.8510 (t) cc_final: 0.8260 (m) REVERT: F 1315 ILE cc_start: 0.6867 (pp) cc_final: 0.6625 (pp) REVERT: F 1494 LYS cc_start: 0.8477 (pmtt) cc_final: 0.8150 (mmtt) REVERT: F 1704 ASP cc_start: 0.7541 (m-30) cc_final: 0.7302 (m-30) REVERT: F 1727 GLU cc_start: 0.8071 (mp0) cc_final: 0.7676 (mp0) REVERT: F 1848 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8050 (tt) REVERT: F 1873 MET cc_start: 0.7006 (ttm) cc_final: 0.6703 (tmt) REVERT: F 1879 GLU cc_start: 0.7512 (tt0) cc_final: 0.7072 (tt0) REVERT: F 1895 TYR cc_start: 0.8444 (p90) cc_final: 0.7894 (p90) REVERT: F 1905 LEU cc_start: 0.7549 (mm) cc_final: 0.6859 (tt) REVERT: F 2020 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8098 (ptm-80) REVERT: F 2071 ASP cc_start: 0.7237 (t70) cc_final: 0.6647 (t0) REVERT: F 2130 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7300 (tm-30) REVERT: F 2131 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7900 (mmt) REVERT: F 2228 GLU cc_start: 0.7844 (mp0) cc_final: 0.7535 (mp0) REVERT: F 2331 ASP cc_start: 0.8281 (t0) cc_final: 0.7994 (t0) outliers start: 207 outliers final: 65 residues processed: 894 average time/residue: 1.3451 time to fit residues: 1550.3471 Evaluate side-chains 685 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 604 time to evaluate : 5.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 342 HIS Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 584 ARG Chi-restraints excluded: chain D residue 695 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 342 HIS Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 454 ARG Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 700 VAL Chi-restraints excluded: chain E residue 756 ILE Chi-restraints excluded: chain E residue 854 HIS Chi-restraints excluded: chain E residue 964 THR Chi-restraints excluded: chain E residue 969 LEU Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1249 ASN Chi-restraints excluded: chain E residue 1255 LYS Chi-restraints excluded: chain E residue 1301 ASP Chi-restraints excluded: chain E residue 1477 LYS Chi-restraints excluded: chain E residue 1567 ARG Chi-restraints excluded: chain E residue 1708 GLU Chi-restraints excluded: chain E residue 1747 GLU Chi-restraints excluded: chain E residue 1786 TYR Chi-restraints excluded: chain E residue 1848 LEU Chi-restraints excluded: chain E residue 1902 THR Chi-restraints excluded: chain E residue 2131 MET Chi-restraints excluded: chain E residue 2227 CYS Chi-restraints excluded: chain E residue 2245 ASP Chi-restraints excluded: chain E residue 2260 VAL Chi-restraints excluded: chain E residue 2275 ILE Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2350 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 454 ARG Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 552 SER Chi-restraints excluded: chain F residue 574 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 964 THR Chi-restraints excluded: chain F residue 969 LEU Chi-restraints excluded: chain F residue 1249 ASN Chi-restraints excluded: chain F residue 1477 LYS Chi-restraints excluded: chain F residue 1492 ASP Chi-restraints excluded: chain F residue 1567 ARG Chi-restraints excluded: chain F residue 1747 GLU Chi-restraints excluded: chain F residue 1786 TYR Chi-restraints excluded: chain F residue 1848 LEU Chi-restraints excluded: chain F residue 1852 ILE Chi-restraints excluded: chain F residue 1902 THR Chi-restraints excluded: chain F residue 2020 ARG Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2227 CYS Chi-restraints excluded: chain F residue 2245 ASP Chi-restraints excluded: chain F residue 2275 ILE Chi-restraints excluded: chain F residue 2350 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 515 optimal weight: 20.0000 chunk 392 optimal weight: 7.9990 chunk 271 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 249 optimal weight: 0.9990 chunk 350 optimal weight: 9.9990 chunk 524 optimal weight: 4.9990 chunk 554 optimal weight: 20.0000 chunk 273 optimal weight: 4.9990 chunk 496 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 213 HIS ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 718 GLN C 213 HIS ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 GLN E 525 ASN ** E 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 868 GLN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 951 HIS E1248 ASN E1903 GLN E2088 ASN ** E2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2115 ASN E2301 ASN E2349 GLN F 392 GLN F 506 ASN F 633 GLN F 868 GLN ** F 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 951 HIS F1248 ASN ** F1484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2088 ASN ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2115 ASN F2349 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 47532 Z= 0.436 Angle : 0.777 9.867 64362 Z= 0.402 Chirality : 0.049 0.408 7376 Planarity : 0.005 0.060 8094 Dihedral : 7.723 175.949 6298 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 5.93 % Allowed : 16.73 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.11), residues: 5736 helix: -0.73 (0.08), residues: 3574 sheet: -0.62 (0.60), residues: 62 loop : -2.35 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E1770 HIS 0.013 0.002 HIS F1891 PHE 0.031 0.003 PHE F 386 TYR 0.032 0.002 TYR C 403 ARG 0.008 0.001 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 634 time to evaluate : 5.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 385 GLN cc_start: 0.7984 (mp10) cc_final: 0.7703 (pm20) REVERT: D 624 LYS cc_start: 0.8749 (mppt) cc_final: 0.8526 (tptt) REVERT: D 745 MET cc_start: 0.7685 (mpt) cc_final: 0.7077 (mpt) REVERT: C 385 GLN cc_start: 0.7913 (mp10) cc_final: 0.7637 (pm20) REVERT: C 624 LYS cc_start: 0.8770 (mppt) cc_final: 0.8550 (tptt) REVERT: C 661 ARG cc_start: 0.7927 (ppp80) cc_final: 0.7704 (ptt180) REVERT: E 96 ASN cc_start: 0.7269 (p0) cc_final: 0.6595 (m-40) REVERT: E 230 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: E 454 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7229 (mtp85) REVERT: E 506 ASN cc_start: 0.8397 (t0) cc_final: 0.8191 (t0) REVERT: E 574 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8061 (mp10) REVERT: E 640 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8166 (p0) REVERT: E 674 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8260 (tptp) REVERT: E 750 ASP cc_start: 0.6734 (m-30) cc_final: 0.6497 (p0) REVERT: E 923 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7524 (mp) REVERT: E 1048 ASN cc_start: 0.7798 (m-40) cc_final: 0.7412 (t0) REVERT: E 1144 TYR cc_start: 0.8443 (m-80) cc_final: 0.8141 (m-80) REVERT: E 1177 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: E 1301 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8388 (m-30) REVERT: E 1324 ASP cc_start: 0.7194 (t70) cc_final: 0.6883 (t70) REVERT: E 1340 ASP cc_start: 0.8728 (t0) cc_final: 0.8433 (m-30) REVERT: E 1362 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7752 (tm-30) REVERT: E 1399 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8468 (tt) REVERT: E 1488 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8229 (mmmt) REVERT: E 1494 LYS cc_start: 0.8576 (pmtt) cc_final: 0.8289 (mmmt) REVERT: E 1727 GLU cc_start: 0.8116 (mp0) cc_final: 0.7588 (mp0) REVERT: E 1747 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: E 1879 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8143 (pt0) REVERT: E 1887 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: E 1895 TYR cc_start: 0.8566 (p90) cc_final: 0.8199 (p90) REVERT: E 1907 ARG cc_start: 0.7365 (mtt-85) cc_final: 0.7036 (mtt-85) REVERT: E 2056 PHE cc_start: 0.5823 (OUTLIER) cc_final: 0.4240 (p90) REVERT: E 2071 ASP cc_start: 0.7285 (t70) cc_final: 0.6718 (t0) REVERT: E 2131 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8159 (mmt) REVERT: E 2228 GLU cc_start: 0.7890 (mp0) cc_final: 0.7484 (mp0) REVERT: E 2364 TRP cc_start: 0.7384 (t60) cc_final: 0.7164 (t60) REVERT: F 96 ASN cc_start: 0.7290 (p0) cc_final: 0.6698 (m-40) REVERT: F 132 LYS cc_start: 0.6390 (OUTLIER) cc_final: 0.5831 (ptmm) REVERT: F 231 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8078 (tt) REVERT: F 454 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7480 (mtp85) REVERT: F 484 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7972 (tmm) REVERT: F 574 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: F 640 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8280 (p0) REVERT: F 664 MET cc_start: 0.8582 (mtt) cc_final: 0.8316 (mtt) REVERT: F 874 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8381 (tmmm) REVERT: F 923 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7062 (mt) REVERT: F 1067 VAL cc_start: 0.8741 (t) cc_final: 0.8455 (m) REVERT: F 1324 ASP cc_start: 0.7238 (t70) cc_final: 0.6919 (t70) REVERT: F 1389 ASP cc_start: 0.8343 (m-30) cc_final: 0.8123 (m-30) REVERT: F 1488 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8135 (mmmt) REVERT: F 1494 LYS cc_start: 0.8613 (pmtt) cc_final: 0.8239 (mmmt) REVERT: F 1704 ASP cc_start: 0.7629 (m-30) cc_final: 0.7358 (m-30) REVERT: F 1727 GLU cc_start: 0.8123 (mp0) cc_final: 0.7666 (mp0) REVERT: F 1744 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: F 1827 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6912 (t80) REVERT: F 1848 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8182 (tt) REVERT: F 1873 MET cc_start: 0.7347 (ttm) cc_final: 0.6875 (tmt) REVERT: F 1895 TYR cc_start: 0.8561 (p90) cc_final: 0.8086 (p90) REVERT: F 2071 ASP cc_start: 0.7318 (t70) cc_final: 0.6830 (t0) REVERT: F 2131 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8207 (mmt) REVERT: F 2228 GLU cc_start: 0.7844 (mp0) cc_final: 0.7453 (mp0) REVERT: F 2331 ASP cc_start: 0.8423 (t0) cc_final: 0.8143 (t0) outliers start: 304 outliers final: 124 residues processed: 863 average time/residue: 1.3074 time to fit residues: 1459.2364 Evaluate side-chains 713 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 563 time to evaluate : 5.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 695 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 454 ARG Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 640 ASN Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 700 VAL Chi-restraints excluded: chain E residue 744 ILE Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 854 HIS Chi-restraints excluded: chain E residue 923 ILE Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 964 THR Chi-restraints excluded: chain E residue 969 LEU Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1023 LEU Chi-restraints excluded: chain E residue 1090 ASP Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1143 VAL Chi-restraints excluded: chain E residue 1177 GLN Chi-restraints excluded: chain E residue 1248 ASN Chi-restraints excluded: chain E residue 1249 ASN Chi-restraints excluded: chain E residue 1255 LYS Chi-restraints excluded: chain E residue 1256 ILE Chi-restraints excluded: chain E residue 1270 THR Chi-restraints excluded: chain E residue 1301 ASP Chi-restraints excluded: chain E residue 1337 LEU Chi-restraints excluded: chain E residue 1399 LEU Chi-restraints excluded: chain E residue 1477 LYS Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1492 ASP Chi-restraints excluded: chain E residue 1499 MET Chi-restraints excluded: chain E residue 1567 ARG Chi-restraints excluded: chain E residue 1626 SER Chi-restraints excluded: chain E residue 1708 GLU Chi-restraints excluded: chain E residue 1747 GLU Chi-restraints excluded: chain E residue 1835 LEU Chi-restraints excluded: chain E residue 1848 LEU Chi-restraints excluded: chain E residue 1852 ILE Chi-restraints excluded: chain E residue 1887 GLU Chi-restraints excluded: chain E residue 1902 THR Chi-restraints excluded: chain E residue 1934 ILE Chi-restraints excluded: chain E residue 1950 VAL Chi-restraints excluded: chain E residue 2056 PHE Chi-restraints excluded: chain E residue 2105 ILE Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2131 MET Chi-restraints excluded: chain E residue 2171 LEU Chi-restraints excluded: chain E residue 2215 MET Chi-restraints excluded: chain E residue 2227 CYS Chi-restraints excluded: chain E residue 2244 LEU Chi-restraints excluded: chain E residue 2260 VAL Chi-restraints excluded: chain E residue 2275 ILE Chi-restraints excluded: chain E residue 2280 THR Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2320 LEU Chi-restraints excluded: chain E residue 2350 GLU Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 454 ARG Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 484 MET Chi-restraints excluded: chain F residue 552 SER Chi-restraints excluded: chain F residue 566 ILE Chi-restraints excluded: chain F residue 574 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 640 ASN Chi-restraints excluded: chain F residue 641 ASP Chi-restraints excluded: chain F residue 657 ASP Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 874 LYS Chi-restraints excluded: chain F residue 892 HIS Chi-restraints excluded: chain F residue 923 ILE Chi-restraints excluded: chain F residue 939 LEU Chi-restraints excluded: chain F residue 964 THR Chi-restraints excluded: chain F residue 969 LEU Chi-restraints excluded: chain F residue 1010 THR Chi-restraints excluded: chain F residue 1023 LEU Chi-restraints excluded: chain F residue 1090 ASP Chi-restraints excluded: chain F residue 1143 VAL Chi-restraints excluded: chain F residue 1248 ASN Chi-restraints excluded: chain F residue 1249 ASN Chi-restraints excluded: chain F residue 1270 THR Chi-restraints excluded: chain F residue 1337 LEU Chi-restraints excluded: chain F residue 1477 LYS Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1492 ASP Chi-restraints excluded: chain F residue 1549 GLN Chi-restraints excluded: chain F residue 1567 ARG Chi-restraints excluded: chain F residue 1626 SER Chi-restraints excluded: chain F residue 1708 GLU Chi-restraints excluded: chain F residue 1734 GLU Chi-restraints excluded: chain F residue 1744 GLU Chi-restraints excluded: chain F residue 1747 GLU Chi-restraints excluded: chain F residue 1827 TYR Chi-restraints excluded: chain F residue 1848 LEU Chi-restraints excluded: chain F residue 1852 ILE Chi-restraints excluded: chain F residue 1902 THR Chi-restraints excluded: chain F residue 1934 ILE Chi-restraints excluded: chain F residue 1950 VAL Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2215 MET Chi-restraints excluded: chain F residue 2227 CYS Chi-restraints excluded: chain F residue 2260 VAL Chi-restraints excluded: chain F residue 2275 ILE Chi-restraints excluded: chain F residue 2280 THR Chi-restraints excluded: chain F residue 2297 VAL Chi-restraints excluded: chain F residue 2320 LEU Chi-restraints excluded: chain F residue 2350 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 462 optimal weight: 0.9990 chunk 314 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 413 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 473 optimal weight: 10.0000 chunk 383 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 283 optimal weight: 20.0000 chunk 498 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 633 GLN ** F 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1248 ASN ** F1484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1903 GLN ** F2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2088 ASN ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2115 ASN F2356 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 47532 Z= 0.239 Angle : 0.673 9.317 64362 Z= 0.345 Chirality : 0.044 0.337 7376 Planarity : 0.004 0.054 8094 Dihedral : 7.358 178.473 6298 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.84 % Allowed : 18.92 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.11), residues: 5736 helix: -0.45 (0.09), residues: 3576 sheet: -0.83 (0.60), residues: 66 loop : -2.23 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E1770 HIS 0.011 0.001 HIS F1891 PHE 0.023 0.002 PHE E1673 TYR 0.028 0.002 TYR F2361 ARG 0.010 0.000 ARG E1393 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 662 time to evaluate : 5.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 346 MET cc_start: 0.6898 (mmm) cc_final: 0.6473 (mmm) REVERT: D 385 GLN cc_start: 0.7857 (mp10) cc_final: 0.7598 (pm20) REVERT: D 542 GLU cc_start: 0.7340 (tt0) cc_final: 0.7092 (tt0) REVERT: D 624 LYS cc_start: 0.8631 (mppt) cc_final: 0.8399 (tptt) REVERT: D 699 MET cc_start: 0.7331 (tmm) cc_final: 0.7107 (tmm) REVERT: C 308 GLN cc_start: 0.8287 (pp30) cc_final: 0.8079 (pp30) REVERT: C 624 LYS cc_start: 0.8637 (mppt) cc_final: 0.8399 (tptt) REVERT: C 661 ARG cc_start: 0.7828 (ppp80) cc_final: 0.7614 (ptt180) REVERT: C 699 MET cc_start: 0.7324 (tmm) cc_final: 0.7095 (tmm) REVERT: E 11 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7677 (tm) REVERT: E 96 ASN cc_start: 0.7179 (p0) cc_final: 0.6564 (m-40) REVERT: E 454 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7258 (mtp85) REVERT: E 574 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: E 674 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8217 (tptp) REVERT: E 1048 ASN cc_start: 0.7738 (m-40) cc_final: 0.7491 (t0) REVERT: E 1144 TYR cc_start: 0.8383 (m-80) cc_final: 0.8095 (m-80) REVERT: E 1177 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: E 1301 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8403 (m-30) REVERT: E 1324 ASP cc_start: 0.7121 (t70) cc_final: 0.6870 (t70) REVERT: E 1488 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8183 (mmmt) REVERT: E 1494 LYS cc_start: 0.8564 (pmtt) cc_final: 0.8344 (mmtt) REVERT: E 1727 GLU cc_start: 0.8070 (mp0) cc_final: 0.7682 (mp0) REVERT: E 1747 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: E 1853 THR cc_start: 0.8798 (t) cc_final: 0.8570 (t) REVERT: E 1879 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8134 (pt0) REVERT: E 1895 TYR cc_start: 0.8484 (p90) cc_final: 0.7936 (p90) REVERT: E 1907 ARG cc_start: 0.7333 (mtt-85) cc_final: 0.6756 (mtt-85) REVERT: E 2071 ASP cc_start: 0.7205 (t70) cc_final: 0.6713 (t0) REVERT: E 2105 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8533 (tp) REVERT: E 2123 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7546 (ttp-110) REVERT: E 2130 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7338 (tm-30) REVERT: E 2131 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8045 (mmt) REVERT: E 2228 GLU cc_start: 0.7791 (mp0) cc_final: 0.7364 (mp0) REVERT: E 2364 TRP cc_start: 0.7398 (t60) cc_final: 0.7143 (t60) REVERT: F 11 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.6597 (mt) REVERT: F 96 ASN cc_start: 0.7199 (p0) cc_final: 0.6583 (m-40) REVERT: F 132 LYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5656 (ptmm) REVERT: F 154 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7753 (mtp) REVERT: F 231 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8062 (tt) REVERT: F 454 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7491 (mtp85) REVERT: F 574 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: F 664 MET cc_start: 0.8526 (mtt) cc_final: 0.8286 (mtt) REVERT: F 674 LYS cc_start: 0.8621 (ttmm) cc_final: 0.8304 (tptp) REVERT: F 1067 VAL cc_start: 0.8644 (t) cc_final: 0.8373 (m) REVERT: F 1177 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.6916 (tm-30) REVERT: F 1324 ASP cc_start: 0.7185 (t70) cc_final: 0.6918 (t70) REVERT: F 1488 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8060 (mmmt) REVERT: F 1494 LYS cc_start: 0.8582 (pmtt) cc_final: 0.8225 (mmmt) REVERT: F 1622 MET cc_start: 0.8883 (ptp) cc_final: 0.8673 (ptp) REVERT: F 1685 ASP cc_start: 0.8013 (t0) cc_final: 0.7704 (t70) REVERT: F 1704 ASP cc_start: 0.7613 (m-30) cc_final: 0.7346 (m-30) REVERT: F 1727 GLU cc_start: 0.8113 (mp0) cc_final: 0.7682 (mp0) REVERT: F 1744 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: F 1848 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8144 (tt) REVERT: F 1873 MET cc_start: 0.6948 (ttm) cc_final: 0.6564 (tmt) REVERT: F 1895 TYR cc_start: 0.8500 (p90) cc_final: 0.7967 (p90) REVERT: F 1905 LEU cc_start: 0.7700 (mm) cc_final: 0.6930 (tt) REVERT: F 2056 PHE cc_start: 0.5803 (OUTLIER) cc_final: 0.3773 (p90) REVERT: F 2071 ASP cc_start: 0.7219 (t70) cc_final: 0.6765 (t0) REVERT: F 2131 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8118 (mmt) REVERT: F 2228 GLU cc_start: 0.7673 (mp0) cc_final: 0.7259 (mp0) REVERT: F 2306 ILE cc_start: 0.7910 (mm) cc_final: 0.7541 (mm) REVERT: F 2323 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8334 (tm) REVERT: F 2331 ASP cc_start: 0.8429 (t0) cc_final: 0.8204 (t0) outliers start: 248 outliers final: 113 residues processed: 847 average time/residue: 1.3007 time to fit residues: 1426.8649 Evaluate side-chains 718 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 582 time to evaluate : 5.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 342 HIS Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 661 ARG Chi-restraints excluded: chain D residue 665 HIS Chi-restraints excluded: chain D residue 695 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 342 HIS Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 454 ARG Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 597 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 700 VAL Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 854 HIS Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 969 LEU Chi-restraints excluded: chain E residue 991 ILE Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1143 VAL Chi-restraints excluded: chain E residue 1177 GLN Chi-restraints excluded: chain E residue 1249 ASN Chi-restraints excluded: chain E residue 1255 LYS Chi-restraints excluded: chain E residue 1270 THR Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1301 ASP Chi-restraints excluded: chain E residue 1477 LYS Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1499 MET Chi-restraints excluded: chain E residue 1549 GLN Chi-restraints excluded: chain E residue 1567 ARG Chi-restraints excluded: chain E residue 1606 ILE Chi-restraints excluded: chain E residue 1626 SER Chi-restraints excluded: chain E residue 1708 GLU Chi-restraints excluded: chain E residue 1747 GLU Chi-restraints excluded: chain E residue 1835 LEU Chi-restraints excluded: chain E residue 1848 LEU Chi-restraints excluded: chain E residue 1852 ILE Chi-restraints excluded: chain E residue 1902 THR Chi-restraints excluded: chain E residue 1934 ILE Chi-restraints excluded: chain E residue 1950 VAL Chi-restraints excluded: chain E residue 2105 ILE Chi-restraints excluded: chain E residue 2123 ARG Chi-restraints excluded: chain E residue 2131 MET Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2171 LEU Chi-restraints excluded: chain E residue 2227 CYS Chi-restraints excluded: chain E residue 2244 LEU Chi-restraints excluded: chain E residue 2245 ASP Chi-restraints excluded: chain E residue 2260 VAL Chi-restraints excluded: chain E residue 2275 ILE Chi-restraints excluded: chain E residue 2280 THR Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2350 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 454 ARG Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 552 SER Chi-restraints excluded: chain F residue 566 ILE Chi-restraints excluded: chain F residue 574 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain F residue 744 ILE Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 939 LEU Chi-restraints excluded: chain F residue 969 LEU Chi-restraints excluded: chain F residue 991 ILE Chi-restraints excluded: chain F residue 1010 THR Chi-restraints excluded: chain F residue 1143 VAL Chi-restraints excluded: chain F residue 1177 GLN Chi-restraints excluded: chain F residue 1249 ASN Chi-restraints excluded: chain F residue 1256 ILE Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1349 ILE Chi-restraints excluded: chain F residue 1477 LYS Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1492 ASP Chi-restraints excluded: chain F residue 1567 ARG Chi-restraints excluded: chain F residue 1606 ILE Chi-restraints excluded: chain F residue 1708 GLU Chi-restraints excluded: chain F residue 1734 GLU Chi-restraints excluded: chain F residue 1744 GLU Chi-restraints excluded: chain F residue 1747 GLU Chi-restraints excluded: chain F residue 1835 LEU Chi-restraints excluded: chain F residue 1848 LEU Chi-restraints excluded: chain F residue 1852 ILE Chi-restraints excluded: chain F residue 1902 THR Chi-restraints excluded: chain F residue 1934 ILE Chi-restraints excluded: chain F residue 1950 VAL Chi-restraints excluded: chain F residue 2056 PHE Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2227 CYS Chi-restraints excluded: chain F residue 2245 ASP Chi-restraints excluded: chain F residue 2260 VAL Chi-restraints excluded: chain F residue 2270 ASP Chi-restraints excluded: chain F residue 2275 ILE Chi-restraints excluded: chain F residue 2280 THR Chi-restraints excluded: chain F residue 2297 VAL Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain F residue 2350 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 186 optimal weight: 20.0000 chunk 499 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 325 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 555 optimal weight: 7.9990 chunk 461 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 46 optimal weight: 0.0010 chunk 183 optimal weight: 8.9990 chunk 291 optimal weight: 5.9990 overall best weight: 3.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN D 718 GLN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 GLN E 506 ASN ** E 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1371 HIS ** E1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2349 GLN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 633 GLN ** F 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1048 ASN ** F1484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1903 GLN ** F2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2088 ASN ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 47532 Z= 0.299 Angle : 0.704 11.062 64362 Z= 0.359 Chirality : 0.046 0.322 7376 Planarity : 0.004 0.056 8094 Dihedral : 7.246 177.485 6298 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 5.29 % Allowed : 19.40 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.57 (0.11), residues: 5736 helix: -0.37 (0.09), residues: 3592 sheet: -0.70 (0.61), residues: 66 loop : -2.15 (0.14), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E1770 HIS 0.010 0.001 HIS F1891 PHE 0.026 0.002 PHE E 386 TYR 0.033 0.002 TYR D 403 ARG 0.011 0.001 ARG F 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 638 time to evaluate : 6.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 308 GLN cc_start: 0.8286 (pp30) cc_final: 0.8071 (pp30) REVERT: D 624 LYS cc_start: 0.8677 (mppt) cc_final: 0.8410 (tptt) REVERT: D 628 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7040 (tp30) REVERT: D 699 MET cc_start: 0.7481 (tmm) cc_final: 0.7209 (tmm) REVERT: C 308 GLN cc_start: 0.8305 (pp30) cc_final: 0.8092 (pp30) REVERT: C 624 LYS cc_start: 0.8685 (mppt) cc_final: 0.8433 (tptt) REVERT: C 661 ARG cc_start: 0.7894 (ppp80) cc_final: 0.7674 (ptt180) REVERT: C 699 MET cc_start: 0.7481 (tmm) cc_final: 0.7213 (tmm) REVERT: E 11 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7656 (tm) REVERT: E 438 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: E 454 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7336 (mtp85) REVERT: E 574 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8094 (mp10) REVERT: E 640 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.8007 (p0) REVERT: E 674 LYS cc_start: 0.8611 (ttmm) cc_final: 0.8293 (tptp) REVERT: E 750 ASP cc_start: 0.6660 (m-30) cc_final: 0.6403 (p0) REVERT: E 1144 TYR cc_start: 0.8356 (m-80) cc_final: 0.8093 (m-80) REVERT: E 1177 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: E 1301 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8392 (m-30) REVERT: E 1324 ASP cc_start: 0.7153 (t70) cc_final: 0.6881 (t70) REVERT: E 1354 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: E 1488 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8253 (mmmt) REVERT: E 1494 LYS cc_start: 0.8666 (pmtt) cc_final: 0.8380 (mmtt) REVERT: E 1727 GLU cc_start: 0.8072 (mp0) cc_final: 0.7665 (mp0) REVERT: E 1747 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: E 1887 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: E 1895 TYR cc_start: 0.8511 (p90) cc_final: 0.8145 (p90) REVERT: E 1907 ARG cc_start: 0.7387 (mtt-85) cc_final: 0.6774 (mtt-85) REVERT: E 2056 PHE cc_start: 0.6050 (OUTLIER) cc_final: 0.4603 (p90) REVERT: E 2071 ASP cc_start: 0.7212 (t70) cc_final: 0.6760 (t0) REVERT: E 2105 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8554 (tp) REVERT: E 2131 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8223 (mmt) REVERT: E 2228 GLU cc_start: 0.7704 (mp0) cc_final: 0.7259 (mp0) REVERT: F 11 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7570 (tm) REVERT: F 96 ASN cc_start: 0.7174 (p0) cc_final: 0.6623 (m-40) REVERT: F 132 LYS cc_start: 0.6182 (OUTLIER) cc_final: 0.5655 (ptmm) REVERT: F 231 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8089 (tt) REVERT: F 454 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7478 (mtp85) REVERT: F 574 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8072 (mp10) REVERT: F 664 MET cc_start: 0.8638 (mtt) cc_final: 0.8361 (mtt) REVERT: F 674 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8376 (tptp) REVERT: F 1067 VAL cc_start: 0.8720 (t) cc_final: 0.8470 (m) REVERT: F 1177 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: F 1324 ASP cc_start: 0.7184 (t70) cc_final: 0.6927 (t70) REVERT: F 1354 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: F 1488 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8207 (mmmt) REVERT: F 1494 LYS cc_start: 0.8627 (pmtt) cc_final: 0.8259 (mmtt) REVERT: F 1704 ASP cc_start: 0.7637 (m-30) cc_final: 0.7374 (m-30) REVERT: F 1727 GLU cc_start: 0.8100 (mp0) cc_final: 0.7682 (mp0) REVERT: F 1747 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6230 (mp0) REVERT: F 1848 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8128 (tt) REVERT: F 1873 MET cc_start: 0.7122 (ttm) cc_final: 0.6766 (tmt) REVERT: F 1895 TYR cc_start: 0.8479 (p90) cc_final: 0.7934 (p90) REVERT: F 2056 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.3977 (p90) REVERT: F 2131 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8097 (mmt) REVERT: F 2228 GLU cc_start: 0.7716 (mp0) cc_final: 0.7251 (mp0) REVERT: F 2306 ILE cc_start: 0.7849 (mm) cc_final: 0.7622 (mm) REVERT: F 2323 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8327 (tm) REVERT: F 2331 ASP cc_start: 0.8431 (t0) cc_final: 0.8214 (t0) outliers start: 271 outliers final: 140 residues processed: 843 average time/residue: 1.3161 time to fit residues: 1440.1726 Evaluate side-chains 756 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 589 time to evaluate : 5.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 661 ARG Chi-restraints excluded: chain D residue 695 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 454 ARG Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 603 SER Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 640 ASN Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 700 VAL Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain E residue 744 ILE Chi-restraints excluded: chain E residue 784 LEU Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 854 HIS Chi-restraints excluded: chain E residue 892 HIS Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 969 LEU Chi-restraints excluded: chain E residue 991 ILE Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1023 LEU Chi-restraints excluded: chain E residue 1090 ASP Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1143 VAL Chi-restraints excluded: chain E residue 1177 GLN Chi-restraints excluded: chain E residue 1249 ASN Chi-restraints excluded: chain E residue 1255 LYS Chi-restraints excluded: chain E residue 1270 THR Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1301 ASP Chi-restraints excluded: chain E residue 1312 TYR Chi-restraints excluded: chain E residue 1337 LEU Chi-restraints excluded: chain E residue 1343 ARG Chi-restraints excluded: chain E residue 1354 GLU Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1408 ASP Chi-restraints excluded: chain E residue 1477 LYS Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1499 MET Chi-restraints excluded: chain E residue 1549 GLN Chi-restraints excluded: chain E residue 1567 ARG Chi-restraints excluded: chain E residue 1606 ILE Chi-restraints excluded: chain E residue 1626 SER Chi-restraints excluded: chain E residue 1708 GLU Chi-restraints excluded: chain E residue 1747 GLU Chi-restraints excluded: chain E residue 1835 LEU Chi-restraints excluded: chain E residue 1848 LEU Chi-restraints excluded: chain E residue 1852 ILE Chi-restraints excluded: chain E residue 1887 GLU Chi-restraints excluded: chain E residue 1902 THR Chi-restraints excluded: chain E residue 1934 ILE Chi-restraints excluded: chain E residue 1950 VAL Chi-restraints excluded: chain E residue 2056 PHE Chi-restraints excluded: chain E residue 2105 ILE Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2131 MET Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2171 LEU Chi-restraints excluded: chain E residue 2227 CYS Chi-restraints excluded: chain E residue 2244 LEU Chi-restraints excluded: chain E residue 2245 ASP Chi-restraints excluded: chain E residue 2260 VAL Chi-restraints excluded: chain E residue 2275 ILE Chi-restraints excluded: chain E residue 2280 THR Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2320 LEU Chi-restraints excluded: chain E residue 2350 GLU Chi-restraints excluded: chain E residue 2365 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 454 ARG Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 552 SER Chi-restraints excluded: chain F residue 566 ILE Chi-restraints excluded: chain F residue 574 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 641 ASP Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain F residue 744 ILE Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 939 LEU Chi-restraints excluded: chain F residue 969 LEU Chi-restraints excluded: chain F residue 991 ILE Chi-restraints excluded: chain F residue 1010 THR Chi-restraints excluded: chain F residue 1090 ASP Chi-restraints excluded: chain F residue 1143 VAL Chi-restraints excluded: chain F residue 1177 GLN Chi-restraints excluded: chain F residue 1249 ASN Chi-restraints excluded: chain F residue 1256 ILE Chi-restraints excluded: chain F residue 1270 THR Chi-restraints excluded: chain F residue 1337 LEU Chi-restraints excluded: chain F residue 1354 GLU Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1399 LEU Chi-restraints excluded: chain F residue 1408 ASP Chi-restraints excluded: chain F residue 1477 LYS Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1492 ASP Chi-restraints excluded: chain F residue 1567 ARG Chi-restraints excluded: chain F residue 1606 ILE Chi-restraints excluded: chain F residue 1626 SER Chi-restraints excluded: chain F residue 1708 GLU Chi-restraints excluded: chain F residue 1734 GLU Chi-restraints excluded: chain F residue 1747 GLU Chi-restraints excluded: chain F residue 1786 TYR Chi-restraints excluded: chain F residue 1835 LEU Chi-restraints excluded: chain F residue 1848 LEU Chi-restraints excluded: chain F residue 1852 ILE Chi-restraints excluded: chain F residue 1934 ILE Chi-restraints excluded: chain F residue 1950 VAL Chi-restraints excluded: chain F residue 2056 PHE Chi-restraints excluded: chain F residue 2105 ILE Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2227 CYS Chi-restraints excluded: chain F residue 2245 ASP Chi-restraints excluded: chain F residue 2260 VAL Chi-restraints excluded: chain F residue 2270 ASP Chi-restraints excluded: chain F residue 2280 THR Chi-restraints excluded: chain F residue 2297 VAL Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain F residue 2350 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 535 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 316 optimal weight: 9.9990 chunk 405 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 467 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 chunk 553 optimal weight: 0.0030 chunk 346 optimal weight: 5.9990 chunk 337 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1903 GLN ** E2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2115 ASN E2349 GLN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1048 ASN F1371 HIS ** F1484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2301 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 47532 Z= 0.244 Angle : 0.683 10.544 64362 Z= 0.346 Chirality : 0.044 0.295 7376 Planarity : 0.004 0.054 8094 Dihedral : 7.103 178.367 6298 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.78 % Allowed : 20.55 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.11), residues: 5736 helix: -0.25 (0.09), residues: 3606 sheet: -0.62 (0.62), residues: 66 loop : -2.10 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F1770 HIS 0.009 0.001 HIS F1891 PHE 0.031 0.002 PHE F1673 TYR 0.032 0.002 TYR E1312 ARG 0.013 0.000 ARG F 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 638 time to evaluate : 5.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 308 GLN cc_start: 0.8230 (pp30) cc_final: 0.8015 (pp30) REVERT: D 346 MET cc_start: 0.7001 (mmm) cc_final: 0.6443 (mmm) REVERT: D 624 LYS cc_start: 0.8648 (mppt) cc_final: 0.8422 (tptt) REVERT: D 628 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7028 (tp30) REVERT: C 308 GLN cc_start: 0.8243 (pp30) cc_final: 0.8038 (pp30) REVERT: C 624 LYS cc_start: 0.8690 (mppt) cc_final: 0.8459 (tptt) REVERT: C 628 GLU cc_start: 0.7552 (tm-30) cc_final: 0.6926 (tp30) REVERT: C 661 ARG cc_start: 0.7851 (ppp80) cc_final: 0.7647 (ptt180) REVERT: C 699 MET cc_start: 0.7475 (tmm) cc_final: 0.7182 (tmm) REVERT: E 11 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7611 (tm) REVERT: E 96 ASN cc_start: 0.7072 (p0) cc_final: 0.6502 (m-40) REVERT: E 452 ILE cc_start: 0.6028 (OUTLIER) cc_final: 0.5551 (mt) REVERT: E 454 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7354 (mtp85) REVERT: E 574 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: E 640 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.8070 (p0) REVERT: E 674 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8289 (tptp) REVERT: E 1177 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: E 1301 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8381 (m-30) REVERT: E 1324 ASP cc_start: 0.7131 (t70) cc_final: 0.6878 (t70) REVERT: E 1354 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: E 1436 LYS cc_start: 0.7412 (pttm) cc_final: 0.7202 (pttm) REVERT: E 1494 LYS cc_start: 0.8702 (pmtt) cc_final: 0.8364 (mmtt) REVERT: E 1747 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: E 1853 THR cc_start: 0.8810 (t) cc_final: 0.8585 (t) REVERT: E 1879 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8085 (pp20) REVERT: E 1887 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: E 1895 TYR cc_start: 0.8480 (p90) cc_final: 0.7957 (p90) REVERT: E 1905 LEU cc_start: 0.7652 (mm) cc_final: 0.6933 (tt) REVERT: E 1907 ARG cc_start: 0.7327 (mtt-85) cc_final: 0.6583 (mtt-85) REVERT: E 2056 PHE cc_start: 0.5897 (OUTLIER) cc_final: 0.4448 (p90) REVERT: E 2105 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8538 (tp) REVERT: E 2228 GLU cc_start: 0.7768 (mp0) cc_final: 0.7338 (mp0) REVERT: F 11 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7626 (tm) REVERT: F 132 LYS cc_start: 0.6157 (OUTLIER) cc_final: 0.5629 (ptmm) REVERT: F 154 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7748 (mtp) REVERT: F 231 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8079 (tt) REVERT: F 454 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7517 (mtp85) REVERT: F 574 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8094 (mp10) REVERT: F 664 MET cc_start: 0.8611 (mtt) cc_final: 0.8352 (mtt) REVERT: F 674 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8365 (tptp) REVERT: F 1067 VAL cc_start: 0.8729 (t) cc_final: 0.8465 (m) REVERT: F 1177 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: F 1324 ASP cc_start: 0.7132 (t70) cc_final: 0.6902 (t70) REVERT: F 1399 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8367 (tt) REVERT: F 1436 LYS cc_start: 0.7506 (pttm) cc_final: 0.7229 (pttm) REVERT: F 1488 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8117 (mmmt) REVERT: F 1494 LYS cc_start: 0.8603 (pmtt) cc_final: 0.8261 (mmtt) REVERT: F 1685 ASP cc_start: 0.8044 (t0) cc_final: 0.7737 (t70) REVERT: F 1704 ASP cc_start: 0.7624 (m-30) cc_final: 0.7365 (m-30) REVERT: F 1727 GLU cc_start: 0.8138 (mp0) cc_final: 0.7739 (mp0) REVERT: F 1747 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6209 (mp0) REVERT: F 1845 ARG cc_start: 0.8246 (mtp85) cc_final: 0.8027 (ttt-90) REVERT: F 1848 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8125 (tt) REVERT: F 1873 MET cc_start: 0.7055 (ttm) cc_final: 0.6681 (tmt) REVERT: F 1895 TYR cc_start: 0.8439 (p90) cc_final: 0.7937 (p90) REVERT: F 2056 PHE cc_start: 0.5808 (OUTLIER) cc_final: 0.3864 (p90) REVERT: F 2089 GLN cc_start: 0.7504 (tp40) cc_final: 0.7296 (tp40) REVERT: F 2131 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8138 (mmt) REVERT: F 2228 GLU cc_start: 0.7646 (mp0) cc_final: 0.7233 (mp0) REVERT: F 2323 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8326 (tm) REVERT: F 2331 ASP cc_start: 0.8457 (t0) cc_final: 0.8217 (t0) outliers start: 245 outliers final: 138 residues processed: 820 average time/residue: 1.3197 time to fit residues: 1403.0013 Evaluate side-chains 737 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 571 time to evaluate : 5.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 628 GLU Chi-restraints excluded: chain D residue 661 ARG Chi-restraints excluded: chain D residue 695 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 332 HIS Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 452 ILE Chi-restraints excluded: chain E residue 454 ARG Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 467 CYS Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 603 SER Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 640 ASN Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 700 VAL Chi-restraints excluded: chain E residue 744 ILE Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 854 HIS Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 969 LEU Chi-restraints excluded: chain E residue 991 ILE Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1023 LEU Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1177 GLN Chi-restraints excluded: chain E residue 1249 ASN Chi-restraints excluded: chain E residue 1255 LYS Chi-restraints excluded: chain E residue 1256 ILE Chi-restraints excluded: chain E residue 1270 THR Chi-restraints excluded: chain E residue 1278 VAL Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1301 ASP Chi-restraints excluded: chain E residue 1343 ARG Chi-restraints excluded: chain E residue 1354 GLU Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1399 LEU Chi-restraints excluded: chain E residue 1408 ASP Chi-restraints excluded: chain E residue 1477 LYS Chi-restraints excluded: chain E residue 1499 MET Chi-restraints excluded: chain E residue 1549 GLN Chi-restraints excluded: chain E residue 1567 ARG Chi-restraints excluded: chain E residue 1606 ILE Chi-restraints excluded: chain E residue 1626 SER Chi-restraints excluded: chain E residue 1659 ASP Chi-restraints excluded: chain E residue 1708 GLU Chi-restraints excluded: chain E residue 1747 GLU Chi-restraints excluded: chain E residue 1786 TYR Chi-restraints excluded: chain E residue 1835 LEU Chi-restraints excluded: chain E residue 1848 LEU Chi-restraints excluded: chain E residue 1852 ILE Chi-restraints excluded: chain E residue 1879 GLU Chi-restraints excluded: chain E residue 1887 GLU Chi-restraints excluded: chain E residue 1934 ILE Chi-restraints excluded: chain E residue 1950 VAL Chi-restraints excluded: chain E residue 2056 PHE Chi-restraints excluded: chain E residue 2105 ILE Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2171 LEU Chi-restraints excluded: chain E residue 2227 CYS Chi-restraints excluded: chain E residue 2244 LEU Chi-restraints excluded: chain E residue 2245 ASP Chi-restraints excluded: chain E residue 2260 VAL Chi-restraints excluded: chain E residue 2280 THR Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2350 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 454 ARG Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 552 SER Chi-restraints excluded: chain F residue 566 ILE Chi-restraints excluded: chain F residue 574 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 603 SER Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 641 ASP Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain F residue 744 ILE Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 854 HIS Chi-restraints excluded: chain F residue 891 ILE Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 939 LEU Chi-restraints excluded: chain F residue 969 LEU Chi-restraints excluded: chain F residue 991 ILE Chi-restraints excluded: chain F residue 1010 THR Chi-restraints excluded: chain F residue 1143 VAL Chi-restraints excluded: chain F residue 1177 GLN Chi-restraints excluded: chain F residue 1249 ASN Chi-restraints excluded: chain F residue 1256 ILE Chi-restraints excluded: chain F residue 1270 THR Chi-restraints excluded: chain F residue 1278 VAL Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1312 TYR Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1399 LEU Chi-restraints excluded: chain F residue 1408 ASP Chi-restraints excluded: chain F residue 1477 LYS Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1492 ASP Chi-restraints excluded: chain F residue 1567 ARG Chi-restraints excluded: chain F residue 1606 ILE Chi-restraints excluded: chain F residue 1626 SER Chi-restraints excluded: chain F residue 1659 ASP Chi-restraints excluded: chain F residue 1708 GLU Chi-restraints excluded: chain F residue 1734 GLU Chi-restraints excluded: chain F residue 1747 GLU Chi-restraints excluded: chain F residue 1786 TYR Chi-restraints excluded: chain F residue 1835 LEU Chi-restraints excluded: chain F residue 1848 LEU Chi-restraints excluded: chain F residue 1852 ILE Chi-restraints excluded: chain F residue 1934 ILE Chi-restraints excluded: chain F residue 1950 VAL Chi-restraints excluded: chain F residue 2056 PHE Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2227 CYS Chi-restraints excluded: chain F residue 2245 ASP Chi-restraints excluded: chain F residue 2260 VAL Chi-restraints excluded: chain F residue 2270 ASP Chi-restraints excluded: chain F residue 2275 ILE Chi-restraints excluded: chain F residue 2280 THR Chi-restraints excluded: chain F residue 2297 VAL Chi-restraints excluded: chain F residue 2320 LEU Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain F residue 2350 GLU Chi-restraints excluded: chain F residue 2365 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 342 optimal weight: 40.0000 chunk 220 optimal weight: 9.9990 chunk 330 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 107 optimal weight: 0.0270 chunk 351 optimal weight: 6.9990 chunk 376 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 434 optimal weight: 0.8980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 481 HIS ** D 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN C 481 HIS ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 GLN E 444 GLN E 525 ASN E 531 ASN E 868 GLN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 GLN E1048 ASN E1059 ASN ** E1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1903 GLN ** E2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2115 ASN ** E2333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 ASN F 640 ASN ** F 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1048 ASN F1059 ASN ** F1484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 47532 Z= 0.177 Angle : 0.649 11.196 64362 Z= 0.328 Chirality : 0.042 0.260 7376 Planarity : 0.004 0.052 8094 Dihedral : 6.860 179.685 6298 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.95 % Allowed : 21.82 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.19 (0.11), residues: 5736 helix: -0.06 (0.09), residues: 3588 sheet: -0.74 (0.61), residues: 66 loop : -2.02 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E1770 HIS 0.010 0.001 HIS F1891 PHE 0.023 0.001 PHE F1673 TYR 0.089 0.001 TYR F1312 ARG 0.016 0.000 ARG F 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 675 time to evaluate : 5.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 308 GLN cc_start: 0.8124 (pp30) cc_final: 0.7869 (pp30) REVERT: D 573 GLU cc_start: 0.7672 (mp0) cc_final: 0.7352 (pm20) REVERT: D 624 LYS cc_start: 0.8617 (mppt) cc_final: 0.8407 (tptt) REVERT: C 308 GLN cc_start: 0.8129 (pp30) cc_final: 0.7875 (pp30) REVERT: C 624 LYS cc_start: 0.8675 (mppt) cc_final: 0.8460 (tptt) REVERT: C 628 GLU cc_start: 0.7446 (tm-30) cc_final: 0.6778 (tp30) REVERT: C 699 MET cc_start: 0.7439 (tmm) cc_final: 0.7127 (tmm) REVERT: E 11 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7563 (tm) REVERT: E 438 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: E 452 ILE cc_start: 0.5734 (OUTLIER) cc_final: 0.5337 (mt) REVERT: E 574 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: E 578 MET cc_start: 0.8001 (ptm) cc_final: 0.7792 (ptp) REVERT: E 674 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8285 (tptp) REVERT: E 1177 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: E 1225 TYR cc_start: 0.8064 (t80) cc_final: 0.7754 (t80) REVERT: E 1301 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8416 (m-30) REVERT: E 1328 THR cc_start: 0.8030 (p) cc_final: 0.7821 (p) REVERT: E 1393 ARG cc_start: 0.7512 (mtm110) cc_final: 0.7179 (mtm110) REVERT: E 1436 LYS cc_start: 0.7397 (pttm) cc_final: 0.7146 (pttm) REVERT: E 1477 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8025 (tppt) REVERT: E 1488 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7916 (tppt) REVERT: E 1549 GLN cc_start: 0.7890 (tp40) cc_final: 0.7623 (mm-40) REVERT: E 1708 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: E 1895 TYR cc_start: 0.8409 (p90) cc_final: 0.7850 (p90) REVERT: E 1905 LEU cc_start: 0.7378 (mm) cc_final: 0.6770 (tt) REVERT: E 1907 ARG cc_start: 0.7088 (mtt-85) cc_final: 0.6391 (mtt-85) REVERT: E 2056 PHE cc_start: 0.5765 (OUTLIER) cc_final: 0.4256 (p90) REVERT: E 2228 GLU cc_start: 0.7630 (mp0) cc_final: 0.7202 (mp0) REVERT: E 2333 GLN cc_start: 0.8293 (pp30) cc_final: 0.7824 (pp30) REVERT: F 11 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7486 (tm) REVERT: F 132 LYS cc_start: 0.6330 (OUTLIER) cc_final: 0.5168 (ptmt) REVERT: F 452 ILE cc_start: 0.6003 (OUTLIER) cc_final: 0.5680 (mt) REVERT: F 664 MET cc_start: 0.8612 (mtt) cc_final: 0.8337 (mtt) REVERT: F 674 LYS cc_start: 0.8531 (ttmm) cc_final: 0.8317 (tptp) REVERT: F 830 ASP cc_start: 0.7975 (m-30) cc_final: 0.7110 (p0) REVERT: F 1067 VAL cc_start: 0.8613 (t) cc_final: 0.8347 (m) REVERT: F 1177 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7040 (tm-30) REVERT: F 1225 TYR cc_start: 0.8019 (t80) cc_final: 0.7739 (t80) REVERT: F 1399 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8356 (tt) REVERT: F 1436 LYS cc_start: 0.7539 (pttm) cc_final: 0.7262 (pttm) REVERT: F 1477 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8123 (tppt) REVERT: F 1488 LYS cc_start: 0.8374 (mmmt) cc_final: 0.7858 (tppt) REVERT: F 1494 LYS cc_start: 0.8532 (pmtt) cc_final: 0.8238 (mmtt) REVERT: F 1685 ASP cc_start: 0.8013 (t0) cc_final: 0.7766 (t70) REVERT: F 1704 ASP cc_start: 0.7574 (m-30) cc_final: 0.7324 (m-30) REVERT: F 1708 GLU cc_start: 0.7784 (pp20) cc_final: 0.7494 (pt0) REVERT: F 1727 GLU cc_start: 0.8108 (mp0) cc_final: 0.7728 (mp0) REVERT: F 1734 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: F 1747 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6175 (mp0) REVERT: F 1848 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8161 (tt) REVERT: F 1873 MET cc_start: 0.6833 (ttm) cc_final: 0.6555 (tmt) REVERT: F 1895 TYR cc_start: 0.8378 (p90) cc_final: 0.7839 (p90) REVERT: F 2131 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8137 (mmt) REVERT: F 2228 GLU cc_start: 0.7709 (mp0) cc_final: 0.7318 (mp0) REVERT: F 2331 ASP cc_start: 0.8516 (t0) cc_final: 0.8227 (t0) outliers start: 202 outliers final: 91 residues processed: 823 average time/residue: 1.3034 time to fit residues: 1397.1557 Evaluate side-chains 696 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 585 time to evaluate : 5.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 452 ILE Chi-restraints excluded: chain E residue 467 CYS Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 603 SER Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 700 VAL Chi-restraints excluded: chain E residue 744 ILE Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 920 LYS Chi-restraints excluded: chain E residue 969 LEU Chi-restraints excluded: chain E residue 991 ILE Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1036 ILE Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1177 GLN Chi-restraints excluded: chain E residue 1249 ASN Chi-restraints excluded: chain E residue 1278 VAL Chi-restraints excluded: chain E residue 1301 ASP Chi-restraints excluded: chain E residue 1310 THR Chi-restraints excluded: chain E residue 1343 ARG Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1477 LYS Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1499 MET Chi-restraints excluded: chain E residue 1567 ARG Chi-restraints excluded: chain E residue 1626 SER Chi-restraints excluded: chain E residue 1708 GLU Chi-restraints excluded: chain E residue 1786 TYR Chi-restraints excluded: chain E residue 1835 LEU Chi-restraints excluded: chain E residue 1848 LEU Chi-restraints excluded: chain E residue 1852 ILE Chi-restraints excluded: chain E residue 1934 ILE Chi-restraints excluded: chain E residue 1950 VAL Chi-restraints excluded: chain E residue 2016 VAL Chi-restraints excluded: chain E residue 2056 PHE Chi-restraints excluded: chain E residue 2227 CYS Chi-restraints excluded: chain E residue 2244 LEU Chi-restraints excluded: chain E residue 2245 ASP Chi-restraints excluded: chain E residue 2260 VAL Chi-restraints excluded: chain E residue 2275 ILE Chi-restraints excluded: chain E residue 2280 THR Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2320 LEU Chi-restraints excluded: chain E residue 2350 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 566 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain F residue 744 ILE Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 969 LEU Chi-restraints excluded: chain F residue 991 ILE Chi-restraints excluded: chain F residue 1010 THR Chi-restraints excluded: chain F residue 1143 VAL Chi-restraints excluded: chain F residue 1177 GLN Chi-restraints excluded: chain F residue 1270 THR Chi-restraints excluded: chain F residue 1278 VAL Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1399 LEU Chi-restraints excluded: chain F residue 1477 LYS Chi-restraints excluded: chain F residue 1492 ASP Chi-restraints excluded: chain F residue 1567 ARG Chi-restraints excluded: chain F residue 1626 SER Chi-restraints excluded: chain F residue 1734 GLU Chi-restraints excluded: chain F residue 1747 GLU Chi-restraints excluded: chain F residue 1786 TYR Chi-restraints excluded: chain F residue 1835 LEU Chi-restraints excluded: chain F residue 1848 LEU Chi-restraints excluded: chain F residue 1934 ILE Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2227 CYS Chi-restraints excluded: chain F residue 2260 VAL Chi-restraints excluded: chain F residue 2280 THR Chi-restraints excluded: chain F residue 2297 VAL Chi-restraints excluded: chain F residue 2320 LEU Chi-restraints excluded: chain F residue 2350 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 503 optimal weight: 8.9990 chunk 530 optimal weight: 0.2980 chunk 483 optimal weight: 1.9990 chunk 515 optimal weight: 20.0000 chunk 529 optimal weight: 1.9990 chunk 310 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 404 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 465 optimal weight: 8.9990 chunk 487 optimal weight: 7.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 444 GLN ** E 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 868 GLN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1048 ASN ** E1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 633 GLN F 640 ASN ** F 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 928 GLN ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 47532 Z= 0.280 Angle : 0.705 11.317 64362 Z= 0.355 Chirality : 0.045 0.311 7376 Planarity : 0.004 0.059 8094 Dihedral : 6.899 177.648 6298 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.89 % Allowed : 22.95 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.16 (0.11), residues: 5736 helix: -0.04 (0.09), residues: 3576 sheet: -0.77 (0.61), residues: 66 loop : -1.99 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F1169 HIS 0.008 0.001 HIS C 334 PHE 0.034 0.002 PHE E1673 TYR 0.032 0.002 TYR F2361 ARG 0.016 0.001 ARG F 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 596 time to evaluate : 6.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 308 GLN cc_start: 0.8237 (pp30) cc_final: 0.8023 (pp30) REVERT: D 624 LYS cc_start: 0.8671 (mppt) cc_final: 0.8395 (tptt) REVERT: C 308 GLN cc_start: 0.8237 (pp30) cc_final: 0.8028 (pp30) REVERT: C 624 LYS cc_start: 0.8712 (mppt) cc_final: 0.8444 (tptt) REVERT: C 628 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6910 (tp30) REVERT: C 699 MET cc_start: 0.7453 (tmm) cc_final: 0.7133 (tmm) REVERT: E 438 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: E 452 ILE cc_start: 0.5846 (OUTLIER) cc_final: 0.5398 (mt) REVERT: E 574 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7960 (mp10) REVERT: E 578 MET cc_start: 0.8126 (ptm) cc_final: 0.7693 (ptp) REVERT: E 674 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8354 (tptp) REVERT: E 923 ILE cc_start: 0.7927 (mm) cc_final: 0.7703 (tp) REVERT: E 1177 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: E 1225 TYR cc_start: 0.8121 (t80) cc_final: 0.7785 (t80) REVERT: E 1301 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: E 1393 ARG cc_start: 0.7573 (mtm110) cc_final: 0.7230 (mtm110) REVERT: E 1436 LYS cc_start: 0.7529 (pttm) cc_final: 0.7328 (pttm) REVERT: E 1488 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7885 (tppt) REVERT: E 1494 LYS cc_start: 0.8557 (pmtt) cc_final: 0.8286 (mmmt) REVERT: E 1708 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7534 (pt0) REVERT: E 1747 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: E 1887 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: E 1895 TYR cc_start: 0.8453 (p90) cc_final: 0.8037 (p90) REVERT: E 1905 LEU cc_start: 0.7502 (mm) cc_final: 0.6744 (tt) REVERT: E 1907 ARG cc_start: 0.7362 (mtt-85) cc_final: 0.6659 (mtt-85) REVERT: E 2056 PHE cc_start: 0.5900 (OUTLIER) cc_final: 0.4466 (p90) REVERT: E 2228 GLU cc_start: 0.7789 (mp0) cc_final: 0.7319 (mp0) REVERT: E 2333 GLN cc_start: 0.8419 (pp30) cc_final: 0.7814 (pp30) REVERT: F 132 LYS cc_start: 0.6389 (OUTLIER) cc_final: 0.5756 (ptmm) REVERT: F 452 ILE cc_start: 0.6030 (OUTLIER) cc_final: 0.5696 (mt) REVERT: F 578 MET cc_start: 0.8143 (ptm) cc_final: 0.7924 (ptp) REVERT: F 664 MET cc_start: 0.8670 (mtt) cc_final: 0.8372 (mtt) REVERT: F 674 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8336 (tptp) REVERT: F 830 ASP cc_start: 0.8002 (m-30) cc_final: 0.7136 (p0) REVERT: F 1067 VAL cc_start: 0.8719 (t) cc_final: 0.8468 (m) REVERT: F 1177 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: F 1225 TYR cc_start: 0.8135 (t80) cc_final: 0.7832 (t80) REVERT: F 1399 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8352 (tt) REVERT: F 1494 LYS cc_start: 0.8617 (pmtt) cc_final: 0.8288 (mmtt) REVERT: F 1704 ASP cc_start: 0.7604 (m-30) cc_final: 0.7342 (m-30) REVERT: F 1708 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7537 (pt0) REVERT: F 1718 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8237 (mp) REVERT: F 1727 GLU cc_start: 0.8126 (mp0) cc_final: 0.7736 (mp0) REVERT: F 1747 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: F 1848 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8173 (tt) REVERT: F 1873 MET cc_start: 0.6933 (ttm) cc_final: 0.6603 (tmt) REVERT: F 1895 TYR cc_start: 0.8428 (p90) cc_final: 0.7890 (p90) REVERT: F 2056 PHE cc_start: 0.5883 (OUTLIER) cc_final: 0.3924 (p90) REVERT: F 2105 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8496 (tp) REVERT: F 2131 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8101 (mmt) REVERT: F 2228 GLU cc_start: 0.7620 (mp0) cc_final: 0.7193 (mp0) REVERT: F 2331 ASP cc_start: 0.8531 (t0) cc_final: 0.8307 (t0) outliers start: 199 outliers final: 116 residues processed: 736 average time/residue: 1.3466 time to fit residues: 1280.3743 Evaluate side-chains 709 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 571 time to evaluate : 5.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 695 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 291 ASN Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 332 HIS Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 452 ILE Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 467 CYS Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 700 VAL Chi-restraints excluded: chain E residue 744 ILE Chi-restraints excluded: chain E residue 755 LEU Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 920 LYS Chi-restraints excluded: chain E residue 969 LEU Chi-restraints excluded: chain E residue 991 ILE Chi-restraints excluded: chain E residue 1023 LEU Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1177 GLN Chi-restraints excluded: chain E residue 1270 THR Chi-restraints excluded: chain E residue 1278 VAL Chi-restraints excluded: chain E residue 1301 ASP Chi-restraints excluded: chain E residue 1310 THR Chi-restraints excluded: chain E residue 1312 TYR Chi-restraints excluded: chain E residue 1343 ARG Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1477 LYS Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1499 MET Chi-restraints excluded: chain E residue 1567 ARG Chi-restraints excluded: chain E residue 1606 ILE Chi-restraints excluded: chain E residue 1626 SER Chi-restraints excluded: chain E residue 1708 GLU Chi-restraints excluded: chain E residue 1747 GLU Chi-restraints excluded: chain E residue 1786 TYR Chi-restraints excluded: chain E residue 1835 LEU Chi-restraints excluded: chain E residue 1848 LEU Chi-restraints excluded: chain E residue 1852 ILE Chi-restraints excluded: chain E residue 1887 GLU Chi-restraints excluded: chain E residue 1934 ILE Chi-restraints excluded: chain E residue 2016 VAL Chi-restraints excluded: chain E residue 2056 PHE Chi-restraints excluded: chain E residue 2121 SER Chi-restraints excluded: chain E residue 2227 CYS Chi-restraints excluded: chain E residue 2245 ASP Chi-restraints excluded: chain E residue 2260 VAL Chi-restraints excluded: chain E residue 2280 THR Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2350 GLU Chi-restraints excluded: chain E residue 2365 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 552 SER Chi-restraints excluded: chain F residue 566 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 603 SER Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain F residue 744 ILE Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 969 LEU Chi-restraints excluded: chain F residue 991 ILE Chi-restraints excluded: chain F residue 1023 LEU Chi-restraints excluded: chain F residue 1177 GLN Chi-restraints excluded: chain F residue 1249 ASN Chi-restraints excluded: chain F residue 1270 THR Chi-restraints excluded: chain F residue 1278 VAL Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1312 TYR Chi-restraints excluded: chain F residue 1343 ARG Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1399 LEU Chi-restraints excluded: chain F residue 1408 ASP Chi-restraints excluded: chain F residue 1477 LYS Chi-restraints excluded: chain F residue 1492 ASP Chi-restraints excluded: chain F residue 1567 ARG Chi-restraints excluded: chain F residue 1626 SER Chi-restraints excluded: chain F residue 1708 GLU Chi-restraints excluded: chain F residue 1718 LEU Chi-restraints excluded: chain F residue 1734 GLU Chi-restraints excluded: chain F residue 1747 GLU Chi-restraints excluded: chain F residue 1786 TYR Chi-restraints excluded: chain F residue 1835 LEU Chi-restraints excluded: chain F residue 1848 LEU Chi-restraints excluded: chain F residue 1852 ILE Chi-restraints excluded: chain F residue 1934 ILE Chi-restraints excluded: chain F residue 2016 VAL Chi-restraints excluded: chain F residue 2056 PHE Chi-restraints excluded: chain F residue 2105 ILE Chi-restraints excluded: chain F residue 2121 SER Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2215 MET Chi-restraints excluded: chain F residue 2227 CYS Chi-restraints excluded: chain F residue 2260 VAL Chi-restraints excluded: chain F residue 2280 THR Chi-restraints excluded: chain F residue 2297 VAL Chi-restraints excluded: chain F residue 2320 LEU Chi-restraints excluded: chain F residue 2350 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 513 optimal weight: 0.9980 chunk 338 optimal weight: 0.0010 chunk 545 optimal weight: 10.0000 chunk 332 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 378 optimal weight: 8.9990 chunk 571 optimal weight: 3.9990 chunk 526 optimal weight: 20.0000 chunk 455 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 351 optimal weight: 0.6980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 HIS ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 GLN E 640 ASN E 868 GLN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1048 ASN ** E1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1903 GLN ** E2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 633 GLN F 640 ASN ** F 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 47532 Z= 0.181 Angle : 0.672 11.765 64362 Z= 0.336 Chirality : 0.043 0.258 7376 Planarity : 0.004 0.055 8094 Dihedral : 6.747 179.789 6298 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.71 % Allowed : 24.28 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.11), residues: 5736 helix: 0.10 (0.09), residues: 3548 sheet: -0.74 (0.61), residues: 66 loop : -1.95 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F1169 HIS 0.007 0.001 HIS E1891 PHE 0.030 0.001 PHE E1673 TYR 0.032 0.001 TYR F2361 ARG 0.015 0.000 ARG F 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11472 Ramachandran restraints generated. 5736 Oldfield, 0 Emsley, 5736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 635 time to evaluate : 5.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 308 GLN cc_start: 0.8177 (pp30) cc_final: 0.7923 (pp30) REVERT: D 573 GLU cc_start: 0.7585 (mp0) cc_final: 0.7356 (pm20) REVERT: C 308 GLN cc_start: 0.8180 (pp30) cc_final: 0.7930 (pp30) REVERT: C 699 MET cc_start: 0.7473 (tmm) cc_final: 0.7148 (tmm) REVERT: E 11 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.6734 (mt) REVERT: E 249 ASP cc_start: 0.7298 (m-30) cc_final: 0.7075 (m-30) REVERT: E 438 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: E 452 ILE cc_start: 0.5799 (OUTLIER) cc_final: 0.5395 (mt) REVERT: E 574 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: E 578 MET cc_start: 0.7987 (ptm) cc_final: 0.7785 (ptp) REVERT: E 1225 TYR cc_start: 0.7993 (t80) cc_final: 0.7600 (t80) REVERT: E 1393 ARG cc_start: 0.7514 (mtm110) cc_final: 0.7242 (mpt90) REVERT: E 1477 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8029 (tppt) REVERT: E 1488 LYS cc_start: 0.8404 (mmmt) cc_final: 0.7913 (tppt) REVERT: E 1494 LYS cc_start: 0.8505 (pmtt) cc_final: 0.8242 (mmmt) REVERT: E 1499 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8492 (tmm) REVERT: E 1549 GLN cc_start: 0.7860 (tp40) cc_final: 0.7637 (mm-40) REVERT: E 1708 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7423 (pt0) REVERT: E 1827 TYR cc_start: 0.7893 (t80) cc_final: 0.7660 (t80) REVERT: E 1887 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: E 1895 TYR cc_start: 0.8388 (p90) cc_final: 0.7831 (p90) REVERT: E 1905 LEU cc_start: 0.7350 (mm) cc_final: 0.6680 (tt) REVERT: E 1907 ARG cc_start: 0.7272 (mtt-85) cc_final: 0.6551 (mtt-85) REVERT: E 2056 PHE cc_start: 0.5661 (OUTLIER) cc_final: 0.4165 (p90) REVERT: E 2130 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7113 (tm-30) REVERT: E 2131 MET cc_start: 0.8416 (mmm) cc_final: 0.7359 (mpp) REVERT: E 2228 GLU cc_start: 0.7769 (mp0) cc_final: 0.7295 (mp0) REVERT: E 2333 GLN cc_start: 0.8283 (pp30) cc_final: 0.7772 (pp30) REVERT: F 11 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.6693 (mt) REVERT: F 132 LYS cc_start: 0.6262 (OUTLIER) cc_final: 0.5097 (ptmt) REVERT: F 452 ILE cc_start: 0.5925 (OUTLIER) cc_final: 0.5671 (mt) REVERT: F 830 ASP cc_start: 0.7953 (m-30) cc_final: 0.7103 (p0) REVERT: F 1067 VAL cc_start: 0.8612 (t) cc_final: 0.8345 (m) REVERT: F 1225 TYR cc_start: 0.8005 (t80) cc_final: 0.7645 (t80) REVERT: F 1399 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8332 (tt) REVERT: F 1477 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8120 (tppt) REVERT: F 1488 LYS cc_start: 0.8393 (mmmt) cc_final: 0.7908 (tppt) REVERT: F 1494 LYS cc_start: 0.8545 (pmtt) cc_final: 0.8239 (mmtt) REVERT: F 1502 SER cc_start: 0.9019 (m) cc_final: 0.8678 (p) REVERT: F 1549 GLN cc_start: 0.7899 (tp40) cc_final: 0.7642 (mm-40) REVERT: F 1685 ASP cc_start: 0.8019 (t0) cc_final: 0.7764 (t70) REVERT: F 1704 ASP cc_start: 0.7571 (m-30) cc_final: 0.7327 (m-30) REVERT: F 1708 GLU cc_start: 0.7724 (pp20) cc_final: 0.7448 (pt0) REVERT: F 1718 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8221 (mp) REVERT: F 1734 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: F 1747 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6160 (mp0) REVERT: F 1873 MET cc_start: 0.6750 (ttm) cc_final: 0.6337 (tmm) REVERT: F 1895 TYR cc_start: 0.8327 (p90) cc_final: 0.7749 (p90) REVERT: F 2130 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7135 (tm-30) REVERT: F 2131 MET cc_start: 0.8401 (mmm) cc_final: 0.7573 (mpp) REVERT: F 2228 GLU cc_start: 0.7736 (mp0) cc_final: 0.7325 (mp0) REVERT: F 2331 ASP cc_start: 0.8547 (t0) cc_final: 0.8220 (t0) outliers start: 138 outliers final: 78 residues processed: 743 average time/residue: 1.3441 time to fit residues: 1296.9777 Evaluate side-chains 684 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 589 time to evaluate : 5.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 291 ASN Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 332 HIS Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 452 ILE Chi-restraints excluded: chain E residue 467 CYS Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 700 VAL Chi-restraints excluded: chain E residue 744 ILE Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 854 HIS Chi-restraints excluded: chain E residue 920 LYS Chi-restraints excluded: chain E residue 969 LEU Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1270 THR Chi-restraints excluded: chain E residue 1310 THR Chi-restraints excluded: chain E residue 1312 TYR Chi-restraints excluded: chain E residue 1343 ARG Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1408 ASP Chi-restraints excluded: chain E residue 1477 LYS Chi-restraints excluded: chain E residue 1499 MET Chi-restraints excluded: chain E residue 1567 ARG Chi-restraints excluded: chain E residue 1626 SER Chi-restraints excluded: chain E residue 1708 GLU Chi-restraints excluded: chain E residue 1786 TYR Chi-restraints excluded: chain E residue 1835 LEU Chi-restraints excluded: chain E residue 1852 ILE Chi-restraints excluded: chain E residue 1887 GLU Chi-restraints excluded: chain E residue 1934 ILE Chi-restraints excluded: chain E residue 2016 VAL Chi-restraints excluded: chain E residue 2056 PHE Chi-restraints excluded: chain E residue 2227 CYS Chi-restraints excluded: chain E residue 2260 VAL Chi-restraints excluded: chain E residue 2280 THR Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2350 GLU Chi-restraints excluded: chain E residue 2365 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 603 SER Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain F residue 744 ILE Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 969 LEU Chi-restraints excluded: chain F residue 991 ILE Chi-restraints excluded: chain F residue 1270 THR Chi-restraints excluded: chain F residue 1278 VAL Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1312 TYR Chi-restraints excluded: chain F residue 1343 ARG Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1399 LEU Chi-restraints excluded: chain F residue 1477 LYS Chi-restraints excluded: chain F residue 1567 ARG Chi-restraints excluded: chain F residue 1626 SER Chi-restraints excluded: chain F residue 1718 LEU Chi-restraints excluded: chain F residue 1734 GLU Chi-restraints excluded: chain F residue 1747 GLU Chi-restraints excluded: chain F residue 1786 TYR Chi-restraints excluded: chain F residue 1835 LEU Chi-restraints excluded: chain F residue 1934 ILE Chi-restraints excluded: chain F residue 2016 VAL Chi-restraints excluded: chain F residue 2227 CYS Chi-restraints excluded: chain F residue 2260 VAL Chi-restraints excluded: chain F residue 2280 THR Chi-restraints excluded: chain F residue 2320 LEU Chi-restraints excluded: chain F residue 2334 ASP Chi-restraints excluded: chain F residue 2350 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 279 optimal weight: 9.9990 chunk 361 optimal weight: 0.8980 chunk 485 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 419 optimal weight: 0.0470 chunk 67 optimal weight: 0.5980 chunk 126 optimal weight: 7.9990 chunk 456 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 468 optimal weight: 10.0000 chunk 57 optimal weight: 0.0770 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 718 GLN ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 GLN ** E1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1273 ASN ** E1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1847 ASN E1891 HIS E1903 GLN ** E2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2115 ASN ** E2333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 633 GLN F 708 ASN ** F 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1273 ASN ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.146490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.120376 restraints weight = 125358.709| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.16 r_work: 0.3529 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 47532 Z= 0.180 Angle : 0.673 11.502 64362 Z= 0.337 Chirality : 0.042 0.232 7376 Planarity : 0.004 0.061 8094 Dihedral : 6.645 179.386 6296 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.59 % Allowed : 24.79 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.11), residues: 5736 helix: 0.13 (0.09), residues: 3560 sheet: -0.67 (0.61), residues: 66 loop : -1.96 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F1169 HIS 0.006 0.001 HIS E 892 PHE 0.040 0.001 PHE F 551 TYR 0.031 0.001 TYR F2361 ARG 0.015 0.000 ARG F 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20994.97 seconds wall clock time: 370 minutes 23.42 seconds (22223.42 seconds total)