Starting phenix.real_space_refine on Mon Mar 25 06:00:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2x_11051/03_2024/6z2x_11051_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2x_11051/03_2024/6z2x_11051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2x_11051/03_2024/6z2x_11051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2x_11051/03_2024/6z2x_11051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2x_11051/03_2024/6z2x_11051_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2x_11051/03_2024/6z2x_11051_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.819 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 29986 2.51 5 N 7772 2.21 5 O 8634 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 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 PHE 1279": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 2328": "NH1" <-> "NH2" 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 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 PHE 1279": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 2328": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46604 Number of models: 1 Model: "" Number of chains: 6 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: 18692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2325, 18692 Classifications: {'peptide': 2325} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 2255} Chain breaks: 6 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 Chain: "F" Number of atoms: 18692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2325, 18692 Classifications: {'peptide': 2325} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 2255} Chain breaks: 6 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12938 SG CYS E 490 36.489 157.346 115.038 1.00 89.12 S ATOM 12962 SG CYS E 493 36.010 160.926 116.055 1.00 83.56 S ATOM 31630 SG CYS F 490 92.994 69.608 114.995 1.00 88.94 S ATOM 31654 SG CYS F 493 93.486 66.030 116.013 1.00 84.08 S 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: 28.90, per 1000 atoms: 0.62 Number of scatterers: 46604 At special positions: 0 Unit cell: (131.44, 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 8634 8.00 N 7772 7.00 C 29986 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: 18.11 Conformation dependent library (CDL) restraints added in 9.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E2402 " pdb="ZN ZN E2402 " - pdb=" NE2 HIS E 553 " pdb="ZN ZN E2402 " - pdb=" SG CYS E 493 " pdb="ZN ZN E2402 " - pdb=" SG CYS E 490 " pdb=" ZN F2402 " pdb="ZN ZN F2402 " - pdb=" NE2 HIS F 553 " pdb="ZN ZN F2402 " - pdb=" SG CYS F 493 " pdb="ZN ZN F2402 " - pdb=" SG CYS F 490 " 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: 280 helices and 6 sheets defined 57.2% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 17.36 Creating SS restraints... Processing helix chain 'D' and resid 202 through 211 Processing helix chain 'D' and resid 222 through 228 removed outlier: 4.087A pdb=" N AARG D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 264 removed outlier: 4.060A pdb=" N LYS D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 286 removed outlier: 3.760A pdb=" N ASP D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 307 removed outlier: 4.581A 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: 4.003A pdb=" N SER D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 433 " --> pdb=" O THR D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 442 Processing helix chain 'D' and resid 447 through 461 removed outlier: 4.392A pdb=" N THR D 455 " --> pdb=" O ARG D 451 " (cutoff:3.500A) removed outlier: 3.831A 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 502 through 507 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: 4.130A pdb=" N SER D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET D 589 " --> pdb=" O GLU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 621 removed outlier: 3.954A pdb=" N ILE D 608 " --> pdb=" O ARG D 604 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU D 609 " --> pdb=" O CYS D 605 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR D 613 " --> pdb=" O GLU D 609 " (cutoff:3.500A) removed outlier: 3.992A 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: 3.654A pdb=" N LYS D 632 " --> pdb=" O GLU D 628 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 649 removed outlier: 3.592A pdb=" N PHE D 645 " --> pdb=" O SER D 641 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N CYS D 648 " --> pdb=" O ARG D 644 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN D 649 " --> pdb=" O PHE D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 667 removed outlier: 3.722A 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: 5.077A pdb=" N ASN D 702 " --> pdb=" O LYS D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 725 removed outlier: 3.755A pdb=" N ILE D 724 " --> pdb=" O MET D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 744 removed outlier: 3.653A pdb=" N ASP D 739 " --> pdb=" O LEU D 735 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER D 740 " --> pdb=" O GLU D 736 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER D 744 " --> pdb=" O SER D 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 211 Processing helix chain 'C' and resid 222 through 228 removed outlier: 4.113A pdb=" N AARG C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 264 removed outlier: 4.057A pdb=" N LYS C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 286 removed outlier: 3.742A pdb=" N ASP C 272 " --> pdb=" O ASP C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 307 removed outlier: 4.554A 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: 3.998A pdb=" N SER C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 433 " --> pdb=" O THR C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 442 Processing helix chain 'C' and resid 447 through 461 removed outlier: 4.388A pdb=" N THR C 455 " --> pdb=" O ARG C 451 " (cutoff:3.500A) removed outlier: 3.846A 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 502 through 507 Processing helix chain 'C' and resid 536 through 562 removed outlier: 3.686A pdb=" N MET C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 592 removed outlier: 4.158A pdb=" N SER C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET C 589 " --> pdb=" O GLU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 621 removed outlier: 3.960A pdb=" N ILE C 608 " --> pdb=" O ARG C 604 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU C 609 " --> pdb=" O CYS C 605 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR C 613 " --> pdb=" O GLU C 609 " (cutoff:3.500A) removed outlier: 3.972A 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 633 removed outlier: 3.686A pdb=" N LYS C 632 " --> pdb=" O GLU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 649 removed outlier: 3.582A pdb=" N PHE C 645 " --> pdb=" O SER C 641 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N CYS C 648 " --> pdb=" O ARG C 644 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN C 649 " --> pdb=" O PHE C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 667 removed outlier: 4.017A pdb=" N ASP C 662 " --> pdb=" O ARG C 658 " (cutoff:3.500A) removed outlier: 3.778A 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: 5.097A pdb=" N ASN C 702 " --> pdb=" O LYS C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 725 removed outlier: 3.704A pdb=" N ILE C 724 " --> pdb=" O MET C 720 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 725 " --> pdb=" O ALA C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 744 removed outlier: 3.666A pdb=" N ASP C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER C 740 " --> pdb=" O GLU C 736 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 18 removed outlier: 3.896A pdb=" N LEU E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 57 removed outlier: 3.954A pdb=" N ASP E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 removed outlier: 3.733A pdb=" N THR E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 113 removed outlier: 3.692A pdb=" N ASP E 104 " --> pdb=" O GLN E 100 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP E 105 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE E 109 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 110 " --> pdb=" O PHE E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 131 removed outlier: 4.014A pdb=" N MET E 123 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 4.064A pdb=" N LYS E 143 " --> pdb=" O LYS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 164 removed outlier: 3.729A pdb=" N GLU E 151 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR E 162 " --> pdb=" O GLU E 158 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU E 163 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 188 removed outlier: 3.788A pdb=" N PHE E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 202 No H-bonds generated for 'chain 'E' and resid 200 through 202' Processing helix chain 'E' and resid 210 through 228 removed outlier: 3.657A pdb=" N ASN E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 252 removed outlier: 3.743A pdb=" N LYS E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE E 244 " --> pdb=" O GLN E 240 " (cutoff:3.500A) removed outlier: 3.749A 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 removed outlier: 3.526A pdb=" N CYS E 306 " --> pdb=" O LEU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 318 removed outlier: 3.709A 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 393 through 402 Processing helix chain 'E' and resid 412 through 418 Processing helix chain 'E' and resid 432 through 444 removed outlier: 3.566A pdb=" N LEU E 436 " --> pdb=" O PHE E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 470 removed outlier: 3.610A pdb=" N ALA E 466 " --> pdb=" O LEU E 462 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU E 468 " --> pdb=" O ARG E 464 " (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: 4.332A pdb=" N ARG E 590 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE E 591 " --> pdb=" O LEU E 587 " (cutoff:3.500A) removed outlier: 4.046A 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 606 through 617 removed outlier: 4.532A pdb=" N SER E 617 " --> pdb=" O LYS E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 637 removed outlier: 3.845A pdb=" N VAL E 628 " --> pdb=" O LYS E 624 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 634 " --> pdb=" O ALA E 630 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR E 637 " --> pdb=" O GLN E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 654 removed outlier: 3.693A pdb=" N ILE E 653 " --> pdb=" O LYS E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 659 through 676 Processing helix chain 'E' and resid 680 through 691 Proline residue: E 686 - end of helix Proline residue: E 689 - end of helix 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 722 No H-bonds generated for 'chain 'E' and resid 719 through 722' Processing helix chain 'E' and resid 725 through 732 removed outlier: 3.627A 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: 4.117A pdb=" N LEU E 819 " --> pdb=" O GLU E 815 " (cutoff:3.500A) Processing helix chain 'E' and resid 828 through 844 removed outlier: 3.744A pdb=" N ALA E 834 " --> pdb=" O ASP E 830 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 879 removed outlier: 4.684A pdb=" N GLN E 870 " --> pdb=" O ASP E 867 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA E 871 " --> pdb=" O GLN E 868 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU E 876 " --> pdb=" O GLN E 873 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN E 877 " --> pdb=" O LYS E 874 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP E 878 " --> pdb=" O LYS E 875 " (cutoff:3.500A) Processing helix chain 'E' and resid 881 through 891 Processing helix chain 'E' and resid 901 through 915 Processing helix chain 'E' and resid 920 through 924 Processing helix chain 'E' and resid 926 through 938 removed outlier: 4.173A pdb=" N ILE E 931 " --> pdb=" O ALA E 927 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 943 through 955 removed outlier: 3.854A pdb=" N ARG E 955 " --> pdb=" O HIS E 951 " (cutoff:3.500A) Processing helix chain 'E' and resid 959 through 964 removed outlier: 3.738A pdb=" N SER E 963 " --> pdb=" O ASP E 959 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N THR E 964 " --> pdb=" O GLU E 960 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 959 through 964' Processing helix chain 'E' and resid 967 through 975 removed outlier: 4.061A pdb=" N PHE E 972 " --> pdb=" O SER E 968 " (cutoff:3.500A) Processing helix chain 'E' and resid 982 through 997 removed outlier: 3.736A 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: 3.621A pdb=" N LEU E1014 " --> pdb=" O THR E1010 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1036 removed outlier: 3.676A pdb=" N MET E1032 " --> pdb=" O GLN E1028 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS E1035 " --> pdb=" O ARG E1031 " (cutoff:3.500A) Processing helix chain 'E' and resid 1043 through 1050 removed outlier: 3.501A pdb=" N ASN E1048 " --> pdb=" O PRO E1044 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN E1049 " --> pdb=" O ILE E1045 " (cutoff:3.500A) Processing helix chain 'E' and resid 1057 through 1075 removed outlier: 4.423A pdb=" N LEU E1062 " --> pdb=" O ILE E1058 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL E1067 " --> pdb=" O ASP E1063 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG E1070 " --> pdb=" O GLU E1066 " (cutoff:3.500A) removed outlier: 3.678A 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: 3.873A pdb=" N LYS E1154 " --> pdb=" O VAL E1150 " (cutoff:3.500A) Processing helix chain 'E' and resid 1164 through 1169 removed outlier: 3.664A pdb=" N TRP E1169 " --> pdb=" O VAL E1165 " (cutoff:3.500A) Processing helix chain 'E' and resid 1174 through 1190 removed outlier: 3.905A pdb=" N LEU E1188 " --> pdb=" O ILE E1184 " (cutoff:3.500A) Processing helix chain 'E' and resid 1207 through 1215 removed outlier: 4.095A pdb=" N LYS E1215 " --> pdb=" O LYS E1211 " (cutoff:3.500A) Processing helix chain 'E' and resid 1218 through 1224 removed outlier: 4.707A 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: 3.554A 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 1311 through 1327 removed outlier: 3.666A pdb=" N LEU E1316 " --> pdb=" O TYR E1312 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE E1321 " --> pdb=" O ASN E1317 " (cutoff:3.500A) Processing helix chain 'E' and resid 1338 through 1369 removed outlier: 3.694A pdb=" N ILE E1349 " --> pdb=" O CYS E1345 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL E1352 " --> pdb=" O SER E1348 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE E1353 " --> pdb=" O ILE E1349 " (cutoff:3.500A) Processing helix chain 'E' and resid 1381 through 1391 removed outlier: 4.002A pdb=" N ARG E1387 " --> pdb=" O ASN E1383 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE E1388 " --> pdb=" O MET E1384 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP E1389 " --> pdb=" O LEU E1385 " (cutoff:3.500A) Processing helix chain 'E' and resid 1402 through 1405 No H-bonds generated for 'chain 'E' and resid 1402 through 1405' Processing helix chain 'E' and resid 1410 through 1422 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 1467 Processing helix chain 'E' and resid 1470 through 1472 No H-bonds generated for 'chain 'E' and resid 1470 through 1472' Processing helix chain 'E' and resid 1476 through 1486 removed outlier: 3.585A pdb=" N ASP E1481 " --> pdb=" O LYS E1477 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS E1482 " --> pdb=" O LEU E1478 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL E1485 " --> pdb=" O ASP E1481 " (cutoff:3.500A) Processing helix chain 'E' and resid 1494 through 1506 removed outlier: 3.926A pdb=" N MET E1499 " --> pdb=" O THR E1495 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS E1506 " --> pdb=" O SER E1502 " (cutoff:3.500A) Processing helix chain 'E' and resid 1509 through 1513 Processing helix chain 'E' and resid 1531 through 1544 removed outlier: 3.651A pdb=" N ILE E1537 " --> pdb=" O GLU E1533 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU E1540 " --> pdb=" O SER E1536 " (cutoff:3.500A) Processing helix chain 'E' and resid 1548 through 1560 removed outlier: 3.980A pdb=" N TRP E1554 " --> pdb=" O THR E1550 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER E1560 " --> pdb=" O GLU E1556 " (cutoff:3.500A) Processing helix chain 'E' and resid 1569 through 1583 Processing helix chain 'E' and resid 1587 through 1603 Processing helix chain 'E' and resid 1618 through 1634 removed outlier: 4.109A pdb=" N LYS E1623 " --> pdb=" O ASN E1619 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP E1629 " --> pdb=" O HIS E1625 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU E1630 " --> pdb=" O SER E1626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER E1631 " --> pdb=" O LEU E1627 " (cutoff:3.500A) Processing helix chain 'E' and resid 1639 through 1652 removed outlier: 4.146A 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: 3.587A pdb=" N LYS E1688 " --> pdb=" O ALA E1684 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN E1699 " --> pdb=" O GLN E1695 " (cutoff:3.500A) Processing helix chain 'E' and resid 1703 through 1715 removed outlier: 3.597A pdb=" N SER E1707 " --> pdb=" O LEU E1703 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU E1708 " --> pdb=" O ASP E1704 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N HIS E1712 " --> pdb=" O GLU E1708 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N CYS E1713 " --> pdb=" O SER E1709 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU E1714 " --> pdb=" O LEU E1710 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU E1715 " --> pdb=" O MET E1711 " (cutoff:3.500A) Processing helix chain 'E' and resid 1721 through 1732 removed outlier: 3.610A pdb=" N ALA E1726 " --> pdb=" O GLU E1722 " (cutoff:3.500A) Processing helix chain 'E' and resid 1736 through 1750 removed outlier: 3.785A 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: 3.902A pdb=" N GLN E1785 " --> pdb=" O GLN E1781 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP E1788 " --> pdb=" O LYS E1784 " (cutoff:3.500A) Processing helix chain 'E' and resid 1798 through 1815 removed outlier: 5.233A pdb=" N GLU E1812 " --> pdb=" O SER E1808 " (cutoff:3.500A) Processing helix chain 'E' and resid 1824 through 1836 removed outlier: 3.715A pdb=" N ALA E1829 " --> pdb=" O PHE E1825 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E1835 " --> pdb=" O SER E1831 " (cutoff:3.500A) Processing helix chain 'E' and resid 1848 through 1854 removed outlier: 3.760A pdb=" N PHE E1854 " --> pdb=" O LYS E1850 " (cutoff:3.500A) Processing helix chain 'E' and resid 1858 through 1864 removed outlier: 3.510A pdb=" N ILE E1863 " --> pdb=" O ALA E1859 " (cutoff:3.500A) Processing helix chain 'E' and resid 1873 through 1891 removed outlier: 3.808A pdb=" N ASP E1880 " --> pdb=" O LYS E1876 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N CYS E1882 " --> pdb=" O THR E1878 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER E1883 " --> pdb=" O GLU E1879 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN E1890 " --> pdb=" O GLU E1886 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS E1891 " --> pdb=" O GLU E1887 " (cutoff:3.500A) Processing helix chain 'E' and resid 1895 through 1905 removed outlier: 3.900A pdb=" N PHE E1899 " --> pdb=" O ILE E1896 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR E1902 " --> pdb=" O PHE E1899 " (cutoff:3.500A) Processing helix chain 'E' and resid 1916 through 1928 removed outlier: 3.667A pdb=" N LEU E1923 " --> pdb=" O ILE E1919 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E1926 " --> pdb=" O ILE E1922 " (cutoff:3.500A) Processing helix chain 'E' and resid 1931 through 1941 removed outlier: 4.714A pdb=" N TRP E1936 " --> pdb=" O SER E1932 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR E1937 " --> pdb=" O HIS E1933 " (cutoff:3.500A) Processing helix chain 'E' and resid 1949 through 1962 removed outlier: 3.741A pdb=" N HIS E1955 " --> pdb=" O LEU E1951 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E1959 " --> pdb=" O HIS E1955 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR E1960 " --> pdb=" O ILE E1956 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG E1961 " --> pdb=" O LEU E1957 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN E1962 " --> pdb=" O GLU E1958 " (cutoff:3.500A) Processing helix chain 'E' and resid 1970 through 1983 removed outlier: 3.644A 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: 3.614A pdb=" N GLN E2089 " --> pdb=" O ARG E2085 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE E2099 " --> pdb=" O THR E2095 " (cutoff:3.500A) removed outlier: 3.959A 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: 3.630A pdb=" N THR E2144 " --> pdb=" O SER E2140 " (cutoff:3.500A) Processing helix chain 'E' and resid 2159 through 2164 Processing helix chain 'E' and resid 2169 through 2180 Processing helix chain 'E' and resid 2185 through 2192 removed outlier: 3.777A pdb=" N PHE E2189 " --> pdb=" O LEU E2185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E2190 " --> pdb=" O TYR E2186 " (cutoff:3.500A) Processing helix chain 'E' and resid 2196 through 2219 removed outlier: 3.766A pdb=" N MET E2213 " --> pdb=" O SER E2209 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET E2215 " --> pdb=" O ALA E2211 " (cutoff:3.500A) removed outlier: 3.976A 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: 4.277A pdb=" N ASP E2270 " --> pdb=" O PRO E2266 " (cutoff:3.500A) Processing helix chain 'E' and resid 2280 through 2294 Processing helix chain 'E' and resid 2296 through 2309 removed outlier: 4.566A pdb=" N THR E2305 " --> pdb=" O ASN E2301 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE E2306 " --> pdb=" O VAL E2302 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N MET E2307 " --> pdb=" O ILE E2303 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR E2308 " --> pdb=" O GLU E2304 " (cutoff:3.500A) Processing helix chain 'E' and resid 2315 through 2328 Processing helix chain 'E' and resid 2340 through 2351 Processing helix chain 'E' and resid 2354 through 2357 No H-bonds generated for 'chain 'E' and resid 2354 through 2357' Processing helix chain 'E' and resid 2362 through 2364 No H-bonds generated for 'chain 'E' and resid 2362 through 2364' Processing helix chain 'F' and resid 5 through 18 removed outlier: 3.896A pdb=" N LEU F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU F 18 " --> pdb=" O ALA F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 57 removed outlier: 3.955A pdb=" N ASP F 57 " --> pdb=" O ARG F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 3.732A pdb=" N THR F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 113 removed outlier: 3.692A pdb=" N ASP F 104 " --> pdb=" O GLN F 100 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER F 110 " --> pdb=" O PHE F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 131 removed outlier: 4.013A pdb=" N MET F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS F 126 " --> pdb=" O PHE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 removed outlier: 4.063A pdb=" N LYS F 143 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 164 removed outlier: 3.729A pdb=" N GLU F 151 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR F 157 " --> pdb=" O THR F 153 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR F 162 " --> pdb=" O GLU F 158 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU F 163 " --> pdb=" O GLN F 159 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 188 removed outlier: 3.788A pdb=" N PHE F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 202 No H-bonds generated for 'chain 'F' and resid 200 through 202' Processing helix chain 'F' and resid 210 through 228 removed outlier: 3.658A pdb=" N ASN F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 252 removed outlier: 3.742A pdb=" N LYS F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR F 243 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE F 244 " --> pdb=" O GLN F 240 " (cutoff:3.500A) removed outlier: 3.749A 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 removed outlier: 3.526A pdb=" N CYS F 306 " --> pdb=" O LEU F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 318 removed outlier: 3.709A 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 393 through 402 Processing helix chain 'F' and resid 412 through 418 Processing helix chain 'F' and resid 432 through 444 removed outlier: 3.565A pdb=" N LEU F 436 " --> pdb=" O PHE F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 470 removed outlier: 3.609A pdb=" N ALA F 466 " --> pdb=" O LEU F 462 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS F 467 " --> pdb=" O GLY F 463 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU F 468 " --> pdb=" O ARG F 464 " (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: 4.333A pdb=" N ARG F 590 " --> pdb=" O LEU F 586 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE F 591 " --> pdb=" O LEU F 587 " (cutoff:3.500A) removed outlier: 4.046A 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 606 through 617 removed outlier: 4.532A pdb=" N SER F 617 " --> pdb=" O LYS F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 624 through 637 removed outlier: 3.844A pdb=" N VAL F 628 " --> pdb=" O LYS F 624 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 634 " --> pdb=" O ALA F 630 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR F 637 " --> pdb=" O GLN F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 654 removed outlier: 3.691A pdb=" N ILE F 653 " --> pdb=" O LYS F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 659 through 676 Processing helix chain 'F' and resid 680 through 691 Proline residue: F 686 - end of helix Proline residue: F 689 - end of helix 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 722 No H-bonds generated for 'chain 'F' and resid 719 through 722' Processing helix chain 'F' and resid 725 through 732 removed outlier: 3.626A 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: 4.116A pdb=" N LEU F 819 " --> pdb=" O GLU F 815 " (cutoff:3.500A) Processing helix chain 'F' and resid 828 through 844 removed outlier: 3.742A pdb=" N ALA F 834 " --> pdb=" O ASP F 830 " (cutoff:3.500A) Processing helix chain 'F' and resid 866 through 879 removed outlier: 4.683A pdb=" N GLN F 870 " --> pdb=" O ASP F 867 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 871 " --> pdb=" O GLN F 868 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU F 876 " --> pdb=" O GLN F 873 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN F 877 " --> pdb=" O LYS F 874 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP F 878 " --> pdb=" O LYS F 875 " (cutoff:3.500A) Processing helix chain 'F' and resid 881 through 891 Processing helix chain 'F' and resid 901 through 915 Processing helix chain 'F' and resid 920 through 924 Processing helix chain 'F' and resid 926 through 938 removed outlier: 4.173A pdb=" N ILE F 931 " --> pdb=" O ALA F 927 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR F 935 " --> pdb=" O ILE F 931 " (cutoff:3.500A) Processing helix chain 'F' and resid 943 through 955 removed outlier: 3.855A pdb=" N ARG F 955 " --> pdb=" O HIS F 951 " (cutoff:3.500A) Processing helix chain 'F' and resid 959 through 964 removed outlier: 3.738A pdb=" N SER F 963 " --> pdb=" O ASP F 959 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N THR F 964 " --> pdb=" O GLU F 960 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 959 through 964' Processing helix chain 'F' and resid 967 through 975 removed outlier: 4.063A pdb=" N PHE F 972 " --> pdb=" O SER F 968 " (cutoff:3.500A) Processing helix chain 'F' and resid 982 through 997 removed outlier: 3.735A 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: 3.621A pdb=" N LEU F1014 " --> pdb=" O THR F1010 " (cutoff:3.500A) Processing helix chain 'F' and resid 1028 through 1036 removed outlier: 3.676A pdb=" N MET F1032 " --> pdb=" O GLN F1028 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS F1035 " --> pdb=" O ARG F1031 " (cutoff:3.500A) Processing helix chain 'F' and resid 1043 through 1050 removed outlier: 3.501A pdb=" N ASN F1048 " --> pdb=" O PRO F1044 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN F1049 " --> pdb=" O ILE F1045 " (cutoff:3.500A) Processing helix chain 'F' and resid 1057 through 1075 removed outlier: 4.423A pdb=" N LEU F1062 " --> pdb=" O ILE F1058 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL F1067 " --> pdb=" O ASP F1063 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG F1070 " --> pdb=" O GLU F1066 " (cutoff:3.500A) removed outlier: 3.678A 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: 3.874A pdb=" N LYS F1154 " --> pdb=" O VAL F1150 " (cutoff:3.500A) Processing helix chain 'F' and resid 1164 through 1169 removed outlier: 3.665A pdb=" N TRP F1169 " --> pdb=" O VAL F1165 " (cutoff:3.500A) Processing helix chain 'F' and resid 1174 through 1190 removed outlier: 3.906A pdb=" N LEU F1188 " --> pdb=" O ILE F1184 " (cutoff:3.500A) Processing helix chain 'F' and resid 1207 through 1215 removed outlier: 4.095A pdb=" N LYS F1215 " --> pdb=" O LYS F1211 " (cutoff:3.500A) Processing helix chain 'F' and resid 1218 through 1224 removed outlier: 4.708A 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: 3.553A 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 1311 through 1327 removed outlier: 3.666A pdb=" N LEU F1316 " --> pdb=" O TYR F1312 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE F1321 " --> pdb=" O ASN F1317 " (cutoff:3.500A) Processing helix chain 'F' and resid 1338 through 1369 removed outlier: 3.694A pdb=" N ILE F1349 " --> pdb=" O CYS F1345 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL F1352 " --> pdb=" O SER F1348 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE F1353 " --> pdb=" O ILE F1349 " (cutoff:3.500A) Processing helix chain 'F' and resid 1381 through 1391 removed outlier: 4.003A pdb=" N ARG F1387 " --> pdb=" O ASN F1383 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE F1388 " --> pdb=" O MET F1384 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP F1389 " --> pdb=" O LEU F1385 " (cutoff:3.500A) Processing helix chain 'F' and resid 1402 through 1405 No H-bonds generated for 'chain 'F' and resid 1402 through 1405' Processing helix chain 'F' and resid 1410 through 1422 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 1467 Processing helix chain 'F' and resid 1470 through 1472 No H-bonds generated for 'chain 'F' and resid 1470 through 1472' Processing helix chain 'F' and resid 1476 through 1486 removed outlier: 3.586A pdb=" N ASP F1481 " --> pdb=" O LYS F1477 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS F1482 " --> pdb=" O LEU F1478 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL F1485 " --> pdb=" O ASP F1481 " (cutoff:3.500A) Processing helix chain 'F' and resid 1494 through 1506 removed outlier: 3.926A pdb=" N MET F1499 " --> pdb=" O THR F1495 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS F1506 " --> pdb=" O SER F1502 " (cutoff:3.500A) Processing helix chain 'F' and resid 1509 through 1513 Processing helix chain 'F' and resid 1531 through 1544 removed outlier: 3.653A pdb=" N ILE F1537 " --> pdb=" O GLU F1533 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU F1540 " --> pdb=" O SER F1536 " (cutoff:3.500A) Processing helix chain 'F' and resid 1548 through 1560 removed outlier: 3.980A pdb=" N TRP F1554 " --> pdb=" O THR F1550 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER F1560 " --> pdb=" O GLU F1556 " (cutoff:3.500A) Processing helix chain 'F' and resid 1569 through 1583 Processing helix chain 'F' and resid 1587 through 1603 Processing helix chain 'F' and resid 1618 through 1634 removed outlier: 4.109A pdb=" N LYS F1623 " --> pdb=" O ASN F1619 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP F1629 " --> pdb=" O HIS F1625 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU F1630 " --> pdb=" O SER F1626 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER F1631 " --> pdb=" O LEU F1627 " (cutoff:3.500A) Processing helix chain 'F' and resid 1639 through 1652 removed outlier: 4.147A 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: 3.587A pdb=" N LYS F1688 " --> pdb=" O ALA F1684 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN F1699 " --> pdb=" O GLN F1695 " (cutoff:3.500A) Processing helix chain 'F' and resid 1703 through 1715 removed outlier: 3.597A pdb=" N SER F1707 " --> pdb=" O LEU F1703 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU F1708 " --> pdb=" O ASP F1704 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N HIS F1712 " --> pdb=" O GLU F1708 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N CYS F1713 " --> pdb=" O SER F1709 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU F1714 " --> pdb=" O LEU F1710 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU F1715 " --> pdb=" O MET F1711 " (cutoff:3.500A) Processing helix chain 'F' and resid 1721 through 1732 removed outlier: 3.611A pdb=" N ALA F1726 " --> pdb=" O GLU F1722 " (cutoff:3.500A) Processing helix chain 'F' and resid 1736 through 1750 removed outlier: 3.786A 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: 3.902A pdb=" N GLN F1785 " --> pdb=" O GLN F1781 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP F1788 " --> pdb=" O LYS F1784 " (cutoff:3.500A) Processing helix chain 'F' and resid 1798 through 1815 removed outlier: 5.233A pdb=" N GLU F1812 " --> pdb=" O SER F1808 " (cutoff:3.500A) Processing helix chain 'F' and resid 1824 through 1836 removed outlier: 3.714A pdb=" N ALA F1829 " --> pdb=" O PHE F1825 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU F1835 " --> pdb=" O SER F1831 " (cutoff:3.500A) Processing helix chain 'F' and resid 1848 through 1854 removed outlier: 3.761A pdb=" N PHE F1854 " --> pdb=" O LYS F1850 " (cutoff:3.500A) Processing helix chain 'F' and resid 1858 through 1864 removed outlier: 3.510A pdb=" N ILE F1863 " --> pdb=" O ALA F1859 " (cutoff:3.500A) Processing helix chain 'F' and resid 1873 through 1891 removed outlier: 3.809A pdb=" N ASP F1880 " --> pdb=" O LYS F1876 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N CYS F1882 " --> pdb=" O THR F1878 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER F1883 " --> pdb=" O GLU F1879 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN F1890 " --> pdb=" O GLU F1886 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS F1891 " --> pdb=" O GLU F1887 " (cutoff:3.500A) Processing helix chain 'F' and resid 1895 through 1905 removed outlier: 3.900A pdb=" N PHE F1899 " --> pdb=" O ILE F1896 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR F1902 " --> pdb=" O PHE F1899 " (cutoff:3.500A) Processing helix chain 'F' and resid 1916 through 1928 removed outlier: 3.668A pdb=" N LEU F1923 " --> pdb=" O ILE F1919 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F1926 " --> pdb=" O ILE F1922 " (cutoff:3.500A) Processing helix chain 'F' and resid 1931 through 1941 removed outlier: 4.714A pdb=" N TRP F1936 " --> pdb=" O SER F1932 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR F1937 " --> pdb=" O HIS F1933 " (cutoff:3.500A) Processing helix chain 'F' and resid 1949 through 1962 removed outlier: 3.741A pdb=" N HIS F1955 " --> pdb=" O LEU F1951 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS F1959 " --> pdb=" O HIS F1955 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR F1960 " --> pdb=" O ILE F1956 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG F1961 " --> pdb=" O LEU F1957 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN F1962 " --> pdb=" O GLU F1958 " (cutoff:3.500A) Processing helix chain 'F' and resid 1970 through 1983 removed outlier: 3.645A 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: 3.614A pdb=" N GLN F2089 " --> pdb=" O ARG F2085 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE F2099 " --> pdb=" O THR F2095 " (cutoff:3.500A) removed outlier: 3.959A 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: 3.632A pdb=" N THR F2144 " --> pdb=" O SER F2140 " (cutoff:3.500A) Processing helix chain 'F' and resid 2159 through 2164 Processing helix chain 'F' and resid 2169 through 2180 Processing helix chain 'F' and resid 2185 through 2192 removed outlier: 3.777A pdb=" N PHE F2189 " --> pdb=" O LEU F2185 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU F2190 " --> pdb=" O TYR F2186 " (cutoff:3.500A) Processing helix chain 'F' and resid 2196 through 2219 removed outlier: 3.767A pdb=" N MET F2213 " --> pdb=" O SER F2209 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET F2215 " --> pdb=" O ALA F2211 " (cutoff:3.500A) removed outlier: 3.975A 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: 4.278A pdb=" N ASP F2270 " --> pdb=" O PRO F2266 " (cutoff:3.500A) Processing helix chain 'F' and resid 2280 through 2294 Processing helix chain 'F' and resid 2296 through 2309 removed outlier: 4.566A pdb=" N THR F2305 " --> pdb=" O ASN F2301 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE F2306 " --> pdb=" O VAL F2302 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N MET F2307 " --> pdb=" O ILE F2303 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR F2308 " --> pdb=" O GLU F2304 " (cutoff:3.500A) Processing helix chain 'F' and resid 2315 through 2328 Processing helix chain 'F' and resid 2340 through 2351 Processing helix chain 'F' and resid 2354 through 2357 No H-bonds generated for 'chain 'F' and resid 2354 through 2357' Processing helix chain 'F' and resid 2362 through 2364 No H-bonds generated for 'chain 'F' and resid 2362 through 2364' 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: 3.726A pdb=" N ILE E2077 " --> pdb=" O LEU E2065 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY E2076 " --> pdb=" O MET E2131 " (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: 3.725A pdb=" N ILE F2077 " --> pdb=" O LEU F2065 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY F2076 " --> pdb=" O MET F2131 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 2135 through 2137 1879 hydrogen bonds defined for protein. 5535 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: 19.57 Time building geometry restraints manager: 19.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13800 1.34 - 1.46: 8817 1.46 - 1.58: 24609 1.58 - 1.70: 6 1.70 - 1.82: 320 Bond restraints: 47552 Sorted by residual: bond pdb=" O3A ANP E2401 " pdb=" PB ANP E2401 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" O3A ANP F2401 " pdb=" PB ANP F2401 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.62e+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 2.93e+01 bond pdb=" N3B ANP F2401 " pdb=" PG ANP F2401 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" O5' ANP E2401 " pdb=" PA ANP E2401 " ideal model delta sigma weight residual 1.655 1.569 0.086 2.00e-02 2.50e+03 1.85e+01 ... (remaining 47547 not shown) Histogram of bond angle deviations from ideal: 97.48 - 105.83: 786 105.83 - 114.18: 27936 114.18 - 122.53: 30771 122.53 - 130.89: 4667 130.89 - 139.24: 228 Bond angle restraints: 64388 Sorted by residual: angle pdb=" PB ANP E2401 " pdb=" N3B ANP E2401 " pdb=" PG ANP E2401 " ideal model delta sigma weight residual 126.95 109.28 17.67 3.00e+00 1.11e-01 3.47e+01 angle pdb=" PB ANP F2401 " pdb=" N3B ANP F2401 " pdb=" PG ANP F2401 " ideal model delta sigma weight residual 126.95 109.63 17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" C THR E1407 " pdb=" N ASP E1408 " pdb=" CA ASP E1408 " ideal model delta sigma weight residual 124.82 134.99 -10.17 1.78e+00 3.16e-01 3.27e+01 angle pdb=" C THR F1407 " pdb=" N ASP F1408 " pdb=" CA ASP F1408 " ideal model delta sigma weight residual 124.82 134.98 -10.16 1.78e+00 3.16e-01 3.26e+01 angle pdb=" C GLN C 596 " pdb=" N ASP C 597 " pdb=" CA ASP C 597 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 ... (remaining 64383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 28536 35.97 - 71.93: 234 71.93 - 107.90: 8 107.90 - 143.87: 0 143.87 - 179.83: 2 Dihedral angle restraints: 28780 sinusoidal: 11650 harmonic: 17130 Sorted by residual: 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 0.00 179.83 -179.83 1 1.00e+01 1.00e-02 1.92e+02 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 0.00 179.77 -179.77 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA GLU F1307 " pdb=" C GLU F1307 " pdb=" N LYS F1308 " pdb=" CA LYS F1308 " ideal model delta harmonic sigma weight residual -180.00 -135.79 -44.21 0 5.00e+00 4.00e-02 7.82e+01 ... (remaining 28777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5692 0.069 - 0.138: 1459 0.138 - 0.207: 176 0.207 - 0.276: 46 0.276 - 0.344: 5 Chirality restraints: 7378 Sorted by residual: chirality pdb=" CB ILE E 597 " pdb=" CA ILE E 597 " pdb=" CG1 ILE E 597 " pdb=" CG2 ILE E 597 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB ILE F 597 " pdb=" CA ILE F 597 " pdb=" CG1 ILE F 597 " pdb=" CG2 ILE F 597 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CB VAL E1942 " pdb=" CA VAL E1942 " pdb=" CG1 VAL E1942 " pdb=" CG2 VAL E1942 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 7375 not shown) Planarity restraints: 8098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F1770 " -0.039 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP F1770 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP F1770 " -0.028 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 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F1770 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP F1770 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP F1770 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F1770 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E1770 " 0.040 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP E1770 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP E1770 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP E1770 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP E1770 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E1770 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E1770 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP E1770 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP E1770 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E1770 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 470 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C VAL C 470 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL C 470 " -0.022 2.00e-02 2.50e+03 pdb=" N TYR C 471 " -0.020 2.00e-02 2.50e+03 ... (remaining 8095 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 795 2.66 - 3.22: 45176 3.22 - 3.78: 75443 3.78 - 4.34: 102699 4.34 - 4.90: 160994 Nonbonded interactions: 385107 Sorted by model distance: nonbonded pdb=" O1A ANP F2401 " pdb="MG MG F2403 " model vdw 2.101 2.170 nonbonded pdb=" O1A ANP E2401 " pdb="MG MG E2403 " model vdw 2.104 2.170 nonbonded pdb=" O1B ANP E2401 " pdb="MG MG E2404 " model vdw 2.115 2.170 nonbonded pdb=" O1G ANP E2401 " pdb="MG MG E2403 " model vdw 2.119 2.170 nonbonded pdb=" O1B ANP F2401 " pdb="MG MG F2404 " model vdw 2.120 2.170 ... (remaining 385102 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: 3.800 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: 0.060 Extract box with map and model: 9.990 Check model and map are aligned: 0.740 Set scattering table: 0.440 Process input model: 136.600 Find NCS groups from input model: 2.300 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 : 0.007 0.150 47552 Z= 0.473 Angle : 1.099 17.674 64388 Z= 0.574 Chirality : 0.062 0.344 7378 Planarity : 0.007 0.078 8098 Dihedral : 11.797 179.832 17636 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.20 % Favored : 91.76 % Rotamer: Outliers : 0.46 % Allowed : 6.05 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.50 (0.08), residues: 5736 helix: -2.90 (0.06), residues: 3524 sheet: -1.28 (0.66), residues: 40 loop : -2.91 (0.11), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.005 TRP F1770 HIS 0.021 0.003 HIS C 665 PHE 0.048 0.004 PHE F1833 TYR 0.031 0.003 TYR F1535 ARG 0.016 0.002 ARG C 664 *********************** 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 1746 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1724 time to evaluate : 5.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 346 MET cc_start: 0.8286 (mmm) cc_final: 0.8030 (mmm) REVERT: D 593 TYR cc_start: 0.9002 (m-80) cc_final: 0.8645 (m-80) REVERT: D 600 ASN cc_start: 0.7739 (m-40) cc_final: 0.7349 (m-40) REVERT: C 308 GLN cc_start: 0.8764 (pp30) cc_final: 0.8555 (pp30) REVERT: C 346 MET cc_start: 0.8277 (mmm) cc_final: 0.7982 (mmm) REVERT: C 593 TYR cc_start: 0.9055 (m-80) cc_final: 0.8841 (m-80) REVERT: C 600 ASN cc_start: 0.7744 (m-40) cc_final: 0.7401 (m-40) REVERT: E 91 LYS cc_start: 0.7457 (tptt) cc_final: 0.7239 (tptt) REVERT: E 102 LEU cc_start: 0.8687 (tm) cc_final: 0.8457 (tp) REVERT: E 122 PHE cc_start: 0.8488 (t80) cc_final: 0.8211 (t80) REVERT: E 154 MET cc_start: 0.8462 (ttp) cc_final: 0.8195 (ttp) REVERT: E 270 GLN cc_start: 0.8249 (mt0) cc_final: 0.7714 (mt0) REVERT: E 563 ASN cc_start: 0.7146 (m-40) cc_final: 0.6833 (t0) REVERT: E 570 PHE cc_start: 0.8384 (t80) cc_final: 0.7990 (t80) REVERT: E 577 PHE cc_start: 0.8747 (t80) cc_final: 0.8471 (t80) REVERT: E 633 GLN cc_start: 0.8299 (pt0) cc_final: 0.8082 (pt0) REVERT: E 764 LEU cc_start: 0.8604 (tp) cc_final: 0.8163 (mt) REVERT: E 821 LYS cc_start: 0.8644 (pttt) cc_final: 0.8167 (pttt) REVERT: E 1023 LEU cc_start: 0.7583 (mp) cc_final: 0.7257 (tt) REVERT: E 1063 ASP cc_start: 0.8127 (m-30) cc_final: 0.7524 (m-30) REVERT: E 1119 CYS cc_start: 0.8532 (m) cc_final: 0.8258 (m) REVERT: E 1148 ASP cc_start: 0.7508 (p0) cc_final: 0.7135 (t0) REVERT: E 1200 MET cc_start: 0.6705 (pmm) cc_final: 0.6428 (pmm) REVERT: E 1290 LEU cc_start: 0.9128 (tm) cc_final: 0.8869 (mt) REVERT: E 1334 MET cc_start: 0.6022 (ptp) cc_final: 0.5810 (mmt) REVERT: E 1436 LYS cc_start: 0.6842 (pmtt) cc_final: 0.6381 (ttmm) REVERT: E 1465 SER cc_start: 0.8879 (p) cc_final: 0.8411 (p) REVERT: E 1501 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8299 (tttt) REVERT: E 1505 ASP cc_start: 0.8358 (m-30) cc_final: 0.8078 (m-30) REVERT: E 1545 GLU cc_start: 0.7947 (tp30) cc_final: 0.7733 (mm-30) REVERT: E 1592 LYS cc_start: 0.8850 (tmtt) cc_final: 0.8639 (tttm) REVERT: E 1681 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7402 (mm-40) REVERT: E 1785 GLN cc_start: 0.7808 (pt0) cc_final: 0.7597 (pt0) REVERT: E 1805 LEU cc_start: 0.9129 (mt) cc_final: 0.8896 (mm) REVERT: E 1827 TYR cc_start: 0.7739 (t80) cc_final: 0.7527 (t80) REVERT: E 1880 ASP cc_start: 0.7319 (p0) cc_final: 0.7046 (p0) REVERT: E 1901 LEU cc_start: 0.8093 (tm) cc_final: 0.7703 (tm) REVERT: E 1905 LEU cc_start: 0.8206 (mt) cc_final: 0.7903 (mp) REVERT: E 1958 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6598 (tt0) REVERT: E 1979 LYS cc_start: 0.8140 (ptmm) cc_final: 0.7815 (mmtp) REVERT: E 2049 PHE cc_start: 0.7710 (t80) cc_final: 0.7200 (t80) REVERT: E 2071 ASP cc_start: 0.8642 (t70) cc_final: 0.8301 (t70) REVERT: E 2077 ILE cc_start: 0.8330 (mm) cc_final: 0.8047 (mm) REVERT: E 2115 ASN cc_start: 0.7834 (m110) cc_final: 0.7430 (m110) REVERT: E 2224 ASP cc_start: 0.7690 (t0) cc_final: 0.7345 (t0) REVERT: E 2326 LYS cc_start: 0.9169 (mttt) cc_final: 0.8896 (mtpp) REVERT: E 2359 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7853 (ttpp) REVERT: F 48 LEU cc_start: 0.8668 (tt) cc_final: 0.8402 (tp) REVERT: F 113 ASN cc_start: 0.8540 (m110) cc_final: 0.8265 (m110) REVERT: F 154 MET cc_start: 0.8248 (ttp) cc_final: 0.8030 (ttp) REVERT: F 212 ASP cc_start: 0.7437 (m-30) cc_final: 0.7216 (m-30) REVERT: F 270 GLN cc_start: 0.8197 (mt0) cc_final: 0.7575 (mt0) REVERT: F 347 TYR cc_start: 0.8504 (t80) cc_final: 0.8196 (t80) REVERT: F 494 ASP cc_start: 0.7523 (m-30) cc_final: 0.7201 (m-30) REVERT: F 563 ASN cc_start: 0.7353 (m-40) cc_final: 0.6785 (t0) REVERT: F 764 LEU cc_start: 0.8940 (tp) cc_final: 0.8714 (tt) REVERT: F 821 LYS cc_start: 0.8571 (pttt) cc_final: 0.8121 (pttt) REVERT: F 861 ILE cc_start: 0.8947 (mp) cc_final: 0.8746 (mt) REVERT: F 1023 LEU cc_start: 0.7640 (mp) cc_final: 0.7108 (tt) REVERT: F 1119 CYS cc_start: 0.8528 (m) cc_final: 0.8277 (m) REVERT: F 1148 ASP cc_start: 0.7236 (p0) cc_final: 0.6965 (t70) REVERT: F 1436 LYS cc_start: 0.6703 (pmtt) cc_final: 0.6326 (ttmm) REVERT: F 1492 ASP cc_start: 0.7412 (m-30) cc_final: 0.7134 (m-30) REVERT: F 1515 ASN cc_start: 0.7945 (t0) cc_final: 0.7744 (t0) REVERT: F 1539 LEU cc_start: 0.7992 (mt) cc_final: 0.7678 (mt) REVERT: F 1545 GLU cc_start: 0.7852 (tp30) cc_final: 0.7652 (mm-30) REVERT: F 1560 SER cc_start: 0.8845 (m) cc_final: 0.8348 (p) REVERT: F 1592 LYS cc_start: 0.8900 (tmtt) cc_final: 0.8676 (tttm) REVERT: F 1650 ASP cc_start: 0.8180 (m-30) cc_final: 0.7968 (m-30) REVERT: F 1732 GLN cc_start: 0.8829 (tp40) cc_final: 0.8402 (tp40) REVERT: F 1734 GLU cc_start: 0.6661 (tt0) cc_final: 0.5727 (tt0) REVERT: F 1785 GLN cc_start: 0.7860 (pt0) cc_final: 0.7648 (pt0) REVERT: F 1805 LEU cc_start: 0.9122 (mt) cc_final: 0.8891 (mm) REVERT: F 1826 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8284 (mt-10) REVERT: F 1827 TYR cc_start: 0.7711 (t80) cc_final: 0.7503 (t80) REVERT: F 1880 ASP cc_start: 0.7402 (p0) cc_final: 0.7099 (p0) REVERT: F 1901 LEU cc_start: 0.8058 (tm) cc_final: 0.7657 (tm) REVERT: F 1905 LEU cc_start: 0.8235 (mt) cc_final: 0.7919 (mp) REVERT: F 1958 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6855 (tt0) REVERT: F 1979 LYS cc_start: 0.8087 (ptmm) cc_final: 0.7753 (mmtp) REVERT: F 2071 ASP cc_start: 0.8533 (t70) cc_final: 0.8234 (t70) REVERT: F 2077 ILE cc_start: 0.8372 (mm) cc_final: 0.8139 (mm) REVERT: F 2115 ASN cc_start: 0.7680 (m110) cc_final: 0.7335 (m110) REVERT: F 2224 ASP cc_start: 0.7747 (t0) cc_final: 0.7230 (t0) REVERT: F 2326 LYS cc_start: 0.9167 (mttt) cc_final: 0.8884 (mtpp) REVERT: F 2359 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7835 (ttpp) outliers start: 22 outliers final: 2 residues processed: 1735 average time/residue: 0.6259 time to fit residues: 1772.6204 Evaluate side-chains 911 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 909 time to evaluate : 5.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain F residue 120 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 484 optimal weight: 6.9990 chunk 435 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 293 optimal weight: 10.0000 chunk 232 optimal weight: 1.9990 chunk 449 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 273 optimal weight: 0.7980 chunk 334 optimal weight: 0.9990 chunk 521 optimal weight: 7.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 213 HIS ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 633 GLN D 637 GLN D 665 HIS D 702 ASN C 213 HIS C 305 GLN C 380 GLN C 426 ASN C 474 ASN C 554 ASN C 665 HIS E 84 ASN E 525 ASN ** E 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN E 682 GLN E 879 ASN E 928 GLN E 934 GLN E1034 ASN E1273 ASN E1365 GLN E1462 ASN E1557 GLN E1675 GLN E1712 HIS E1847 ASN ** E1963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1968 HIS E2092 GLN ** E2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN F 84 ASN F 149 HIS ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 682 GLN F 879 ASN F 928 GLN F 951 HIS F1439 GLN F1462 ASN F1557 GLN F1675 GLN ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1712 HIS F1776 ASN F1847 ASN ** F1963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2092 GLN ** F2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 47552 Z= 0.200 Angle : 0.699 11.602 64388 Z= 0.359 Chirality : 0.044 0.259 7378 Planarity : 0.005 0.085 8098 Dihedral : 8.015 179.893 6300 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.82 % Allowed : 15.20 % Favored : 81.97 % 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: -3.01 (0.10), residues: 5736 helix: -1.54 (0.08), residues: 3540 sheet: -0.68 (0.64), residues: 60 loop : -2.67 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E1770 HIS 0.015 0.001 HIS F 892 PHE 0.043 0.002 PHE C 489 TYR 0.037 0.001 TYR D 563 ARG 0.007 0.001 ARG D 617 *********************** 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 1218 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1074 time to evaluate : 5.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 542 GLU cc_start: 0.7523 (tt0) cc_final: 0.7271 (tt0) REVERT: D 682 TYR cc_start: 0.9072 (m-80) cc_final: 0.8440 (m-10) REVERT: C 308 GLN cc_start: 0.8754 (pp30) cc_final: 0.8478 (pp30) REVERT: C 542 GLU cc_start: 0.7547 (tt0) cc_final: 0.7287 (tt0) REVERT: C 660 MET cc_start: 0.8521 (mtp) cc_final: 0.8139 (mtp) REVERT: E 91 LYS cc_start: 0.7381 (tptt) cc_final: 0.6932 (ttpt) REVERT: E 208 PHE cc_start: 0.6927 (t80) cc_final: 0.6690 (t80) REVERT: E 231 LEU cc_start: 0.8201 (tp) cc_final: 0.7931 (tt) REVERT: E 278 MET cc_start: 0.8442 (ptp) cc_final: 0.8159 (mtp) REVERT: E 395 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8816 (mtmt) REVERT: E 563 ASN cc_start: 0.7192 (m-40) cc_final: 0.6909 (t0) REVERT: E 577 PHE cc_start: 0.8604 (t80) cc_final: 0.8293 (t80) REVERT: E 719 THR cc_start: 0.8650 (m) cc_final: 0.8405 (t) REVERT: E 764 LEU cc_start: 0.8660 (tp) cc_final: 0.8256 (mt) REVERT: E 849 GLU cc_start: 0.8487 (pm20) cc_final: 0.8143 (pm20) REVERT: E 1023 LEU cc_start: 0.7710 (mp) cc_final: 0.7389 (tt) REVERT: E 1119 CYS cc_start: 0.8563 (m) cc_final: 0.8272 (m) REVERT: E 1148 ASP cc_start: 0.7434 (p0) cc_final: 0.7040 (t0) REVERT: E 1225 TYR cc_start: 0.8637 (t80) cc_final: 0.8231 (t80) REVERT: E 1436 LYS cc_start: 0.6953 (pmtt) cc_final: 0.6498 (ttmm) REVERT: E 1444 GLU cc_start: 0.7966 (pm20) cc_final: 0.7736 (pm20) REVERT: E 1465 SER cc_start: 0.9048 (p) cc_final: 0.8828 (m) REVERT: E 1501 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8305 (tttt) REVERT: E 1505 ASP cc_start: 0.8348 (m-30) cc_final: 0.8095 (m-30) REVERT: E 1643 LYS cc_start: 0.8819 (mttt) cc_final: 0.8584 (mtmt) REVERT: E 1685 ASP cc_start: 0.8108 (t0) cc_final: 0.7507 (t0) REVERT: E 1727 GLU cc_start: 0.8249 (mp0) cc_final: 0.7924 (mp0) REVERT: E 1827 TYR cc_start: 0.7845 (t80) cc_final: 0.7436 (t80) REVERT: E 1901 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7738 (tm) REVERT: E 1905 LEU cc_start: 0.8129 (mt) cc_final: 0.7817 (mp) REVERT: E 2071 ASP cc_start: 0.8537 (t70) cc_final: 0.8163 (t0) REVERT: E 2077 ILE cc_start: 0.8414 (mm) cc_final: 0.8213 (mm) REVERT: E 2131 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8023 (mpp) REVERT: E 2224 ASP cc_start: 0.7740 (t0) cc_final: 0.7429 (t0) REVERT: E 2258 GLU cc_start: 0.6320 (mm-30) cc_final: 0.6075 (tp30) REVERT: E 2326 LYS cc_start: 0.9230 (mttt) cc_final: 0.8977 (mtpp) REVERT: E 2331 ASP cc_start: 0.7807 (t0) cc_final: 0.7590 (p0) REVERT: F 58 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: F 113 ASN cc_start: 0.8518 (m110) cc_final: 0.8085 (m110) REVERT: F 212 ASP cc_start: 0.7437 (m-30) cc_final: 0.7158 (m-30) REVERT: F 270 GLN cc_start: 0.8127 (mt0) cc_final: 0.7527 (mt0) REVERT: F 300 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8849 (mm) REVERT: F 328 SER cc_start: 0.8560 (m) cc_final: 0.8004 (p) REVERT: F 395 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8681 (mtmt) REVERT: F 437 ASN cc_start: 0.7727 (m110) cc_final: 0.7244 (m110) REVERT: F 462 LEU cc_start: 0.9001 (mt) cc_final: 0.8592 (mm) REVERT: F 482 LYS cc_start: 0.5227 (mppt) cc_final: 0.4907 (tppt) REVERT: F 494 ASP cc_start: 0.7326 (m-30) cc_final: 0.7046 (m-30) REVERT: F 563 ASN cc_start: 0.7144 (m-40) cc_final: 0.6813 (t0) REVERT: F 591 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8356 (mt) REVERT: F 644 ASP cc_start: 0.8235 (m-30) cc_final: 0.7857 (p0) REVERT: F 821 LYS cc_start: 0.8556 (pttt) cc_final: 0.8064 (pttt) REVERT: F 1023 LEU cc_start: 0.7754 (mp) cc_final: 0.7317 (tt) REVERT: F 1118 LYS cc_start: 0.8239 (ttmt) cc_final: 0.8013 (mtmt) REVERT: F 1119 CYS cc_start: 0.8573 (m) cc_final: 0.8239 (m) REVERT: F 1148 ASP cc_start: 0.7203 (p0) cc_final: 0.6980 (t70) REVERT: F 1334 MET cc_start: 0.5895 (ptp) cc_final: 0.5548 (mmt) REVERT: F 1436 LYS cc_start: 0.6937 (pmtt) cc_final: 0.6534 (ttmm) REVERT: F 1444 GLU cc_start: 0.7922 (pm20) cc_final: 0.7722 (pm20) REVERT: F 1465 SER cc_start: 0.9013 (p) cc_final: 0.8802 (m) REVERT: F 1491 ASP cc_start: 0.7279 (p0) cc_final: 0.7004 (p0) REVERT: F 1501 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8457 (tttt) REVERT: F 1643 LYS cc_start: 0.8812 (mttt) cc_final: 0.8544 (mtmt) REVERT: F 1669 MET cc_start: 0.8795 (tpp) cc_final: 0.8187 (mmm) REVERT: F 1685 ASP cc_start: 0.8135 (t0) cc_final: 0.7488 (t0) REVERT: F 1711 MET cc_start: 0.8545 (mmp) cc_final: 0.8254 (mmm) REVERT: F 1727 GLU cc_start: 0.8273 (mp0) cc_final: 0.7970 (mp0) REVERT: F 1754 SER cc_start: 0.6663 (m) cc_final: 0.6209 (p) REVERT: F 1785 GLN cc_start: 0.7782 (pt0) cc_final: 0.7550 (pt0) REVERT: F 1901 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7682 (tm) REVERT: F 1905 LEU cc_start: 0.8215 (mt) cc_final: 0.7879 (mp) REVERT: F 2071 ASP cc_start: 0.8450 (t70) cc_final: 0.8151 (t0) REVERT: F 2115 ASN cc_start: 0.7640 (m110) cc_final: 0.7436 (m110) REVERT: F 2131 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7998 (mpp) REVERT: F 2224 ASP cc_start: 0.7556 (t0) cc_final: 0.7264 (t0) REVERT: F 2258 GLU cc_start: 0.6456 (mm-30) cc_final: 0.6027 (tp30) REVERT: F 2326 LYS cc_start: 0.9177 (mttt) cc_final: 0.8968 (mtpp) outliers start: 144 outliers final: 75 residues processed: 1160 average time/residue: 0.5459 time to fit residues: 1069.9538 Evaluate side-chains 909 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 825 time to evaluate : 5.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 342 HIS Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 699 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 342 HIS Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 395 LYS Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 721 LEU Chi-restraints excluded: chain E residue 879 ASN Chi-restraints excluded: chain E residue 990 SER Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1150 VAL Chi-restraints excluded: chain E residue 1282 LEU Chi-restraints excluded: chain E residue 1342 LEU Chi-restraints excluded: chain E residue 1400 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1672 SER Chi-restraints excluded: chain E residue 1709 SER Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1828 ARG Chi-restraints excluded: chain E residue 1901 LEU Chi-restraints excluded: chain E residue 2016 VAL Chi-restraints excluded: chain E residue 2092 GLN Chi-restraints excluded: chain E residue 2131 MET Chi-restraints excluded: chain E residue 2157 SER Chi-restraints excluded: chain E residue 2260 VAL Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 395 LYS Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 565 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 591 ILE Chi-restraints excluded: chain F residue 605 ASP Chi-restraints excluded: chain F residue 637 THR Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 721 LEU Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 1010 THR Chi-restraints excluded: chain F residue 1112 LEU Chi-restraints excluded: chain F residue 1282 LEU Chi-restraints excluded: chain F residue 1342 LEU Chi-restraints excluded: chain F residue 1400 LEU Chi-restraints excluded: chain F residue 1597 SER Chi-restraints excluded: chain F residue 1601 ILE Chi-restraints excluded: chain F residue 1630 LEU Chi-restraints excluded: chain F residue 1901 LEU Chi-restraints excluded: chain F residue 2016 VAL Chi-restraints excluded: chain F residue 2092 GLN Chi-restraints excluded: chain F residue 2114 ILE Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2260 VAL Chi-restraints excluded: chain F residue 2355 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 289 optimal weight: 0.0370 chunk 161 optimal weight: 10.0000 chunk 433 optimal weight: 9.9990 chunk 354 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 522 optimal weight: 10.0000 chunk 564 optimal weight: 0.9980 chunk 465 optimal weight: 9.9990 chunk 517 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 418 optimal weight: 6.9990 overall best weight: 3.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 426 ASN D 474 ASN D 481 HIS D 649 GLN D 702 ASN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN C 481 HIS E 100 GLN E 149 HIS E 270 GLN ** E 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 ASN ** E1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1776 ASN E1921 HIS E1955 HIS E2092 GLN ** E2301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN F 58 GLN F 525 ASN F 835 ASN F 879 ASN F 892 HIS ** F1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1955 HIS F2092 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 47552 Z= 0.293 Angle : 0.702 11.836 64388 Z= 0.361 Chirality : 0.045 0.279 7378 Planarity : 0.004 0.060 8098 Dihedral : 7.725 179.312 6300 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.18 % Allowed : 15.96 % Favored : 79.86 % 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: -2.19 (0.10), residues: 5736 helix: -0.85 (0.08), residues: 3564 sheet: -0.54 (0.63), residues: 60 loop : -2.43 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F1770 HIS 0.007 0.001 HIS F 892 PHE 0.027 0.002 PHE C 489 TYR 0.025 0.002 TYR E1009 ARG 0.005 0.001 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 1105 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 891 time to evaluate : 5.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 274 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8842 (mm) REVERT: D 541 MET cc_start: 0.8138 (mmm) cc_final: 0.7603 (tpt) REVERT: C 308 GLN cc_start: 0.8855 (pp30) cc_final: 0.8581 (pp30) REVERT: C 541 MET cc_start: 0.8094 (mmm) cc_final: 0.7579 (tpt) REVERT: C 682 TYR cc_start: 0.9040 (m-80) cc_final: 0.8270 (m-10) REVERT: E 100 GLN cc_start: 0.6860 (mt0) cc_final: 0.6627 (mt0) REVERT: E 300 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8853 (mm) REVERT: E 563 ASN cc_start: 0.7167 (m-40) cc_final: 0.6909 (t0) REVERT: E 699 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7543 (tt) REVERT: E 764 LEU cc_start: 0.8799 (tp) cc_final: 0.8402 (mt) REVERT: E 810 TYR cc_start: 0.7506 (m-80) cc_final: 0.7152 (m-80) REVERT: E 879 ASN cc_start: 0.8219 (t0) cc_final: 0.7856 (t0) REVERT: E 993 ASP cc_start: 0.8486 (p0) cc_final: 0.7767 (m-30) REVERT: E 1023 LEU cc_start: 0.7778 (mp) cc_final: 0.7480 (tt) REVERT: E 1119 CYS cc_start: 0.8611 (m) cc_final: 0.8325 (m) REVERT: E 1148 ASP cc_start: 0.7479 (p0) cc_final: 0.7111 (t0) REVERT: E 1187 SER cc_start: 0.8856 (t) cc_final: 0.8566 (m) REVERT: E 1436 LYS cc_start: 0.7120 (pmtt) cc_final: 0.6552 (ttmm) REVERT: E 1444 GLU cc_start: 0.8028 (pm20) cc_final: 0.7793 (pm20) REVERT: E 1643 LYS cc_start: 0.8876 (mttt) cc_final: 0.8639 (mtmt) REVERT: E 1685 ASP cc_start: 0.8145 (t0) cc_final: 0.7514 (t0) REVERT: E 1727 GLU cc_start: 0.8300 (mp0) cc_final: 0.7942 (mp0) REVERT: E 1754 SER cc_start: 0.6729 (m) cc_final: 0.6238 (p) REVERT: E 1929 GLU cc_start: 0.7117 (tt0) cc_final: 0.6748 (tt0) REVERT: E 2071 ASP cc_start: 0.8523 (t70) cc_final: 0.8145 (t0) REVERT: E 2077 ILE cc_start: 0.8423 (mm) cc_final: 0.8197 (mm) REVERT: E 2131 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8062 (mpp) REVERT: E 2215 MET cc_start: 0.7648 (pmm) cc_final: 0.7269 (pmm) REVERT: E 2224 ASP cc_start: 0.7916 (t0) cc_final: 0.7686 (t0) REVERT: E 2326 LYS cc_start: 0.9290 (mttt) cc_final: 0.9076 (mtpp) REVERT: E 2345 GLU cc_start: 0.8278 (tp30) cc_final: 0.7959 (tp30) REVERT: F 113 ASN cc_start: 0.8679 (m110) cc_final: 0.8213 (m110) REVERT: F 212 ASP cc_start: 0.7620 (m-30) cc_final: 0.7339 (m-30) REVERT: F 231 LEU cc_start: 0.8142 (tp) cc_final: 0.7901 (tt) REVERT: F 270 GLN cc_start: 0.8076 (mt0) cc_final: 0.7343 (mt0) REVERT: F 300 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8880 (mm) REVERT: F 333 PHE cc_start: 0.8180 (m-10) cc_final: 0.7936 (m-80) REVERT: F 437 ASN cc_start: 0.7848 (m110) cc_final: 0.7361 (m110) REVERT: F 452 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7019 (mp) REVERT: F 482 LYS cc_start: 0.5245 (mppt) cc_final: 0.4900 (tppt) REVERT: F 563 ASN cc_start: 0.7273 (m-40) cc_final: 0.6844 (t0) REVERT: F 591 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8318 (mt) REVERT: F 821 LYS cc_start: 0.8622 (pttt) cc_final: 0.8091 (pttt) REVERT: F 993 ASP cc_start: 0.8405 (p0) cc_final: 0.7590 (m-30) REVERT: F 1023 LEU cc_start: 0.7782 (mp) cc_final: 0.7356 (tt) REVERT: F 1119 CYS cc_start: 0.8603 (m) cc_final: 0.8315 (m) REVERT: F 1148 ASP cc_start: 0.7329 (p0) cc_final: 0.7049 (t70) REVERT: F 1334 MET cc_start: 0.6031 (ptp) cc_final: 0.5674 (mmt) REVERT: F 1436 LYS cc_start: 0.7106 (pmtt) cc_final: 0.6650 (ttmm) REVERT: F 1439 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: F 1444 GLU cc_start: 0.7999 (pm20) cc_final: 0.7795 (pm20) REVERT: F 1465 SER cc_start: 0.9003 (p) cc_final: 0.8788 (m) REVERT: F 1491 ASP cc_start: 0.7286 (p0) cc_final: 0.6882 (p0) REVERT: F 1492 ASP cc_start: 0.7420 (m-30) cc_final: 0.7210 (m-30) REVERT: F 1501 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8591 (tttt) REVERT: F 1643 LYS cc_start: 0.8868 (mttt) cc_final: 0.8592 (mtmt) REVERT: F 1669 MET cc_start: 0.8787 (tpp) cc_final: 0.8347 (mmm) REVERT: F 1685 ASP cc_start: 0.8193 (t0) cc_final: 0.7560 (t0) REVERT: F 1711 MET cc_start: 0.8630 (mmp) cc_final: 0.8408 (mmm) REVERT: F 1727 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: F 1754 SER cc_start: 0.6530 (m) cc_final: 0.6098 (p) REVERT: F 1765 LEU cc_start: 0.8692 (tp) cc_final: 0.8441 (tp) REVERT: F 1827 TYR cc_start: 0.7699 (t80) cc_final: 0.7256 (t80) REVERT: F 2071 ASP cc_start: 0.8424 (t70) cc_final: 0.8075 (t0) REVERT: F 2131 MET cc_start: 0.8802 (mpp) cc_final: 0.8238 (mpp) REVERT: F 2191 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8081 (mt-10) REVERT: F 2224 ASP cc_start: 0.7917 (t0) cc_final: 0.7593 (t0) REVERT: F 2345 GLU cc_start: 0.8108 (tp30) cc_final: 0.7867 (tp30) REVERT: F 2364 TRP cc_start: 0.7261 (t60) cc_final: 0.6822 (t60) outliers start: 214 outliers final: 132 residues processed: 1038 average time/residue: 0.5400 time to fit residues: 957.6797 Evaluate side-chains 915 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 774 time to evaluate : 5.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 416 ASN Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 661 ARG Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 684 ASP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 252 CYS Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 637 THR Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 777 VAL Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 837 ILE Chi-restraints excluded: chain E residue 990 SER Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1129 THR Chi-restraints excluded: chain E residue 1150 VAL Chi-restraints excluded: chain E residue 1205 LEU Chi-restraints excluded: chain E residue 1208 ASN Chi-restraints excluded: chain E residue 1263 LEU Chi-restraints excluded: chain E residue 1304 ILE Chi-restraints excluded: chain E residue 1326 ILE Chi-restraints excluded: chain E residue 1342 LEU Chi-restraints excluded: chain E residue 1368 SER Chi-restraints excluded: chain E residue 1400 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1624 LEU Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1672 SER Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1709 SER Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1810 LEU Chi-restraints excluded: chain E residue 1828 ARG Chi-restraints excluded: chain E residue 1902 THR Chi-restraints excluded: chain E residue 1924 LEU Chi-restraints excluded: chain E residue 2016 VAL Chi-restraints excluded: chain E residue 2105 ILE Chi-restraints excluded: chain E residue 2114 ILE Chi-restraints excluded: chain E residue 2131 MET Chi-restraints excluded: chain E residue 2157 SER Chi-restraints excluded: chain E residue 2275 ILE Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2344 THR Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 591 ILE Chi-restraints excluded: chain F residue 604 GLU Chi-restraints excluded: chain F residue 605 ASP Chi-restraints excluded: chain F residue 637 THR Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 960 GLU Chi-restraints excluded: chain F residue 990 SER Chi-restraints excluded: chain F residue 1010 THR Chi-restraints excluded: chain F residue 1042 LEU Chi-restraints excluded: chain F residue 1112 LEU Chi-restraints excluded: chain F residue 1129 THR Chi-restraints excluded: chain F residue 1208 ASN Chi-restraints excluded: chain F residue 1272 GLU Chi-restraints excluded: chain F residue 1282 LEU Chi-restraints excluded: chain F residue 1304 ILE Chi-restraints excluded: chain F residue 1342 LEU Chi-restraints excluded: chain F residue 1349 ILE Chi-restraints excluded: chain F residue 1400 LEU Chi-restraints excluded: chain F residue 1439 GLN Chi-restraints excluded: chain F residue 1630 LEU Chi-restraints excluded: chain F residue 1668 SER Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1704 ASP Chi-restraints excluded: chain F residue 1709 SER Chi-restraints excluded: chain F residue 1727 GLU Chi-restraints excluded: chain F residue 1786 TYR Chi-restraints excluded: chain F residue 1902 THR Chi-restraints excluded: chain F residue 2016 VAL Chi-restraints excluded: chain F residue 2105 ILE Chi-restraints excluded: chain F residue 2114 ILE Chi-restraints excluded: chain F residue 2215 MET Chi-restraints excluded: chain F residue 2275 ILE Chi-restraints excluded: chain F residue 2297 VAL Chi-restraints excluded: chain F residue 2344 THR Chi-restraints excluded: chain F residue 2355 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 515 optimal weight: 10.0000 chunk 392 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 chunk 350 optimal weight: 10.0000 chunk 524 optimal weight: 0.7980 chunk 554 optimal weight: 20.0000 chunk 273 optimal weight: 0.0970 chunk 496 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 overall best weight: 4.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 347 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS ** D 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 HIS C 600 ASN C 671 HIS E 426 GLN E 616 GLN ** E 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 GLN ** E1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1371 HIS ** E1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1840 ASN E2092 GLN ** E2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 GLN ** F 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 735 GLN F 879 ASN ** F1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1371 HIS ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1921 HIS F2092 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 47552 Z= 0.326 Angle : 0.700 12.036 64388 Z= 0.359 Chirality : 0.045 0.271 7378 Planarity : 0.004 0.052 8098 Dihedral : 7.555 179.537 6300 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.74 % Allowed : 17.06 % Favored : 78.20 % 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: -1.77 (0.11), residues: 5736 helix: -0.52 (0.09), residues: 3572 sheet: -0.35 (0.63), residues: 60 loop : -2.26 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E2364 HIS 0.006 0.001 HIS E2241 PHE 0.025 0.002 PHE E 386 TYR 0.026 0.002 TYR F2361 ARG 0.012 0.001 ARG F 454 *********************** 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 1107 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 864 time to evaluate : 5.486 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 274 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8876 (mm) REVERT: D 637 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7984 (mt0) REVERT: D 712 LYS cc_start: 0.8492 (tptt) cc_final: 0.7336 (ttmt) REVERT: C 308 GLN cc_start: 0.8941 (pp30) cc_final: 0.8624 (pp30) REVERT: C 600 ASN cc_start: 0.8108 (m-40) cc_final: 0.7797 (m-40) REVERT: C 700 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8134 (tp40) REVERT: C 736 GLU cc_start: 0.8338 (pm20) cc_final: 0.7945 (tm-30) REVERT: E 163 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: E 229 CYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6873 (p) REVERT: E 471 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7386 (tp30) REVERT: E 563 ASN cc_start: 0.7337 (m-40) cc_final: 0.7005 (t0) REVERT: E 694 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7974 (pt0) REVERT: E 699 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7513 (tt) REVERT: E 1023 LEU cc_start: 0.7805 (mp) cc_final: 0.7521 (tt) REVERT: E 1119 CYS cc_start: 0.8627 (m) cc_final: 0.8336 (m) REVERT: E 1148 ASP cc_start: 0.7540 (p0) cc_final: 0.7146 (t0) REVERT: E 1187 SER cc_start: 0.8874 (t) cc_final: 0.8572 (m) REVERT: E 1403 ARG cc_start: 0.8096 (mmt180) cc_final: 0.7748 (mmt180) REVERT: E 1436 LYS cc_start: 0.7236 (pmtt) cc_final: 0.6735 (ttmm) REVERT: E 1643 LYS cc_start: 0.8898 (mttt) cc_final: 0.8643 (mtmt) REVERT: E 1685 ASP cc_start: 0.8183 (t0) cc_final: 0.7561 (t0) REVERT: E 1724 GLU cc_start: 0.8009 (tp30) cc_final: 0.7365 (tp30) REVERT: E 1727 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: E 1954 LYS cc_start: 0.7975 (mmtp) cc_final: 0.7644 (mmtp) REVERT: E 2071 ASP cc_start: 0.8526 (t70) cc_final: 0.8128 (t0) REVERT: E 2131 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8083 (mpp) REVERT: E 2254 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7849 (pp) REVERT: F 212 ASP cc_start: 0.7666 (m-30) cc_final: 0.7402 (m-30) REVERT: F 229 CYS cc_start: 0.7396 (p) cc_final: 0.7089 (p) REVERT: F 452 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7196 (mp) REVERT: F 563 ASN cc_start: 0.7315 (m-40) cc_final: 0.6926 (t0) REVERT: F 591 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8429 (mt) REVERT: F 620 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8049 (tt) REVERT: F 694 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7287 (pm20) REVERT: F 1023 LEU cc_start: 0.7737 (mp) cc_final: 0.7325 (tt) REVERT: F 1066 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: F 1119 CYS cc_start: 0.8607 (m) cc_final: 0.8321 (m) REVERT: F 1148 ASP cc_start: 0.7449 (p0) cc_final: 0.7220 (t0) REVERT: F 1283 ILE cc_start: 0.8970 (pt) cc_final: 0.8674 (mp) REVERT: F 1384 MET cc_start: 0.7912 (mmm) cc_final: 0.7372 (mpp) REVERT: F 1436 LYS cc_start: 0.7179 (pmtt) cc_final: 0.6763 (ttmm) REVERT: F 1439 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7989 (mp10) REVERT: F 1491 ASP cc_start: 0.7304 (p0) cc_final: 0.7079 (p0) REVERT: F 1501 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8782 (tttt) REVERT: F 1592 LYS cc_start: 0.9090 (tttp) cc_final: 0.8823 (tttt) REVERT: F 1643 LYS cc_start: 0.8925 (mttt) cc_final: 0.8676 (mtmt) REVERT: F 1669 MET cc_start: 0.8649 (tpp) cc_final: 0.8389 (mmm) REVERT: F 1685 ASP cc_start: 0.8195 (t0) cc_final: 0.7572 (t0) REVERT: F 1727 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: F 1754 SER cc_start: 0.6652 (m) cc_final: 0.6177 (p) REVERT: F 1765 LEU cc_start: 0.8710 (tp) cc_final: 0.8478 (tp) REVERT: F 2071 ASP cc_start: 0.8443 (t70) cc_final: 0.8096 (t70) REVERT: F 2131 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7747 (mpp) REVERT: F 2224 ASP cc_start: 0.8097 (t0) cc_final: 0.7795 (t0) REVERT: F 2345 GLU cc_start: 0.8225 (tp30) cc_final: 0.7970 (tp30) REVERT: F 2364 TRP cc_start: 0.7222 (t60) cc_final: 0.6975 (t60) outliers start: 243 outliers final: 146 residues processed: 1022 average time/residue: 0.5387 time to fit residues: 941.1868 Evaluate side-chains 930 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 766 time to evaluate : 5.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 661 ARG Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 684 ASP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 252 CYS Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 637 THR Chi-restraints excluded: chain E residue 640 ASN Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 653 ILE Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 694 GLN Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain E residue 709 LEU Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 777 VAL Chi-restraints excluded: chain E residue 798 PHE Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 990 SER Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1150 VAL Chi-restraints excluded: chain E residue 1208 ASN Chi-restraints excluded: chain E residue 1263 LEU Chi-restraints excluded: chain E residue 1326 ILE Chi-restraints excluded: chain E residue 1349 ILE Chi-restraints excluded: chain E residue 1368 SER Chi-restraints excluded: chain E residue 1400 LEU Chi-restraints excluded: chain E residue 1408 ASP Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1597 SER Chi-restraints excluded: chain E residue 1624 LEU Chi-restraints excluded: chain E residue 1672 SER Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1709 SER Chi-restraints excluded: chain E residue 1727 GLU Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1774 SER Chi-restraints excluded: chain E residue 1810 LEU Chi-restraints excluded: chain E residue 1934 ILE Chi-restraints excluded: chain E residue 1950 VAL Chi-restraints excluded: chain E residue 1969 ASP Chi-restraints excluded: chain E residue 2063 LYS Chi-restraints excluded: chain E residue 2086 GLN Chi-restraints excluded: chain E residue 2114 ILE Chi-restraints excluded: chain E residue 2131 MET Chi-restraints excluded: chain E residue 2157 SER Chi-restraints excluded: chain E residue 2254 LEU Chi-restraints excluded: chain E residue 2260 VAL Chi-restraints excluded: chain E residue 2264 LEU Chi-restraints excluded: chain E residue 2275 ILE Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2344 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 591 ILE Chi-restraints excluded: chain F residue 604 GLU Chi-restraints excluded: chain F residue 605 ASP Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 637 THR Chi-restraints excluded: chain F residue 640 ASN Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 694 GLN Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 892 HIS Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 924 SER Chi-restraints excluded: chain F residue 990 SER Chi-restraints excluded: chain F residue 1010 THR Chi-restraints excluded: chain F residue 1066 GLU Chi-restraints excluded: chain F residue 1112 LEU Chi-restraints excluded: chain F residue 1129 THR Chi-restraints excluded: chain F residue 1205 LEU Chi-restraints excluded: chain F residue 1208 ASN Chi-restraints excluded: chain F residue 1272 GLU Chi-restraints excluded: chain F residue 1282 LEU Chi-restraints excluded: chain F residue 1304 ILE Chi-restraints excluded: chain F residue 1349 ILE Chi-restraints excluded: chain F residue 1400 LEU Chi-restraints excluded: chain F residue 1408 ASP Chi-restraints excluded: chain F residue 1439 GLN Chi-restraints excluded: chain F residue 1601 ILE Chi-restraints excluded: chain F residue 1630 LEU Chi-restraints excluded: chain F residue 1668 SER Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1704 ASP Chi-restraints excluded: chain F residue 1709 SER Chi-restraints excluded: chain F residue 1727 GLU Chi-restraints excluded: chain F residue 1786 TYR Chi-restraints excluded: chain F residue 1934 ILE Chi-restraints excluded: chain F residue 1950 VAL Chi-restraints excluded: chain F residue 2016 VAL Chi-restraints excluded: chain F residue 2086 GLN Chi-restraints excluded: chain F residue 2114 ILE Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2215 MET Chi-restraints excluded: chain F residue 2260 VAL Chi-restraints excluded: chain F residue 2275 ILE Chi-restraints excluded: chain F residue 2297 VAL Chi-restraints excluded: chain F residue 2344 THR Chi-restraints excluded: chain F residue 2355 ASP Chi-restraints excluded: chain F residue 2360 MET Chi-restraints excluded: chain F residue 2365 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 462 optimal weight: 7.9990 chunk 314 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 413 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 473 optimal weight: 0.5980 chunk 383 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 498 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS D 554 ASN D 600 ASN D 610 HIS ** D 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 HIS ** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 HIS E 197 ASN ** E 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 633 GLN ** E1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1292 ASN E1371 HIS ** E1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1921 HIS E2092 GLN ** E2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN ** F 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 708 ASN F 735 GLN F1371 HIS ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1840 ASN F1921 HIS F1987 GLN F2092 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 47552 Z= 0.332 Angle : 0.710 13.828 64388 Z= 0.362 Chirality : 0.046 0.313 7378 Planarity : 0.004 0.051 8098 Dihedral : 7.458 179.532 6296 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 5.15 % Allowed : 18.09 % Favored : 76.77 % 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: -1.61 (0.11), residues: 5736 helix: -0.38 (0.09), residues: 3604 sheet: -0.16 (0.63), residues: 62 loop : -2.25 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E2364 HIS 0.007 0.001 HIS F2241 PHE 0.035 0.002 PHE C 399 TYR 0.044 0.002 TYR D 563 ARG 0.006 0.001 ARG F 124 *********************** 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 1085 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 821 time to evaluate : 5.533 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: D 274 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8899 (mm) REVERT: D 482 MET cc_start: 0.8720 (tpp) cc_final: 0.8400 (tpt) REVERT: D 541 MET cc_start: 0.8332 (mmm) cc_final: 0.7945 (tpt) REVERT: D 637 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: D 651 GLU cc_start: 0.6770 (tp30) cc_final: 0.6521 (tp30) REVERT: C 308 GLN cc_start: 0.8984 (pp30) cc_final: 0.8663 (pp30) REVERT: C 482 MET cc_start: 0.8740 (tpp) cc_final: 0.8446 (tpt) REVERT: C 541 MET cc_start: 0.8220 (mmm) cc_final: 0.7622 (tpt) REVERT: C 715 GLU cc_start: 0.7953 (mp0) cc_final: 0.7658 (mp0) REVERT: C 736 GLU cc_start: 0.8296 (pm20) cc_final: 0.7951 (tm-30) REVERT: E 58 GLN cc_start: 0.8584 (tp40) cc_final: 0.8365 (tp40) REVERT: E 126 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8009 (mtpp) REVERT: E 163 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6748 (mt-10) REVERT: E 229 CYS cc_start: 0.7273 (p) cc_final: 0.6972 (p) REVERT: E 471 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7331 (tp30) REVERT: E 563 ASN cc_start: 0.7289 (m-40) cc_final: 0.7057 (t0) REVERT: E 565 GLN cc_start: 0.6315 (tm-30) cc_final: 0.5745 (tt0) REVERT: E 1023 LEU cc_start: 0.7808 (mp) cc_final: 0.7553 (tt) REVERT: E 1119 CYS cc_start: 0.8616 (m) cc_final: 0.8345 (m) REVERT: E 1148 ASP cc_start: 0.7606 (p0) cc_final: 0.7186 (t0) REVERT: E 1187 SER cc_start: 0.8841 (t) cc_final: 0.8555 (m) REVERT: E 1436 LYS cc_start: 0.7296 (pmtt) cc_final: 0.6808 (ttmm) REVERT: E 1643 LYS cc_start: 0.8880 (mttt) cc_final: 0.8644 (mtmt) REVERT: E 1685 ASP cc_start: 0.8216 (t0) cc_final: 0.7587 (t0) REVERT: E 1724 GLU cc_start: 0.8070 (tp30) cc_final: 0.7399 (tp30) REVERT: E 1727 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7770 (mp0) REVERT: E 1896 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7807 (pp) REVERT: E 1954 LYS cc_start: 0.7985 (mmtp) cc_final: 0.7679 (mmtp) REVERT: E 2071 ASP cc_start: 0.8491 (t70) cc_final: 0.8115 (t70) REVERT: E 2131 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.7298 (mpp) REVERT: F 90 MET cc_start: 0.7198 (ppp) cc_final: 0.6499 (ppp) REVERT: F 163 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6758 (mt-10) REVERT: F 212 ASP cc_start: 0.7646 (m-30) cc_final: 0.7281 (m-30) REVERT: F 270 GLN cc_start: 0.8185 (mt0) cc_final: 0.7442 (mt0) REVERT: F 563 ASN cc_start: 0.7363 (m-40) cc_final: 0.6908 (t0) REVERT: F 591 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8419 (mt) REVERT: F 620 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8147 (mp) REVERT: F 694 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7314 (pm20) REVERT: F 767 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8651 (p0) REVERT: F 1023 LEU cc_start: 0.7774 (mp) cc_final: 0.7420 (tt) REVERT: F 1119 CYS cc_start: 0.8630 (m) cc_final: 0.8345 (m) REVERT: F 1148 ASP cc_start: 0.7547 (p0) cc_final: 0.7282 (t0) REVERT: F 1384 MET cc_start: 0.7961 (mmm) cc_final: 0.7388 (mpp) REVERT: F 1436 LYS cc_start: 0.7333 (pmtt) cc_final: 0.6970 (ttmm) REVERT: F 1439 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8123 (mp10) REVERT: F 1592 LYS cc_start: 0.9080 (tttp) cc_final: 0.8840 (tttt) REVERT: F 1643 LYS cc_start: 0.8928 (mttt) cc_final: 0.8674 (mtmt) REVERT: F 1669 MET cc_start: 0.8648 (tpp) cc_final: 0.8369 (mmm) REVERT: F 1685 ASP cc_start: 0.8187 (t0) cc_final: 0.7546 (t0) REVERT: F 1727 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: F 1754 SER cc_start: 0.6712 (m) cc_final: 0.6213 (p) REVERT: F 1896 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7813 (pp) REVERT: F 2071 ASP cc_start: 0.8420 (t70) cc_final: 0.8065 (t70) REVERT: F 2131 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7792 (mpp) REVERT: F 2224 ASP cc_start: 0.8134 (t0) cc_final: 0.7927 (t0) outliers start: 264 outliers final: 167 residues processed: 990 average time/residue: 0.5322 time to fit residues: 904.3643 Evaluate side-chains 934 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 751 time to evaluate : 5.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 342 HIS Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 684 ASP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 597 ILE Chi-restraints excluded: chain E residue 605 ASP Chi-restraints excluded: chain E residue 633 GLN Chi-restraints excluded: chain E residue 637 THR Chi-restraints excluded: chain E residue 640 ASN Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 755 LEU Chi-restraints excluded: chain E residue 777 VAL Chi-restraints excluded: chain E residue 798 PHE Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 957 LEU Chi-restraints excluded: chain E residue 988 VAL Chi-restraints excluded: chain E residue 990 SER Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1129 THR Chi-restraints excluded: chain E residue 1150 VAL Chi-restraints excluded: chain E residue 1205 LEU Chi-restraints excluded: chain E residue 1208 ASN Chi-restraints excluded: chain E residue 1263 LEU Chi-restraints excluded: chain E residue 1304 ILE Chi-restraints excluded: chain E residue 1349 ILE Chi-restraints excluded: chain E residue 1368 SER Chi-restraints excluded: chain E residue 1400 LEU Chi-restraints excluded: chain E residue 1408 ASP Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1597 SER Chi-restraints excluded: chain E residue 1622 MET Chi-restraints excluded: chain E residue 1624 LEU Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1638 ASP Chi-restraints excluded: chain E residue 1672 SER Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1709 SER Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1774 SER Chi-restraints excluded: chain E residue 1810 LEU Chi-restraints excluded: chain E residue 1896 ILE Chi-restraints excluded: chain E residue 1924 LEU Chi-restraints excluded: chain E residue 1934 ILE Chi-restraints excluded: chain E residue 1969 ASP Chi-restraints excluded: chain E residue 2016 VAL Chi-restraints excluded: chain E residue 2063 LYS Chi-restraints excluded: chain E residue 2114 ILE Chi-restraints excluded: chain E residue 2131 MET Chi-restraints excluded: chain E residue 2157 SER Chi-restraints excluded: chain E residue 2215 MET Chi-restraints excluded: chain E residue 2259 ILE Chi-restraints excluded: chain E residue 2260 VAL Chi-restraints excluded: chain E residue 2264 LEU Chi-restraints excluded: chain E residue 2275 ILE Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2344 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 574 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 591 ILE Chi-restraints excluded: chain F residue 604 GLU Chi-restraints excluded: chain F residue 605 ASP Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 637 THR Chi-restraints excluded: chain F residue 640 ASN Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 694 GLN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 990 SER Chi-restraints excluded: chain F residue 1010 THR Chi-restraints excluded: chain F residue 1112 LEU Chi-restraints excluded: chain F residue 1129 THR Chi-restraints excluded: chain F residue 1205 LEU Chi-restraints excluded: chain F residue 1208 ASN Chi-restraints excluded: chain F residue 1272 GLU Chi-restraints excluded: chain F residue 1282 LEU Chi-restraints excluded: chain F residue 1304 ILE Chi-restraints excluded: chain F residue 1349 ILE Chi-restraints excluded: chain F residue 1400 LEU Chi-restraints excluded: chain F residue 1408 ASP Chi-restraints excluded: chain F residue 1439 GLN Chi-restraints excluded: chain F residue 1597 SER Chi-restraints excluded: chain F residue 1630 LEU Chi-restraints excluded: chain F residue 1668 SER Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1704 ASP Chi-restraints excluded: chain F residue 1709 SER Chi-restraints excluded: chain F residue 1727 GLU Chi-restraints excluded: chain F residue 1774 SER Chi-restraints excluded: chain F residue 1786 TYR Chi-restraints excluded: chain F residue 1820 ILE Chi-restraints excluded: chain F residue 1896 ILE Chi-restraints excluded: chain F residue 1924 LEU Chi-restraints excluded: chain F residue 1934 ILE Chi-restraints excluded: chain F residue 1941 LEU Chi-restraints excluded: chain F residue 1950 VAL Chi-restraints excluded: chain F residue 2114 ILE Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2215 MET Chi-restraints excluded: chain F residue 2264 LEU Chi-restraints excluded: chain F residue 2275 ILE Chi-restraints excluded: chain F residue 2297 VAL Chi-restraints excluded: chain F residue 2327 ILE Chi-restraints excluded: chain F residue 2344 THR Chi-restraints excluded: chain F residue 2355 ASP Chi-restraints excluded: chain F residue 2365 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 186 optimal weight: 6.9990 chunk 499 optimal weight: 0.9990 chunk 109 optimal weight: 0.0670 chunk 325 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 555 optimal weight: 5.9990 chunk 461 optimal weight: 10.0000 chunk 257 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 291 optimal weight: 8.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS D 718 GLN ** C 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 HIS ** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 ASN E 633 GLN ** E1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1776 ASN E1921 HIS E2092 GLN ** E2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 668 GLN F1034 ASN ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1987 GLN F2092 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 47552 Z= 0.199 Angle : 0.650 14.098 64388 Z= 0.328 Chirality : 0.043 0.257 7378 Planarity : 0.004 0.052 8098 Dihedral : 7.215 179.937 6296 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.06 % Allowed : 19.77 % Favored : 76.17 % 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: -1.33 (0.11), residues: 5736 helix: -0.14 (0.09), residues: 3592 sheet: -0.13 (0.63), residues: 62 loop : -2.16 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F2364 HIS 0.007 0.001 HIS D 610 PHE 0.027 0.002 PHE C 399 TYR 0.040 0.001 TYR E 810 ARG 0.006 0.000 ARG D 704 *********************** 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 1108 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 900 time to evaluate : 5.178 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: D 376 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8892 (tt) REVERT: D 541 MET cc_start: 0.8236 (mmm) cc_final: 0.7877 (tpt) REVERT: C 308 GLN cc_start: 0.8924 (pp30) cc_final: 0.8610 (pp30) REVERT: C 715 GLU cc_start: 0.8058 (mp0) cc_final: 0.7809 (mp0) REVERT: C 736 GLU cc_start: 0.8182 (pm20) cc_final: 0.7945 (tm-30) REVERT: E 126 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7898 (mtpp) REVERT: E 163 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: E 229 CYS cc_start: 0.7028 (p) cc_final: 0.6760 (p) REVERT: E 471 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7336 (tp30) REVERT: E 563 ASN cc_start: 0.7228 (m-40) cc_final: 0.6932 (t0) REVERT: E 810 TYR cc_start: 0.7843 (m-10) cc_final: 0.7558 (m-80) REVERT: E 888 SER cc_start: 0.9035 (m) cc_final: 0.8756 (p) REVERT: E 1119 CYS cc_start: 0.8590 (m) cc_final: 0.8296 (m) REVERT: E 1122 MET cc_start: 0.8409 (mtt) cc_final: 0.8179 (mtp) REVERT: E 1148 ASP cc_start: 0.7602 (p0) cc_final: 0.7220 (t0) REVERT: E 1187 SER cc_start: 0.8814 (t) cc_final: 0.8589 (m) REVERT: E 1436 LYS cc_start: 0.7146 (pmtt) cc_final: 0.6760 (ttmm) REVERT: E 1501 LYS cc_start: 0.9076 (mmmt) cc_final: 0.8811 (tttt) REVERT: E 1643 LYS cc_start: 0.8881 (mttt) cc_final: 0.8648 (mtmt) REVERT: E 1685 ASP cc_start: 0.8159 (t0) cc_final: 0.7568 (t0) REVERT: E 1724 GLU cc_start: 0.7922 (tp30) cc_final: 0.7277 (tp30) REVERT: E 1727 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7733 (mp0) REVERT: E 1754 SER cc_start: 0.6851 (m) cc_final: 0.6378 (p) REVERT: E 1954 LYS cc_start: 0.7946 (mmtp) cc_final: 0.7656 (mmtp) REVERT: E 2071 ASP cc_start: 0.8390 (t70) cc_final: 0.8025 (t70) REVERT: E 2131 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7226 (mpp) REVERT: E 2224 ASP cc_start: 0.7782 (t0) cc_final: 0.7507 (t0) REVERT: E 2258 GLU cc_start: 0.5995 (mp0) cc_final: 0.5676 (mp0) REVERT: E 2292 MET cc_start: 0.8469 (mtp) cc_final: 0.8265 (mtp) REVERT: F 90 MET cc_start: 0.6938 (ppp) cc_final: 0.6652 (ppp) REVERT: F 113 ASN cc_start: 0.8720 (m110) cc_final: 0.8207 (m110) REVERT: F 117 TYR cc_start: 0.8645 (m-80) cc_final: 0.8367 (m-10) REVERT: F 163 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: F 212 ASP cc_start: 0.7571 (m-30) cc_final: 0.7220 (m-30) REVERT: F 229 CYS cc_start: 0.7297 (p) cc_final: 0.7004 (p) REVERT: F 563 ASN cc_start: 0.7108 (m-40) cc_final: 0.6868 (t0) REVERT: F 620 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8040 (mp) REVERT: F 710 ILE cc_start: 0.9503 (pp) cc_final: 0.9271 (pp) REVERT: F 767 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8543 (p0) REVERT: F 1023 LEU cc_start: 0.7788 (mp) cc_final: 0.7439 (tt) REVERT: F 1066 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: F 1119 CYS cc_start: 0.8594 (m) cc_final: 0.8286 (m) REVERT: F 1122 MET cc_start: 0.8521 (mtt) cc_final: 0.8237 (mtp) REVERT: F 1148 ASP cc_start: 0.7409 (p0) cc_final: 0.7202 (t0) REVERT: F 1384 MET cc_start: 0.7904 (mmm) cc_final: 0.7366 (mpp) REVERT: F 1436 LYS cc_start: 0.7202 (pmtt) cc_final: 0.6896 (ttmm) REVERT: F 1439 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: F 1501 LYS cc_start: 0.9095 (mmmt) cc_final: 0.8789 (tttt) REVERT: F 1643 LYS cc_start: 0.8891 (mttt) cc_final: 0.8637 (mtmt) REVERT: F 1685 ASP cc_start: 0.8094 (t0) cc_final: 0.7479 (t0) REVERT: F 1727 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: F 1754 SER cc_start: 0.6627 (m) cc_final: 0.6136 (p) REVERT: F 2071 ASP cc_start: 0.8427 (t70) cc_final: 0.8089 (t70) REVERT: F 2131 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7676 (mpp) REVERT: F 2162 TRP cc_start: 0.8386 (t60) cc_final: 0.7763 (t60) REVERT: F 2191 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8026 (mt-10) REVERT: F 2303 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8729 (mt) outliers start: 208 outliers final: 136 residues processed: 1034 average time/residue: 0.5383 time to fit residues: 951.0233 Evaluate side-chains 934 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 785 time to evaluate : 5.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 342 HIS Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 661 ARG Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 342 HIS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 637 THR Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 709 LEU Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 957 LEU Chi-restraints excluded: chain E residue 991 ILE Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1208 ASN Chi-restraints excluded: chain E residue 1263 LEU Chi-restraints excluded: chain E residue 1304 ILE Chi-restraints excluded: chain E residue 1349 ILE Chi-restraints excluded: chain E residue 1400 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1622 MET Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1672 SER Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1709 SER Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1774 SER Chi-restraints excluded: chain E residue 1934 ILE Chi-restraints excluded: chain E residue 1941 LEU Chi-restraints excluded: chain E residue 1950 VAL Chi-restraints excluded: chain E residue 1969 ASP Chi-restraints excluded: chain E residue 2016 VAL Chi-restraints excluded: chain E residue 2063 LYS Chi-restraints excluded: chain E residue 2114 ILE Chi-restraints excluded: chain E residue 2131 MET Chi-restraints excluded: chain E residue 2157 SER Chi-restraints excluded: chain E residue 2215 MET Chi-restraints excluded: chain E residue 2264 LEU Chi-restraints excluded: chain E residue 2275 ILE Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2365 LEU Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 574 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 604 GLU Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 637 THR Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 957 LEU Chi-restraints excluded: chain F residue 990 SER Chi-restraints excluded: chain F residue 991 ILE Chi-restraints excluded: chain F residue 1010 THR Chi-restraints excluded: chain F residue 1022 ILE Chi-restraints excluded: chain F residue 1066 GLU Chi-restraints excluded: chain F residue 1112 LEU Chi-restraints excluded: chain F residue 1150 VAL Chi-restraints excluded: chain F residue 1205 LEU Chi-restraints excluded: chain F residue 1208 ASN Chi-restraints excluded: chain F residue 1272 GLU Chi-restraints excluded: chain F residue 1304 ILE Chi-restraints excluded: chain F residue 1349 ILE Chi-restraints excluded: chain F residue 1400 LEU Chi-restraints excluded: chain F residue 1439 GLN Chi-restraints excluded: chain F residue 1630 LEU Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1704 ASP Chi-restraints excluded: chain F residue 1709 SER Chi-restraints excluded: chain F residue 1727 GLU Chi-restraints excluded: chain F residue 1752 ASN Chi-restraints excluded: chain F residue 1786 TYR Chi-restraints excluded: chain F residue 1924 LEU Chi-restraints excluded: chain F residue 1934 ILE Chi-restraints excluded: chain F residue 1941 LEU Chi-restraints excluded: chain F residue 2016 VAL Chi-restraints excluded: chain F residue 2086 GLN Chi-restraints excluded: chain F residue 2114 ILE Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2215 MET Chi-restraints excluded: chain F residue 2264 LEU Chi-restraints excluded: chain F residue 2275 ILE Chi-restraints excluded: chain F residue 2297 VAL Chi-restraints excluded: chain F residue 2303 ILE Chi-restraints excluded: chain F residue 2327 ILE Chi-restraints excluded: chain F residue 2355 ASP Chi-restraints excluded: chain F residue 2360 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 535 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 316 optimal weight: 9.9990 chunk 405 optimal weight: 5.9990 chunk 314 optimal weight: 8.9990 chunk 467 optimal weight: 10.0000 chunk 310 optimal weight: 8.9990 chunk 553 optimal weight: 8.9990 chunk 346 optimal weight: 4.9990 chunk 337 optimal weight: 20.0000 chunk 255 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS ** C 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 HIS ** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 ASN E 565 GLN ** E 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 862 ASN E 868 GLN ** E1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1371 HIS E1675 GLN E1776 ASN E1785 GLN E1987 GLN E2092 GLN ** E2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 633 GLN F 868 GLN ** F1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1371 HIS F1439 GLN ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1675 GLN ** F1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1987 GLN F2092 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 47552 Z= 0.417 Angle : 0.764 12.157 64388 Z= 0.389 Chirality : 0.048 0.291 7378 Planarity : 0.004 0.047 8098 Dihedral : 7.409 179.428 6296 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 5.03 % Allowed : 19.75 % Favored : 75.22 % 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: -1.41 (0.11), residues: 5736 helix: -0.23 (0.09), residues: 3622 sheet: -0.35 (0.62), residues: 62 loop : -2.16 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F2364 HIS 0.008 0.002 HIS D 663 PHE 0.043 0.003 PHE D 206 TYR 0.034 0.002 TYR E 810 ARG 0.006 0.001 ARG F 454 *********************** 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 1036 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 778 time to evaluate : 5.558 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: D 541 MET cc_start: 0.8411 (mmm) cc_final: 0.8035 (tpt) REVERT: C 308 GLN cc_start: 0.9015 (pp30) cc_final: 0.8673 (pp30) REVERT: C 541 MET cc_start: 0.8378 (mmm) cc_final: 0.7956 (tpt) REVERT: C 700 GLN cc_start: 0.8331 (tp40) cc_final: 0.7768 (tt0) REVERT: C 715 GLU cc_start: 0.8043 (mp0) cc_final: 0.7796 (mp0) REVERT: C 736 GLU cc_start: 0.8229 (pm20) cc_final: 0.7921 (tm-30) REVERT: E 126 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8056 (mtpp) REVERT: E 218 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8688 (mm) REVERT: E 471 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7462 (tp30) REVERT: E 563 ASN cc_start: 0.7467 (m-40) cc_final: 0.6818 (t0) REVERT: E 888 SER cc_start: 0.9083 (m) cc_final: 0.8829 (p) REVERT: E 902 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7414 (mm-30) REVERT: E 1119 CYS cc_start: 0.8592 (m) cc_final: 0.8338 (m) REVERT: E 1122 MET cc_start: 0.8543 (mtt) cc_final: 0.8271 (mtp) REVERT: E 1148 ASP cc_start: 0.7832 (p0) cc_final: 0.7230 (t0) REVERT: E 1187 SER cc_start: 0.8890 (t) cc_final: 0.8624 (m) REVERT: E 1436 LYS cc_start: 0.7445 (pmtt) cc_final: 0.7004 (ttmm) REVERT: E 1643 LYS cc_start: 0.8894 (mttt) cc_final: 0.8659 (mtmt) REVERT: E 1685 ASP cc_start: 0.8233 (t0) cc_final: 0.7614 (t0) REVERT: E 1724 GLU cc_start: 0.8145 (tp30) cc_final: 0.7577 (tp30) REVERT: E 1727 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7795 (mp0) REVERT: E 1820 ILE cc_start: 0.8866 (mp) cc_final: 0.8595 (mm) REVERT: E 1954 LYS cc_start: 0.7977 (mmtp) cc_final: 0.7768 (mmtp) REVERT: E 2071 ASP cc_start: 0.8451 (t70) cc_final: 0.8080 (t70) REVERT: E 2131 MET cc_start: 0.8558 (mpp) cc_final: 0.6992 (mpp) REVERT: E 2224 ASP cc_start: 0.8041 (t0) cc_final: 0.7721 (t0) REVERT: E 2258 GLU cc_start: 0.6752 (mp0) cc_final: 0.6422 (mp0) REVERT: F 117 TYR cc_start: 0.8757 (m-80) cc_final: 0.8505 (m-10) REVERT: F 163 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: F 212 ASP cc_start: 0.7619 (m-30) cc_final: 0.7330 (m-30) REVERT: F 455 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8536 (mm) REVERT: F 471 GLU cc_start: 0.7775 (tp30) cc_final: 0.7564 (tp30) REVERT: F 563 ASN cc_start: 0.7373 (m-40) cc_final: 0.6898 (t0) REVERT: F 620 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8046 (mp) REVERT: F 665 MET cc_start: 0.8873 (tpp) cc_final: 0.8607 (tpp) REVERT: F 694 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: F 767 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8717 (p0) REVERT: F 991 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9253 (mt) REVERT: F 1023 LEU cc_start: 0.7789 (mp) cc_final: 0.7433 (tt) REVERT: F 1066 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: F 1119 CYS cc_start: 0.8610 (m) cc_final: 0.8335 (m) REVERT: F 1148 ASP cc_start: 0.7723 (p0) cc_final: 0.7291 (t0) REVERT: F 1334 MET cc_start: 0.5737 (ptp) cc_final: 0.5471 (ptm) REVERT: F 1436 LYS cc_start: 0.7461 (pmtt) cc_final: 0.6873 (ttmm) REVERT: F 1494 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8200 (ptpp) REVERT: F 1643 LYS cc_start: 0.8910 (mttt) cc_final: 0.8661 (mtmt) REVERT: F 1685 ASP cc_start: 0.8211 (t0) cc_final: 0.7611 (t0) REVERT: F 1727 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: F 1801 TYR cc_start: 0.8838 (m-80) cc_final: 0.8546 (m-10) REVERT: F 1820 ILE cc_start: 0.8728 (mp) cc_final: 0.8443 (mm) REVERT: F 2071 ASP cc_start: 0.8432 (t70) cc_final: 0.8077 (t70) REVERT: F 2131 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7395 (mpp) REVERT: F 2191 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8197 (mt-10) outliers start: 258 outliers final: 187 residues processed: 950 average time/residue: 0.5446 time to fit residues: 889.3118 Evaluate side-chains 930 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 730 time to evaluate : 5.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 498 ASN Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 661 ARG Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 684 ASP Chi-restraints excluded: chain D residue 716 LYS Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 660 MET Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 605 ASP Chi-restraints excluded: chain E residue 637 THR Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 709 LEU Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 755 LEU Chi-restraints excluded: chain E residue 797 THR Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 957 LEU Chi-restraints excluded: chain E residue 991 ILE Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1022 ILE Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1129 THR Chi-restraints excluded: chain E residue 1205 LEU Chi-restraints excluded: chain E residue 1208 ASN Chi-restraints excluded: chain E residue 1263 LEU Chi-restraints excluded: chain E residue 1266 LEU Chi-restraints excluded: chain E residue 1273 ASN Chi-restraints excluded: chain E residue 1282 LEU Chi-restraints excluded: chain E residue 1290 LEU Chi-restraints excluded: chain E residue 1304 ILE Chi-restraints excluded: chain E residue 1342 LEU Chi-restraints excluded: chain E residue 1349 ILE Chi-restraints excluded: chain E residue 1368 SER Chi-restraints excluded: chain E residue 1400 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1582 ILE Chi-restraints excluded: chain E residue 1597 SER Chi-restraints excluded: chain E residue 1622 MET Chi-restraints excluded: chain E residue 1624 LEU Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1638 ASP Chi-restraints excluded: chain E residue 1672 SER Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1709 SER Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1774 SER Chi-restraints excluded: chain E residue 1924 LEU Chi-restraints excluded: chain E residue 1930 TYR Chi-restraints excluded: chain E residue 1934 ILE Chi-restraints excluded: chain E residue 1950 VAL Chi-restraints excluded: chain E residue 1969 ASP Chi-restraints excluded: chain E residue 2016 VAL Chi-restraints excluded: chain E residue 2063 LYS Chi-restraints excluded: chain E residue 2086 GLN Chi-restraints excluded: chain E residue 2114 ILE Chi-restraints excluded: chain E residue 2157 SER Chi-restraints excluded: chain E residue 2215 MET Chi-restraints excluded: chain E residue 2264 LEU Chi-restraints excluded: chain E residue 2275 ILE Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2344 THR Chi-restraints excluded: chain E residue 2365 LEU Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 574 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 591 ILE Chi-restraints excluded: chain F residue 604 GLU Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 637 THR Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 694 GLN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 797 THR Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 892 HIS Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 969 LEU Chi-restraints excluded: chain F residue 990 SER Chi-restraints excluded: chain F residue 991 ILE Chi-restraints excluded: chain F residue 1010 THR Chi-restraints excluded: chain F residue 1022 ILE Chi-restraints excluded: chain F residue 1066 GLU Chi-restraints excluded: chain F residue 1112 LEU Chi-restraints excluded: chain F residue 1150 VAL Chi-restraints excluded: chain F residue 1205 LEU Chi-restraints excluded: chain F residue 1208 ASN Chi-restraints excluded: chain F residue 1282 LEU Chi-restraints excluded: chain F residue 1304 ILE Chi-restraints excluded: chain F residue 1342 LEU Chi-restraints excluded: chain F residue 1349 ILE Chi-restraints excluded: chain F residue 1400 LEU Chi-restraints excluded: chain F residue 1494 LYS Chi-restraints excluded: chain F residue 1560 SER Chi-restraints excluded: chain F residue 1582 ILE Chi-restraints excluded: chain F residue 1630 LEU Chi-restraints excluded: chain F residue 1668 SER Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1704 ASP Chi-restraints excluded: chain F residue 1709 SER Chi-restraints excluded: chain F residue 1727 GLU Chi-restraints excluded: chain F residue 1752 ASN Chi-restraints excluded: chain F residue 1774 SER Chi-restraints excluded: chain F residue 1786 TYR Chi-restraints excluded: chain F residue 1805 LEU Chi-restraints excluded: chain F residue 1850 LYS Chi-restraints excluded: chain F residue 1924 LEU Chi-restraints excluded: chain F residue 1930 TYR Chi-restraints excluded: chain F residue 1934 ILE Chi-restraints excluded: chain F residue 1950 VAL Chi-restraints excluded: chain F residue 2016 VAL Chi-restraints excluded: chain F residue 2017 VAL Chi-restraints excluded: chain F residue 2046 ILE Chi-restraints excluded: chain F residue 2078 MET Chi-restraints excluded: chain F residue 2086 GLN Chi-restraints excluded: chain F residue 2114 ILE Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2215 MET Chi-restraints excluded: chain F residue 2260 VAL Chi-restraints excluded: chain F residue 2275 ILE Chi-restraints excluded: chain F residue 2297 VAL Chi-restraints excluded: chain F residue 2327 ILE Chi-restraints excluded: chain F residue 2344 THR Chi-restraints excluded: chain F residue 2355 ASP Chi-restraints excluded: chain F residue 2360 MET 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: 20.0000 chunk 220 optimal weight: 6.9990 chunk 330 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 351 optimal weight: 0.9990 chunk 376 optimal weight: 10.0000 chunk 273 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 434 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 ASN ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS D 702 ASN ** C 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 HIS C 494 ASN ** E 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 633 GLN E 868 GLN E1049 ASN E1371 HIS E1776 ASN E2092 GLN ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 868 GLN ** F1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1049 ASN F1371 HIS F1675 GLN F2092 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 47552 Z= 0.196 Angle : 0.680 15.880 64388 Z= 0.339 Chirality : 0.044 0.296 7378 Planarity : 0.004 0.061 8098 Dihedral : 7.124 179.897 6296 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.58 % Allowed : 21.37 % Favored : 75.05 % 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: -1.14 (0.11), residues: 5736 helix: 0.02 (0.09), residues: 3580 sheet: -0.33 (0.63), residues: 62 loop : -2.08 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F2364 HIS 0.009 0.001 HIS D 663 PHE 0.057 0.002 PHE C 489 TYR 0.023 0.001 TYR E1827 ARG 0.011 0.000 ARG E 454 *********************** 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 1057 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 874 time to evaluate : 5.143 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: D 376 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8900 (tt) REVERT: D 482 MET cc_start: 0.8780 (tpp) cc_final: 0.8500 (tpt) REVERT: D 593 TYR cc_start: 0.9002 (m-80) cc_final: 0.8725 (m-80) REVERT: D 700 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7740 (tt0) REVERT: C 308 GLN cc_start: 0.8951 (pp30) cc_final: 0.8635 (pp30) REVERT: C 541 MET cc_start: 0.8167 (mmm) cc_final: 0.7693 (tpt) REVERT: C 736 GLU cc_start: 0.8082 (pm20) cc_final: 0.7879 (tm-30) REVERT: E 117 TYR cc_start: 0.8651 (m-80) cc_final: 0.8448 (m-10) REVERT: E 163 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7499 (mm-30) REVERT: E 323 GLN cc_start: 0.8356 (pm20) cc_final: 0.8132 (pm20) REVERT: E 471 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: E 574 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: E 665 MET cc_start: 0.7676 (mmm) cc_final: 0.7194 (tpt) REVERT: E 858 TYR cc_start: 0.7775 (m-80) cc_final: 0.7524 (m-80) REVERT: E 888 SER cc_start: 0.9038 (m) cc_final: 0.8789 (p) REVERT: E 1119 CYS cc_start: 0.8568 (m) cc_final: 0.8291 (m) REVERT: E 1148 ASP cc_start: 0.7781 (p0) cc_final: 0.7253 (t0) REVERT: E 1334 MET cc_start: 0.5628 (ptp) cc_final: 0.5385 (ptp) REVERT: E 1384 MET cc_start: 0.8029 (mmm) cc_final: 0.7519 (mpp) REVERT: E 1436 LYS cc_start: 0.7245 (pmtt) cc_final: 0.6849 (ttmm) REVERT: E 1494 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8095 (ptpp) REVERT: E 1643 LYS cc_start: 0.8852 (mttt) cc_final: 0.8600 (mtmt) REVERT: E 1685 ASP cc_start: 0.8137 (t0) cc_final: 0.7670 (t0) REVERT: E 1724 GLU cc_start: 0.7868 (tp30) cc_final: 0.7239 (tp30) REVERT: E 1727 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7747 (mp0) REVERT: E 1754 SER cc_start: 0.6893 (m) cc_final: 0.6402 (p) REVERT: E 1772 ASP cc_start: 0.7749 (t0) cc_final: 0.7445 (t0) REVERT: E 1809 ARG cc_start: 0.8766 (ptp-170) cc_final: 0.8451 (ptp90) REVERT: E 1834 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8907 (mt) REVERT: E 1850 LYS cc_start: 0.8481 (mmmt) cc_final: 0.8250 (tptp) REVERT: E 1905 LEU cc_start: 0.7975 (mp) cc_final: 0.7769 (mp) REVERT: E 1958 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6901 (tt0) REVERT: E 2071 ASP cc_start: 0.8393 (t70) cc_final: 0.8059 (t70) REVERT: E 2089 GLN cc_start: 0.7384 (mt0) cc_final: 0.7110 (mt0) REVERT: E 2131 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7234 (mpp) REVERT: E 2224 ASP cc_start: 0.7992 (t0) cc_final: 0.7723 (t0) REVERT: F 117 TYR cc_start: 0.8674 (m-80) cc_final: 0.8440 (m-10) REVERT: F 163 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: F 212 ASP cc_start: 0.7436 (m-30) cc_final: 0.7131 (m-30) REVERT: F 229 CYS cc_start: 0.7363 (p) cc_final: 0.7085 (p) REVERT: F 455 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8594 (mm) REVERT: F 471 GLU cc_start: 0.7770 (tp30) cc_final: 0.7368 (tp30) REVERT: F 563 ASN cc_start: 0.7108 (m-40) cc_final: 0.6897 (t0) REVERT: F 902 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7043 (mm-30) REVERT: F 1023 LEU cc_start: 0.7780 (mp) cc_final: 0.7445 (tt) REVERT: F 1066 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: F 1119 CYS cc_start: 0.8595 (m) cc_final: 0.8281 (m) REVERT: F 1122 MET cc_start: 0.8524 (mtt) cc_final: 0.8252 (mtp) REVERT: F 1148 ASP cc_start: 0.7679 (p0) cc_final: 0.7271 (t0) REVERT: F 1384 MET cc_start: 0.7902 (mmm) cc_final: 0.7364 (mpp) REVERT: F 1419 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7825 (tp-100) REVERT: F 1436 LYS cc_start: 0.7301 (pmtt) cc_final: 0.6984 (ttmm) REVERT: F 1501 LYS cc_start: 0.9147 (mmmt) cc_final: 0.8817 (tttt) REVERT: F 1643 LYS cc_start: 0.8877 (mttt) cc_final: 0.8619 (mtmt) REVERT: F 1685 ASP cc_start: 0.8153 (t0) cc_final: 0.7553 (t0) REVERT: F 1727 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7819 (mp0) REVERT: F 1754 SER cc_start: 0.6758 (m) cc_final: 0.6287 (p) REVERT: F 1801 TYR cc_start: 0.8690 (m-80) cc_final: 0.8459 (m-10) REVERT: F 1809 ARG cc_start: 0.8762 (ptp-170) cc_final: 0.8518 (ptp90) REVERT: F 1838 GLU cc_start: 0.7839 (pt0) cc_final: 0.7572 (tp30) REVERT: F 2071 ASP cc_start: 0.8403 (t70) cc_final: 0.8101 (t70) REVERT: F 2131 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7626 (mpp) REVERT: F 2191 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8008 (mt-10) REVERT: F 2303 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8785 (mt) outliers start: 183 outliers final: 142 residues processed: 982 average time/residue: 0.5420 time to fit residues: 908.7986 Evaluate side-chains 944 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 790 time to evaluate : 5.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 498 ASN Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 716 LYS Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 342 HIS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 660 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 709 LEU Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 797 THR Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 957 LEU Chi-restraints excluded: chain E residue 991 ILE Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1205 LEU Chi-restraints excluded: chain E residue 1208 ASN Chi-restraints excluded: chain E residue 1263 LEU Chi-restraints excluded: chain E residue 1304 ILE Chi-restraints excluded: chain E residue 1349 ILE Chi-restraints excluded: chain E residue 1368 SER Chi-restraints excluded: chain E residue 1400 LEU Chi-restraints excluded: chain E residue 1494 LYS Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1597 SER Chi-restraints excluded: chain E residue 1622 MET Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1672 SER Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1709 SER Chi-restraints excluded: chain E residue 1734 GLU Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1774 SER Chi-restraints excluded: chain E residue 1834 LEU Chi-restraints excluded: chain E residue 1858 ILE Chi-restraints excluded: chain E residue 1934 ILE Chi-restraints excluded: chain E residue 1950 VAL Chi-restraints excluded: chain E residue 1969 ASP Chi-restraints excluded: chain E residue 2016 VAL Chi-restraints excluded: chain E residue 2063 LYS Chi-restraints excluded: chain E residue 2086 GLN Chi-restraints excluded: chain E residue 2114 ILE Chi-restraints excluded: chain E residue 2131 MET Chi-restraints excluded: chain E residue 2215 MET Chi-restraints excluded: chain E residue 2260 VAL Chi-restraints excluded: chain E residue 2264 LEU Chi-restraints excluded: chain E residue 2275 ILE Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2312 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain F residue 797 THR Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 957 LEU Chi-restraints excluded: chain F residue 969 LEU Chi-restraints excluded: chain F residue 990 SER Chi-restraints excluded: chain F residue 991 ILE Chi-restraints excluded: chain F residue 1010 THR Chi-restraints excluded: chain F residue 1066 GLU Chi-restraints excluded: chain F residue 1112 LEU Chi-restraints excluded: chain F residue 1150 VAL Chi-restraints excluded: chain F residue 1205 LEU Chi-restraints excluded: chain F residue 1208 ASN Chi-restraints excluded: chain F residue 1272 GLU Chi-restraints excluded: chain F residue 1282 LEU Chi-restraints excluded: chain F residue 1304 ILE Chi-restraints excluded: chain F residue 1349 ILE Chi-restraints excluded: chain F residue 1400 LEU Chi-restraints excluded: chain F residue 1630 LEU Chi-restraints excluded: chain F residue 1668 SER Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1704 ASP Chi-restraints excluded: chain F residue 1709 SER Chi-restraints excluded: chain F residue 1752 ASN Chi-restraints excluded: chain F residue 1805 LEU Chi-restraints excluded: chain F residue 1833 PHE Chi-restraints excluded: chain F residue 1934 ILE Chi-restraints excluded: chain F residue 1950 VAL Chi-restraints excluded: chain F residue 2016 VAL Chi-restraints excluded: chain F residue 2017 VAL Chi-restraints excluded: chain F residue 2046 ILE Chi-restraints excluded: chain F residue 2078 MET Chi-restraints excluded: chain F residue 2086 GLN Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2215 MET Chi-restraints excluded: chain F residue 2275 ILE Chi-restraints excluded: chain F residue 2297 VAL Chi-restraints excluded: chain F residue 2303 ILE Chi-restraints excluded: chain F residue 2327 ILE Chi-restraints excluded: chain F residue 2355 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 503 optimal weight: 7.9990 chunk 530 optimal weight: 20.0000 chunk 483 optimal weight: 2.9990 chunk 515 optimal weight: 9.9990 chunk 529 optimal weight: 3.9990 chunk 310 optimal weight: 0.0470 chunk 224 optimal weight: 8.9990 chunk 404 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 465 optimal weight: 1.9990 chunk 487 optimal weight: 10.0000 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS D 649 GLN ** C 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 HIS E1034 ASN E1371 HIS E1574 ASN E1776 ASN E1921 HIS E2092 GLN F 633 GLN ** F1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1049 ASN F1371 HIS F1574 ASN ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1785 GLN F2092 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 47552 Z= 0.201 Angle : 0.680 15.168 64388 Z= 0.338 Chirality : 0.044 0.299 7378 Planarity : 0.004 0.089 8098 Dihedral : 6.993 179.837 6296 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.60 % Allowed : 22.15 % Favored : 74.26 % 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: -1.05 (0.11), residues: 5736 helix: 0.11 (0.09), residues: 3598 sheet: -0.40 (0.62), residues: 62 loop : -2.09 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F2364 HIS 0.007 0.001 HIS F1371 PHE 0.046 0.002 PHE C 206 TYR 0.021 0.001 TYR F2174 ARG 0.019 0.000 ARG D 627 *********************** 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 1032 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 848 time to evaluate : 5.395 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: D 376 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8961 (tt) REVERT: D 482 MET cc_start: 0.8805 (tpp) cc_final: 0.8549 (tpt) REVERT: D 593 TYR cc_start: 0.8963 (m-80) cc_final: 0.8683 (m-80) REVERT: C 308 GLN cc_start: 0.8924 (pp30) cc_final: 0.8601 (pp30) REVERT: C 541 MET cc_start: 0.8175 (mmm) cc_final: 0.7642 (tpt) REVERT: C 736 GLU cc_start: 0.8034 (pm20) cc_final: 0.7833 (tm-30) REVERT: E 471 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7336 (tp30) REVERT: E 574 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: E 711 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7817 (mm-30) REVERT: E 888 SER cc_start: 0.9036 (m) cc_final: 0.8824 (p) REVERT: E 1034 ASN cc_start: 0.7719 (OUTLIER) cc_final: 0.7507 (p0) REVERT: E 1043 ILE cc_start: 0.9130 (mm) cc_final: 0.8901 (mt) REVERT: E 1119 CYS cc_start: 0.8569 (m) cc_final: 0.8280 (m) REVERT: E 1148 ASP cc_start: 0.7864 (p0) cc_final: 0.7290 (t0) REVERT: E 1245 TYR cc_start: 0.7223 (m-80) cc_final: 0.6601 (m-10) REVERT: E 1334 MET cc_start: 0.5734 (ptp) cc_final: 0.5443 (ptp) REVERT: E 1384 MET cc_start: 0.7968 (mmm) cc_final: 0.7453 (mpp) REVERT: E 1436 LYS cc_start: 0.7208 (pmtt) cc_final: 0.6776 (ttmm) REVERT: E 1494 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8128 (ptpp) REVERT: E 1501 LYS cc_start: 0.9136 (mmmt) cc_final: 0.8823 (tttt) REVERT: E 1643 LYS cc_start: 0.8872 (mttt) cc_final: 0.8640 (mtmt) REVERT: E 1685 ASP cc_start: 0.8131 (t0) cc_final: 0.7547 (t0) REVERT: E 1724 GLU cc_start: 0.7913 (tp30) cc_final: 0.7299 (tp30) REVERT: E 1727 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7729 (mp0) REVERT: E 1754 SER cc_start: 0.7013 (m) cc_final: 0.6504 (p) REVERT: E 1772 ASP cc_start: 0.7798 (t0) cc_final: 0.7517 (t0) REVERT: E 1834 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8811 (mt) REVERT: E 1838 GLU cc_start: 0.7716 (pt0) cc_final: 0.7483 (tp30) REVERT: E 1850 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8187 (tptp) REVERT: E 1867 PRO cc_start: 0.4826 (Cg_endo) cc_final: 0.4535 (Cg_exo) REVERT: E 1958 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6925 (tt0) REVERT: E 2071 ASP cc_start: 0.8367 (t70) cc_final: 0.8027 (t70) REVERT: E 2131 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7187 (mpp) REVERT: E 2224 ASP cc_start: 0.8057 (t0) cc_final: 0.7840 (t0) REVERT: F 109 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8595 (mp) REVERT: F 113 ASN cc_start: 0.8701 (m110) cc_final: 0.8179 (m110) REVERT: F 117 TYR cc_start: 0.8677 (m-80) cc_final: 0.8456 (m-10) REVERT: F 163 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: F 212 ASP cc_start: 0.7415 (m-30) cc_final: 0.7115 (m-30) REVERT: F 229 CYS cc_start: 0.7352 (p) cc_final: 0.7069 (p) REVERT: F 455 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8575 (mm) REVERT: F 563 ASN cc_start: 0.6976 (m-40) cc_final: 0.6716 (t0) REVERT: F 694 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7299 (pm20) REVERT: F 767 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8515 (p0) REVERT: F 1023 LEU cc_start: 0.7803 (mp) cc_final: 0.7469 (tt) REVERT: F 1066 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: F 1119 CYS cc_start: 0.8575 (m) cc_final: 0.8274 (m) REVERT: F 1122 MET cc_start: 0.8518 (mtt) cc_final: 0.8231 (mtp) REVERT: F 1148 ASP cc_start: 0.7708 (p0) cc_final: 0.7227 (t0) REVERT: F 1334 MET cc_start: 0.5461 (ptp) cc_final: 0.5189 (ptm) REVERT: F 1384 MET cc_start: 0.7891 (mmm) cc_final: 0.7342 (mpp) REVERT: F 1419 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7880 (tp-100) REVERT: F 1436 LYS cc_start: 0.7311 (pmtt) cc_final: 0.6970 (ttmm) REVERT: F 1501 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8792 (tttt) REVERT: F 1643 LYS cc_start: 0.8886 (mttt) cc_final: 0.8616 (mtmt) REVERT: F 1685 ASP cc_start: 0.8155 (t0) cc_final: 0.7553 (t0) REVERT: F 1727 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7806 (mp0) REVERT: F 1754 SER cc_start: 0.6823 (m) cc_final: 0.6404 (p) REVERT: F 1801 TYR cc_start: 0.8687 (m-80) cc_final: 0.8447 (m-10) REVERT: F 1834 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8804 (mt) REVERT: F 1838 GLU cc_start: 0.7848 (pt0) cc_final: 0.7511 (tp30) REVERT: F 1867 PRO cc_start: 0.5004 (Cg_endo) cc_final: 0.4685 (Cg_exo) REVERT: F 1913 GLN cc_start: 0.7310 (tm-30) cc_final: 0.7053 (mt0) REVERT: F 2071 ASP cc_start: 0.8408 (t70) cc_final: 0.8099 (t70) REVERT: F 2131 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7593 (mpp) REVERT: F 2191 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7968 (mt-10) REVERT: F 2303 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8786 (mt) outliers start: 184 outliers final: 137 residues processed: 957 average time/residue: 0.5554 time to fit residues: 912.4948 Evaluate side-chains 957 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 803 time to evaluate : 5.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 342 HIS Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 342 HIS Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 660 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 709 LEU Chi-restraints excluded: chain E residue 711 GLU Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 797 THR Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 957 LEU Chi-restraints excluded: chain E residue 991 ILE Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1034 ASN Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1205 LEU Chi-restraints excluded: chain E residue 1208 ASN Chi-restraints excluded: chain E residue 1263 LEU Chi-restraints excluded: chain E residue 1304 ILE Chi-restraints excluded: chain E residue 1349 ILE Chi-restraints excluded: chain E residue 1368 SER Chi-restraints excluded: chain E residue 1400 LEU Chi-restraints excluded: chain E residue 1494 LYS Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1597 SER Chi-restraints excluded: chain E residue 1622 MET Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1672 SER Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1709 SER Chi-restraints excluded: chain E residue 1734 GLU Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1834 LEU Chi-restraints excluded: chain E residue 1934 ILE Chi-restraints excluded: chain E residue 1969 ASP Chi-restraints excluded: chain E residue 2016 VAL Chi-restraints excluded: chain E residue 2017 VAL Chi-restraints excluded: chain E residue 2063 LYS Chi-restraints excluded: chain E residue 2078 MET Chi-restraints excluded: chain E residue 2092 GLN Chi-restraints excluded: chain E residue 2114 ILE Chi-restraints excluded: chain E residue 2131 MET Chi-restraints excluded: chain E residue 2215 MET Chi-restraints excluded: chain E residue 2260 VAL Chi-restraints excluded: chain E residue 2264 LEU Chi-restraints excluded: chain E residue 2275 ILE Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2312 MET Chi-restraints excluded: chain E residue 2365 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 574 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 637 THR Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 694 GLN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 957 LEU Chi-restraints excluded: chain F residue 969 LEU Chi-restraints excluded: chain F residue 990 SER Chi-restraints excluded: chain F residue 991 ILE Chi-restraints excluded: chain F residue 1010 THR Chi-restraints excluded: chain F residue 1066 GLU Chi-restraints excluded: chain F residue 1112 LEU Chi-restraints excluded: chain F residue 1150 VAL Chi-restraints excluded: chain F residue 1205 LEU Chi-restraints excluded: chain F residue 1208 ASN Chi-restraints excluded: chain F residue 1272 GLU Chi-restraints excluded: chain F residue 1282 LEU Chi-restraints excluded: chain F residue 1304 ILE Chi-restraints excluded: chain F residue 1349 ILE Chi-restraints excluded: chain F residue 1371 HIS Chi-restraints excluded: chain F residue 1400 LEU Chi-restraints excluded: chain F residue 1630 LEU Chi-restraints excluded: chain F residue 1668 SER Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1704 ASP Chi-restraints excluded: chain F residue 1709 SER Chi-restraints excluded: chain F residue 1752 ASN Chi-restraints excluded: chain F residue 1805 LEU Chi-restraints excluded: chain F residue 1833 PHE Chi-restraints excluded: chain F residue 1834 LEU Chi-restraints excluded: chain F residue 1934 ILE Chi-restraints excluded: chain F residue 1950 VAL Chi-restraints excluded: chain F residue 2016 VAL Chi-restraints excluded: chain F residue 2017 VAL Chi-restraints excluded: chain F residue 2046 ILE Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2215 MET Chi-restraints excluded: chain F residue 2275 ILE Chi-restraints excluded: chain F residue 2297 VAL Chi-restraints excluded: chain F residue 2303 ILE Chi-restraints excluded: chain F residue 2327 ILE Chi-restraints excluded: chain F residue 2355 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 513 optimal weight: 0.5980 chunk 338 optimal weight: 0.8980 chunk 545 optimal weight: 4.9990 chunk 332 optimal weight: 0.9990 chunk 258 optimal weight: 8.9990 chunk 378 optimal weight: 7.9990 chunk 571 optimal weight: 20.0000 chunk 526 optimal weight: 1.9990 chunk 455 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 351 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS ** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 HIS E 908 ASN E1034 ASN E1371 HIS E1776 ASN E1921 HIS ** E1963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2086 GLN E2092 GLN ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 633 GLN ** F1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1921 HIS ** F1963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2086 GLN F2092 GLN ** F2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 47552 Z= 0.201 Angle : 0.694 15.225 64388 Z= 0.343 Chirality : 0.044 0.324 7378 Planarity : 0.004 0.084 8098 Dihedral : 6.939 179.832 6296 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.23 % Allowed : 22.96 % Favored : 73.81 % 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: -0.97 (0.11), residues: 5736 helix: 0.16 (0.09), residues: 3580 sheet: -0.43 (0.62), residues: 62 loop : -2.02 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F2364 HIS 0.010 0.001 HIS F1371 PHE 0.045 0.002 PHE C 206 TYR 0.023 0.001 TYR E1827 ARG 0.020 0.001 ARG D 627 ********************** 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 1002 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 837 time to evaluate : 5.414 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: D 376 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8943 (tt) REVERT: D 482 MET cc_start: 0.8794 (tpp) cc_final: 0.8541 (tpt) REVERT: D 489 PHE cc_start: 0.7743 (m-80) cc_final: 0.7242 (m-80) REVERT: D 593 TYR cc_start: 0.8969 (m-80) cc_final: 0.8761 (m-80) REVERT: C 308 GLN cc_start: 0.8922 (pp30) cc_final: 0.8595 (pp30) REVERT: C 541 MET cc_start: 0.8172 (mmm) cc_final: 0.7604 (tpt) REVERT: E 323 GLN cc_start: 0.8411 (pm20) cc_final: 0.8136 (pm20) REVERT: E 471 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: E 574 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8211 (mp10) REVERT: E 711 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: E 888 SER cc_start: 0.9035 (m) cc_final: 0.8817 (p) REVERT: E 1043 ILE cc_start: 0.9126 (mm) cc_final: 0.8889 (mt) REVERT: E 1119 CYS cc_start: 0.8560 (m) cc_final: 0.8270 (m) REVERT: E 1148 ASP cc_start: 0.7880 (p0) cc_final: 0.7292 (t0) REVERT: E 1334 MET cc_start: 0.5746 (ptp) cc_final: 0.5472 (ptm) REVERT: E 1384 MET cc_start: 0.7962 (mmm) cc_final: 0.7458 (mpp) REVERT: E 1436 LYS cc_start: 0.7227 (pmtt) cc_final: 0.6795 (ttmm) REVERT: E 1494 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8109 (ptpp) REVERT: E 1501 LYS cc_start: 0.9118 (mmmt) cc_final: 0.8790 (tttt) REVERT: E 1643 LYS cc_start: 0.8810 (mttt) cc_final: 0.8589 (mtmt) REVERT: E 1685 ASP cc_start: 0.8120 (t0) cc_final: 0.7544 (t0) REVERT: E 1724 GLU cc_start: 0.7902 (tp30) cc_final: 0.7290 (tp30) REVERT: E 1727 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7730 (mp0) REVERT: E 1754 SER cc_start: 0.6955 (m) cc_final: 0.6479 (p) REVERT: E 1838 GLU cc_start: 0.7733 (pt0) cc_final: 0.7495 (tp30) REVERT: E 1850 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8194 (tptp) REVERT: E 1867 PRO cc_start: 0.4864 (Cg_endo) cc_final: 0.4576 (Cg_exo) REVERT: E 2071 ASP cc_start: 0.8343 (t70) cc_final: 0.8013 (t70) REVERT: E 2131 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7245 (mpp) REVERT: F 90 MET cc_start: 0.6856 (ppp) cc_final: 0.6413 (ppp) REVERT: F 113 ASN cc_start: 0.8693 (m110) cc_final: 0.8193 (m110) REVERT: F 117 TYR cc_start: 0.8684 (m-80) cc_final: 0.8461 (m-10) REVERT: F 212 ASP cc_start: 0.7401 (m-30) cc_final: 0.7109 (m-30) REVERT: F 229 CYS cc_start: 0.7291 (p) cc_final: 0.7001 (p) REVERT: F 455 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8596 (mm) REVERT: F 694 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: F 767 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8491 (p0) REVERT: F 1023 LEU cc_start: 0.7807 (mp) cc_final: 0.7474 (tt) REVERT: F 1043 ILE cc_start: 0.9131 (mm) cc_final: 0.8898 (mt) REVERT: F 1119 CYS cc_start: 0.8573 (m) cc_final: 0.8278 (m) REVERT: F 1148 ASP cc_start: 0.7724 (p0) cc_final: 0.7216 (t0) REVERT: F 1200 MET cc_start: 0.6669 (pmm) cc_final: 0.6362 (pmm) REVERT: F 1334 MET cc_start: 0.5455 (ptp) cc_final: 0.5186 (ptm) REVERT: F 1384 MET cc_start: 0.7887 (mmm) cc_final: 0.7362 (mpp) REVERT: F 1419 GLN cc_start: 0.8129 (tp-100) cc_final: 0.7838 (tp-100) REVERT: F 1436 LYS cc_start: 0.7323 (pmtt) cc_final: 0.6972 (ttmm) REVERT: F 1501 LYS cc_start: 0.9144 (mmmt) cc_final: 0.8782 (tttt) REVERT: F 1615 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7636 (mm) REVERT: F 1643 LYS cc_start: 0.8868 (mttt) cc_final: 0.8613 (mtmt) REVERT: F 1685 ASP cc_start: 0.8144 (t0) cc_final: 0.7546 (t0) REVERT: F 1727 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7816 (mp0) REVERT: F 1754 SER cc_start: 0.6809 (m) cc_final: 0.6378 (p) REVERT: F 1838 GLU cc_start: 0.7824 (pt0) cc_final: 0.7514 (tp30) REVERT: F 1867 PRO cc_start: 0.5034 (Cg_endo) cc_final: 0.4723 (Cg_exo) REVERT: F 1937 TYR cc_start: 0.7939 (m-80) cc_final: 0.7657 (m-80) REVERT: F 2071 ASP cc_start: 0.8398 (t70) cc_final: 0.8090 (t70) REVERT: F 2131 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.7566 (mpp) REVERT: F 2191 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7949 (mt-10) REVERT: F 2303 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8741 (mt) REVERT: F 2308 TYR cc_start: 0.7210 (m-80) cc_final: 0.6879 (m-80) outliers start: 165 outliers final: 132 residues processed: 938 average time/residue: 0.5235 time to fit residues: 845.5497 Evaluate side-chains 941 residues out of total 5314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 797 time to evaluate : 5.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 342 HIS Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 498 ASN Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 342 HIS Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 660 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 709 LEU Chi-restraints excluded: chain E residue 711 GLU Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 797 THR Chi-restraints excluded: chain E residue 803 ILE Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 957 LEU Chi-restraints excluded: chain E residue 991 ILE Chi-restraints excluded: chain E residue 1010 THR Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1205 LEU Chi-restraints excluded: chain E residue 1208 ASN Chi-restraints excluded: chain E residue 1263 LEU Chi-restraints excluded: chain E residue 1304 ILE Chi-restraints excluded: chain E residue 1349 ILE Chi-restraints excluded: chain E residue 1371 HIS Chi-restraints excluded: chain E residue 1400 LEU Chi-restraints excluded: chain E residue 1494 LYS Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1622 MET Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1672 SER Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1709 SER Chi-restraints excluded: chain E residue 1734 GLU Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1924 LEU Chi-restraints excluded: chain E residue 1934 ILE Chi-restraints excluded: chain E residue 1969 ASP Chi-restraints excluded: chain E residue 2016 VAL Chi-restraints excluded: chain E residue 2063 LYS Chi-restraints excluded: chain E residue 2078 MET Chi-restraints excluded: chain E residue 2086 GLN Chi-restraints excluded: chain E residue 2092 GLN Chi-restraints excluded: chain E residue 2114 ILE Chi-restraints excluded: chain E residue 2131 MET Chi-restraints excluded: chain E residue 2215 MET Chi-restraints excluded: chain E residue 2264 LEU Chi-restraints excluded: chain E residue 2275 ILE Chi-restraints excluded: chain E residue 2297 VAL Chi-restraints excluded: chain E residue 2312 MET Chi-restraints excluded: chain E residue 2365 LEU Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 574 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 604 GLU Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 694 GLN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 797 THR Chi-restraints excluded: chain F residue 803 ILE Chi-restraints excluded: chain F residue 957 LEU Chi-restraints excluded: chain F residue 969 LEU Chi-restraints excluded: chain F residue 990 SER Chi-restraints excluded: chain F residue 991 ILE Chi-restraints excluded: chain F residue 1010 THR Chi-restraints excluded: chain F residue 1112 LEU Chi-restraints excluded: chain F residue 1150 VAL Chi-restraints excluded: chain F residue 1205 LEU Chi-restraints excluded: chain F residue 1208 ASN Chi-restraints excluded: chain F residue 1272 GLU Chi-restraints excluded: chain F residue 1282 LEU Chi-restraints excluded: chain F residue 1304 ILE Chi-restraints excluded: chain F residue 1349 ILE Chi-restraints excluded: chain F residue 1400 LEU Chi-restraints excluded: chain F residue 1615 LEU Chi-restraints excluded: chain F residue 1630 LEU Chi-restraints excluded: chain F residue 1668 SER Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1704 ASP Chi-restraints excluded: chain F residue 1709 SER Chi-restraints excluded: chain F residue 1752 ASN Chi-restraints excluded: chain F residue 1934 ILE Chi-restraints excluded: chain F residue 1950 VAL Chi-restraints excluded: chain F residue 2016 VAL Chi-restraints excluded: chain F residue 2017 VAL Chi-restraints excluded: chain F residue 2086 GLN Chi-restraints excluded: chain F residue 2092 GLN Chi-restraints excluded: chain F residue 2131 MET Chi-restraints excluded: chain F residue 2215 MET Chi-restraints excluded: chain F residue 2275 ILE Chi-restraints excluded: chain F residue 2297 VAL Chi-restraints excluded: chain F residue 2303 ILE Chi-restraints excluded: chain F residue 2327 ILE Chi-restraints excluded: chain F residue 2355 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.7025 > 50: distance: 38 - 42: 6.479 distance: 42 - 43: 4.370 distance: 43 - 44: 5.684 distance: 44 - 45: 3.885 distance: 46 - 47: 4.679 distance: 49 - 50: 4.754 distance: 49 - 52: 3.759 distance: 50 - 56: 3.117 distance: 52 - 53: 3.713 distance: 53 - 54: 4.035 distance: 53 - 55: 5.488 distance: 57 - 58: 5.158 distance: 57 - 60: 3.814 distance: 58 - 59: 4.362 distance: 62 - 63: 4.055 distance: 62 - 64: 6.572 distance: 65 - 66: 3.884 distance: 66 - 67: 5.410 distance: 66 - 69: 7.995 distance: 67 - 68: 24.636 distance: 67 - 76: 27.311 distance: 69 - 70: 4.892 distance: 70 - 71: 10.279 distance: 71 - 72: 6.017 distance: 72 - 73: 5.554 distance: 73 - 74: 5.143 distance: 73 - 75: 5.099 distance: 76 - 77: 17.544 distance: 77 - 78: 28.468 distance: 77 - 80: 20.914 distance: 78 - 79: 17.882 distance: 78 - 81: 21.537 distance: 81 - 82: 10.557 distance: 82 - 83: 17.355 distance: 82 - 85: 20.874 distance: 83 - 84: 16.699 distance: 83 - 89: 13.040 distance: 85 - 86: 12.368 distance: 86 - 87: 6.516 distance: 86 - 88: 10.772 distance: 89 - 90: 6.514 distance: 89 - 95: 13.343 distance: 90 - 91: 7.913 distance: 90 - 93: 6.893 distance: 91 - 92: 6.759 distance: 91 - 96: 7.397 distance: 93 - 94: 4.975 distance: 94 - 95: 11.555 distance: 96 - 97: 6.614 distance: 97 - 98: 10.821 distance: 97 - 100: 6.229 distance: 98 - 99: 10.756 distance: 98 - 105: 8.476 distance: 100 - 101: 7.852 distance: 101 - 102: 5.335 distance: 102 - 103: 5.214 distance: 102 - 104: 6.508 distance: 105 - 106: 15.507 distance: 106 - 107: 6.795 distance: 106 - 109: 16.583 distance: 107 - 108: 11.474 distance: 107 - 110: 5.186 distance: 108 - 129: 18.999 distance: 110 - 111: 5.899 distance: 111 - 112: 3.182 distance: 111 - 114: 3.778 distance: 112 - 113: 3.986 distance: 112 - 119: 10.107 distance: 114 - 115: 7.660 distance: 115 - 116: 7.417 distance: 116 - 117: 3.511 distance: 116 - 118: 8.360