Starting phenix.real_space_refine on Fri Jul 26 01:46:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiz_36335/07_2024/8jiz_36335.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiz_36335/07_2024/8jiz_36335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiz_36335/07_2024/8jiz_36335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiz_36335/07_2024/8jiz_36335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiz_36335/07_2024/8jiz_36335.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiz_36335/07_2024/8jiz_36335.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 170 5.16 5 C 19800 2.51 5 N 5177 2.21 5 O 5855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 31002 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5950 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 30, 'TRANS': 730} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6120 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 32, 'TRANS': 749} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 5940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 5940 Classifications: {'peptide': 756} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 28, 'TRANS': 727} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 6094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6094 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "E" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1708 Classifications: {'peptide': 228} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 214} Chain: "F" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1644 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "G" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1650 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205} Chain breaks: 1 Chain: "H" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1644 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 17.58, per 1000 atoms: 0.57 Number of scatterers: 31002 At special positions: 0 Unit cell: (180.36, 226.8, 201.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 170 16.00 O 5855 8.00 N 5177 7.00 C 19800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 79 " - pdb=" SG CYS D 308 " distance=2.04 Simple disulfide: pdb=" SG CYS D 420 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 151 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 900 " - " ASN A 687 " " NAG B 901 " - " ASN B 471 " " NAG B 902 " - " ASN B 203 " " NAG C 900 " - " ASN C 687 " " NAG D 901 " - " ASN D 368 " " NAG D 902 " - " ASN D 471 " " NAG D 903 " - " ASN D 771 " " NAG D 904 " - " ASN D 203 " " NAG I 1 " - " ASN B 61 " " NAG J 1 " - " ASN B 276 " " NAG K 1 " - " ASN B 771 " " NAG L 1 " - " ASN D 61 " " NAG M 1 " - " ASN D 276 " Time building additional restraints: 11.31 Conformation dependent library (CDL) restraints added in 5.9 seconds 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7372 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 49 sheets defined 36.0% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.733A pdb=" N GLN A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 180 through 193 Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 287 through 310 removed outlier: 3.984A pdb=" N PHE A 310 " --> pdb=" O MET A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 515 through 522 removed outlier: 3.587A pdb=" N VAL A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 579 removed outlier: 3.686A pdb=" N LEU A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.836A pdb=" N MET A 630 " --> pdb=" O THR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 653 removed outlier: 3.778A pdb=" N PHE A 637 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.571A pdb=" N ASN A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 708 removed outlier: 3.559A pdb=" N PHE A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 814 through 837 removed outlier: 4.415A pdb=" N ALA A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 52 Processing helix chain 'B' and resid 70 through 83 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 126 through 130 Processing helix chain 'B' and resid 144 through 159 Processing helix chain 'B' and resid 170 through 187 removed outlier: 3.656A pdb=" N GLU B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 224 through 237 removed outlier: 4.246A pdb=" N MET B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.525A pdb=" N GLU B 253 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 276 through 299 removed outlier: 3.514A pdb=" N GLU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 328 Processing helix chain 'B' and resid 457 through 471 removed outlier: 3.876A pdb=" N ASP B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.727A pdb=" N TYR B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 584 Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'B' and resid 628 through 654 removed outlier: 3.668A pdb=" N MET B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 removed outlier: 3.667A pdb=" N ARG B 673 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN B 674 " --> pdb=" O PRO B 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 669 through 674' Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 705 through 708 removed outlier: 3.687A pdb=" N LYS B 708 " --> pdb=" O HIS B 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 705 through 708' Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.725A pdb=" N PHE B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 782 Processing helix chain 'B' and resid 783 through 793 Processing helix chain 'B' and resid 810 through 843 removed outlier: 3.765A pdb=" N ALA B 814 " --> pdb=" O PHE B 810 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 829 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 834 " --> pdb=" O LEU B 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 57 through 60 removed outlier: 3.643A pdb=" N ALA C 60 " --> pdb=" O PRO C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.682A pdb=" N GLN C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 150 through 165 Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.716A pdb=" N PHE C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 222 Processing helix chain 'C' and resid 232 through 246 removed outlier: 3.626A pdb=" N LEU C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 310 Processing helix chain 'C' and resid 379 through 383 removed outlier: 3.789A pdb=" N THR C 382 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 472 Processing helix chain 'C' and resid 494 through 502 removed outlier: 3.545A pdb=" N TYR C 502 " --> pdb=" O GLY C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 522 Processing helix chain 'C' and resid 559 through 579 Processing helix chain 'C' and resid 603 through 611 Processing helix chain 'C' and resid 627 through 632 Processing helix chain 'C' and resid 633 through 652 removed outlier: 3.966A pdb=" N PHE C 637 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.799A pdb=" N GLN C 671 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 676 Processing helix chain 'C' and resid 688 through 698 removed outlier: 3.546A pdb=" N ARG C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN C 697 " --> pdb=" O ASN C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 708 removed outlier: 4.191A pdb=" N GLN C 703 " --> pdb=" O PRO C 699 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR C 704 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 723 removed outlier: 3.739A pdb=" N ALA C 716 " --> pdb=" O GLY C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 741 Processing helix chain 'C' and resid 742 through 745 Processing helix chain 'C' and resid 771 through 785 removed outlier: 4.153A pdb=" N LEU C 777 " --> pdb=" O ARG C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 793 Processing helix chain 'C' and resid 813 through 836 removed outlier: 4.102A pdb=" N MET C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 821 " --> pdb=" O MET C 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 52 removed outlier: 3.984A pdb=" N HIS D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 104 through 114 removed outlier: 4.261A pdb=" N TYR D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 130 Processing helix chain 'D' and resid 144 through 158 Processing helix chain 'D' and resid 170 through 187 removed outlier: 4.074A pdb=" N ARG D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 224 through 237 removed outlier: 3.900A pdb=" N MET D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.950A pdb=" N SER D 255 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 Processing helix chain 'D' and resid 276 through 299 removed outlier: 3.670A pdb=" N HIS D 280 " --> pdb=" O ASN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 457 through 471 Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 561 through 584 Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 627 through 657 removed outlier: 3.901A pdb=" N ILE D 631 " --> pdb=" O PHE D 627 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET D 641 " --> pdb=" O ALA D 637 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE D 643 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 674 removed outlier: 3.777A pdb=" N ASN D 674 " --> pdb=" O PRO D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 699 through 706 Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 removed outlier: 4.080A pdb=" N PHE D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 782 Processing helix chain 'D' and resid 783 through 793 Processing helix chain 'D' and resid 810 through 843 removed outlier: 3.599A pdb=" N PHE D 829 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE D 833 " --> pdb=" O PHE D 829 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.771A pdb=" N ASP E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR E 32 " --> pdb=" O LEU E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 61 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.906A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 removed outlier: 3.646A pdb=" N LEU F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS F 126 " --> pdb=" O ASP F 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 121 through 126' Processing helix chain 'F' and resid 183 through 188 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.633A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 167 through 169 No H-bonds generated for 'chain 'G' and resid 167 through 169' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.637A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.890A pdb=" N VAL A 38 " --> pdb=" O LEU A 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.531A pdb=" N LEU A 125 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 100 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE A 124 " --> pdb=" O PHE A 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 207 removed outlier: 6.315A pdb=" N SER A 171 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N TYR A 230 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL A 173 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 279 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU A 276 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 408 through 410 removed outlier: 6.461A pdb=" N ILE A 408 " --> pdb=" O TYR A 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA7, first strand: chain 'A' and resid 507 through 508 removed outlier: 3.679A pdb=" N ASP A 523 " --> pdb=" O LEU A 765 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AA9, first strand: chain 'A' and resid 729 through 731 Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 62 removed outlier: 7.051A pdb=" N VAL B 27 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN B 28 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA B 89 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LEU B 119 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 90 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL B 118 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 164 through 167 removed outlier: 6.355A pdb=" N ILE B 164 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N SER B 222 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 166 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 267 through 271 removed outlier: 6.354A pdb=" N ASN B 355 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLN B 363 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN B 357 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LEU B 361 " --> pdb=" O GLN B 357 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB5, first strand: chain 'B' and resid 681 through 682 removed outlier: 6.931A pdb=" N ALA B 682 " --> pdb=" O ILE B 730 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 73 removed outlier: 3.782A pdb=" N LEU C 72 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA C 37 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU C 98 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE C 124 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.566A pdb=" N PHE C 170 " --> pdb=" O ASP C 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 204 through 206 removed outlier: 3.711A pdb=" N VAL C 279 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 365 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C 373 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 376 through 377 Processing sheet with id=AC1, first strand: chain 'C' and resid 452 through 456 removed outlier: 8.486A pdb=" N LEU C 479 " --> pdb=" O PRO C 435 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ARG C 437 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET C 507 " --> pdb=" O SER C 407 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 530 through 531 Processing sheet with id=AC3, first strand: chain 'C' and resid 728 through 731 removed outlier: 3.530A pdb=" N VAL C 748 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 28 through 32 removed outlier: 6.787A pdb=" N ASN D 28 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA D 89 " --> pdb=" O ASN D 28 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 194 through 197 removed outlier: 3.552A pdb=" N SER D 168 " --> pdb=" O SER D 222 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 269 through 271 removed outlier: 3.541A pdb=" N GLY D 365 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASN D 355 " --> pdb=" O GLN D 363 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLN D 363 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN D 357 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU D 361 " --> pdb=" O GLN D 357 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE D 366 " --> pdb=" O ILE D 373 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE D 373 " --> pdb=" O ILE D 366 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 330 through 333 removed outlier: 4.697A pdb=" N ASP D 332 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY D 336 " --> pdb=" O ASP D 332 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 477 through 478 Processing sheet with id=AC9, first strand: chain 'D' and resid 412 through 413 removed outlier: 3.527A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AD2, first strand: chain 'D' and resid 681 through 682 removed outlier: 6.708A pdb=" N ALA D 682 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N ASP D 732 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU D 538 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLU D 751 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 747 " --> pdb=" O VAL D 542 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'E' and resid 45 through 51 removed outlier: 5.055A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 92 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL E 120 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 131 through 135 removed outlier: 3.780A pdb=" N GLY E 150 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER E 191 " --> pdb=" O CYS E 151 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR E 187 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 131 through 135 removed outlier: 3.780A pdb=" N GLY E 150 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER E 191 " --> pdb=" O CYS E 151 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR E 187 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 162 through 165 removed outlier: 4.255A pdb=" N TYR E 205 " --> pdb=" O VAL E 222 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.754A pdb=" N SER F 7 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.575A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.595A pdb=" N GLN F 90 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 114 through 118 removed outlier: 3.736A pdb=" N VAL F 133 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 153 through 155 removed outlier: 4.135A pdb=" N TRP F 148 " --> pdb=" O GLN F 155 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR F 192 " --> pdb=" O PHE F 209 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE F 209 " --> pdb=" O TYR F 192 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'G' and resid 11 through 12 removed outlier: 7.279A pdb=" N MET G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 131 through 135 removed outlier: 4.300A pdb=" N GLY G 150 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR G 187 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 131 through 135 removed outlier: 4.300A pdb=" N GLY G 150 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR G 187 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 161 through 165 removed outlier: 3.953A pdb=" N TYR G 205 " --> pdb=" O VAL G 222 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS G 220 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.974A pdb=" N THR H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.690A pdb=" N LEU H 11 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU H 33 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N SER H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.690A pdb=" N LEU H 11 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN H 90 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.929A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 154 through 155 removed outlier: 4.382A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR H 192 " --> pdb=" O PHE H 209 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE H 209 " --> pdb=" O TYR H 192 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS H 194 " --> pdb=" O LYS H 207 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS H 207 " --> pdb=" O CYS H 194 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL H 196 " --> pdb=" O VAL H 205 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL H 205 " --> pdb=" O VAL H 196 " (cutoff:3.500A) 1277 hydrogen bonds defined for protein. 3588 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: 15.02 Time building geometry restraints manager: 12.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9902 1.34 - 1.46: 7610 1.46 - 1.58: 13909 1.58 - 1.70: 0 1.70 - 1.82: 285 Bond restraints: 31706 Sorted by residual: bond pdb=" C1 NAG D 904 " pdb=" O5 NAG D 904 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C1 NAG D 903 " pdb=" O5 NAG D 903 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 ... (remaining 31701 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.04: 986 107.04 - 113.80: 17796 113.80 - 120.55: 11863 120.55 - 127.31: 12007 127.31 - 134.07: 387 Bond angle restraints: 43039 Sorted by residual: angle pdb=" C ASP E 106 " pdb=" CA ASP E 106 " pdb=" CB ASP E 106 " ideal model delta sigma weight residual 117.23 109.58 7.65 1.36e+00 5.41e-01 3.16e+01 angle pdb=" C THR D 35 " pdb=" CA THR D 35 " pdb=" CB THR D 35 " ideal model delta sigma weight residual 115.89 109.47 6.42 1.32e+00 5.74e-01 2.36e+01 angle pdb=" CA ASP E 106 " pdb=" C ASP E 106 " pdb=" N GLY E 107 " ideal model delta sigma weight residual 119.98 116.51 3.47 8.50e-01 1.38e+00 1.67e+01 angle pdb=" C SER A 225 " pdb=" N VAL A 226 " pdb=" CA VAL A 226 " ideal model delta sigma weight residual 120.49 125.04 -4.55 1.38e+00 5.25e-01 1.09e+01 angle pdb=" N ASP E 106 " pdb=" CA ASP E 106 " pdb=" C ASP E 106 " ideal model delta sigma weight residual 108.67 113.92 -5.25 1.67e+00 3.59e-01 9.88e+00 ... (remaining 43034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 18520 24.83 - 49.65: 515 49.65 - 74.48: 38 74.48 - 99.31: 11 99.31 - 124.14: 1 Dihedral angle restraints: 19085 sinusoidal: 7652 harmonic: 11433 Sorted by residual: dihedral pdb=" C2 NAG D 904 " pdb=" C1 NAG D 904 " pdb=" O5 NAG D 904 " pdb=" C5 NAG D 904 " ideal model delta sinusoidal sigma weight residual -62.96 61.18 -124.14 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" CA THR D 35 " pdb=" C THR D 35 " pdb=" N ARG D 36 " pdb=" CA ARG D 36 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" C1 NAG D 904 " pdb=" C5 NAG D 904 " pdb=" O5 NAG D 904 " pdb=" C6 NAG D 904 " ideal model delta sinusoidal sigma weight residual 171.16 -92.60 -96.24 1 3.00e+01 1.11e-03 1.18e+01 ... (remaining 19082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3441 0.035 - 0.070: 1005 0.070 - 0.105: 362 0.105 - 0.141: 107 0.141 - 0.176: 5 Chirality restraints: 4920 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 771 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" C1 NAG D 904 " pdb=" ND2 ASN D 203 " pdb=" C2 NAG D 904 " pdb=" O5 NAG D 904 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN D 61 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 4917 not shown) Planarity restraints: 5446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 159 " 0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO G 160 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 160 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 160 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 515 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO B 516 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 516 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 516 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 56 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 57 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " 0.019 5.00e-02 4.00e+02 ... (remaining 5443 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2273 2.74 - 3.28: 32263 3.28 - 3.82: 52424 3.82 - 4.36: 58976 4.36 - 4.90: 102123 Nonbonded interactions: 248059 Sorted by model distance: nonbonded pdb=" OG1 THR D 486 " pdb=" O GLN D 686 " model vdw 2.200 2.440 nonbonded pdb=" O VAL A 339 " pdb=" OG SER A 349 " model vdw 2.222 2.440 nonbonded pdb=" OG1 THR C 531 " pdb=" OD1 ASP C 731 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR D 205 " pdb=" O7 NAG D 904 " model vdw 2.253 2.440 nonbonded pdb=" NH1 ARG F 108 " pdb=" O ASP F 170 " model vdw 2.264 2.520 ... (remaining 248054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 211 or (resid 212 through 213 and \ (name N or name CA or name C or name O or name CB )) or resid 214 through 395 or \ (resid 396 and (name N or name CA or name C or name O or name CB )) or resid 39 \ 7 through 545 or resid 547 through 580 or resid 599 through 625 or resid 627 thr \ ough 796 or resid 813 through 837 or resid 900)) selection = (chain 'C' and (resid 34 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 58 or (resid 59 throu \ gh 61 and (name N or name CA or name C or name O or name CB )) or resid 62 throu \ gh 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or r \ esid 96 through 193 or (resid 194 and (name N or name CA or name C or name O or \ name CB )) or resid 195 through 292 or (resid 293 and (name N or name CA or name \ C or name O or name CB )) or resid 294 through 535 or (resid 536 and (name N or \ name CA or name C or name O or name CB )) or resid 537 through 654 or resid 660 \ through 665 or (resid 666 and (name N or name CA or name C or name O or name CB \ )) or resid 667 through 796 or resid 813 through 837 or resid 900)) } ncs_group { reference = (chain 'B' and (resid 25 through 294 or (resid 295 and (name N or name CA or nam \ e C or name O or name CB )) or resid 296 through 488 or (resid 489 and (name N o \ r name CA or name C or name O or name CB )) or resid 490 through 553 or resid 55 \ 5 through 601 or resid 604 through 617 or resid 627 through 844 or resid 901 thr \ ough 902)) selection = (chain 'D' and ((resid 25 and (name N or name CA or name C or name O or name CB \ )) or resid 26 through 34 or (resid 35 and (name N or name CA or name C or name \ O or name CB )) or resid 36 through 83 or (resid 84 and (name N or name CA or na \ me C or name O or name CB )) or resid 85 through 326 or (resid 327 and (name N o \ r name CA or name C or name O or name CB )) or resid 328 through 414 or (resid 4 \ 15 and (name N or name CA or name C or name O or name CB )) or resid 416 or (res \ id 417 and (name N or name CA or name C or name O or name CB )) or resid 418 thr \ ough 657 or (resid 658 through 663 and (name N or name CA or name C or name O or \ name CB )) or resid 664 through 844 or resid 901 through 902)) } ncs_group { reference = (chain 'E' and (resid 1 through 138 or resid 145 through 225)) selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.440 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 86.760 Find NCS groups from input model: 3.060 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.002 0.072 31706 Z= 0.135 Angle : 0.479 9.315 43039 Z= 0.258 Chirality : 0.040 0.176 4920 Planarity : 0.003 0.040 5433 Dihedral : 10.593 124.137 11659 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.67 % Favored : 95.12 % Rotamer: Outliers : 4.73 % Allowed : 8.21 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3896 helix: 2.17 (0.15), residues: 1253 sheet: 0.59 (0.20), residues: 774 loop : -0.71 (0.16), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 110 HIS 0.004 0.000 HIS A 119 PHE 0.011 0.001 PHE A 310 TYR 0.008 0.001 TYR G 105 ARG 0.002 0.000 ARG C 386 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 337 time to evaluate : 3.810 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: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.7696 (mm) cc_final: 0.7438 (mm) REVERT: A 323 GLN cc_start: 0.8077 (mt0) cc_final: 0.7560 (tm-30) REVERT: A 408 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8745 (mm) REVERT: A 512 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8814 (pp) REVERT: A 561 MET cc_start: 0.1486 (pmm) cc_final: 0.0156 (mmt) REVERT: A 564 MET cc_start: 0.5825 (tmm) cc_final: 0.5348 (tmm) REVERT: A 677 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8228 (p) REVERT: B 379 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8735 (mt) REVERT: B 785 MET cc_start: 0.9017 (mmt) cc_final: 0.8348 (mpp) REVERT: B 834 GLU cc_start: 0.3618 (OUTLIER) cc_final: 0.2550 (tp30) REVERT: C 69 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8200 (t) REVERT: C 561 MET cc_start: 0.2411 (pmm) cc_final: 0.1640 (pmm) REVERT: C 761 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: D 209 MET cc_start: 0.8079 (tpp) cc_final: 0.7621 (tpp) REVERT: D 315 TRP cc_start: 0.6983 (OUTLIER) cc_final: 0.6070 (t60) REVERT: D 548 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.4991 (tmt170) REVERT: D 695 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7859 (tpp80) REVERT: E 128 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6356 (ptpt) REVERT: G 155 ASP cc_start: 0.8059 (m-30) cc_final: 0.7854 (m-30) REVERT: G 217 LYS cc_start: 0.8841 (mttt) cc_final: 0.8417 (tppt) outliers start: 159 outliers final: 34 residues processed: 476 average time/residue: 0.4640 time to fit residues: 339.3187 Evaluate side-chains 249 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 204 time to evaluate : 3.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 761 TYR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 315 TRP Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain E residue 128 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 330 optimal weight: 0.9990 chunk 296 optimal weight: 9.9990 chunk 164 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 306 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 228 optimal weight: 40.0000 chunk 355 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN A 193 ASN A 216 GLN A 323 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN A 766 GLN B 134 HIS B 363 GLN B 375 ASN B 705 HIS C 35 ASN C 111 GLN C 146 GLN C 356 GLN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 GLN F 38 GLN H 124 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31706 Z= 0.190 Angle : 0.549 11.313 43039 Z= 0.278 Chirality : 0.042 0.188 4920 Planarity : 0.004 0.048 5433 Dihedral : 6.855 113.587 4677 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.16 % Favored : 94.64 % Rotamer: Outliers : 3.51 % Allowed : 11.34 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3896 helix: 1.97 (0.15), residues: 1279 sheet: 0.43 (0.20), residues: 774 loop : -0.76 (0.16), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 55 HIS 0.011 0.001 HIS D 477 PHE 0.014 0.001 PHE A 310 TYR 0.023 0.001 TYR D 703 ARG 0.011 0.000 ARG D 673 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 211 time to evaluate : 3.786 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: A 323 GLN cc_start: 0.8079 (mt0) cc_final: 0.7530 (tm-30) REVERT: A 408 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8750 (mm) REVERT: A 512 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8787 (pp) REVERT: A 561 MET cc_start: 0.1628 (pmm) cc_final: 0.0264 (mmt) REVERT: A 564 MET cc_start: 0.5230 (tmm) cc_final: 0.4721 (tmm) REVERT: A 677 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8227 (p) REVERT: B 379 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8769 (mt) REVERT: B 706 MET cc_start: 0.7557 (mpp) cc_final: 0.7308 (mpp) REVERT: B 834 GLU cc_start: 0.3491 (OUTLIER) cc_final: 0.2365 (tp30) REVERT: C 69 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8400 (t) REVERT: C 74 MET cc_start: 0.7791 (pmm) cc_final: 0.7533 (pmm) REVERT: C 133 MET cc_start: 0.8515 (mpt) cc_final: 0.8281 (mpt) REVERT: C 257 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8808 (p) REVERT: C 761 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: D 209 MET cc_start: 0.8125 (tpp) cc_final: 0.7763 (tpp) REVERT: D 311 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7624 (p0) REVERT: D 315 TRP cc_start: 0.7398 (OUTLIER) cc_final: 0.6524 (t60) REVERT: D 354 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7649 (mpp) REVERT: D 470 MET cc_start: 0.8745 (mtt) cc_final: 0.8425 (mtm) REVERT: D 548 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.5081 (tmt170) REVERT: D 695 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7869 (tpp80) REVERT: D 818 MET cc_start: -0.2375 (mmm) cc_final: -0.3273 (mtm) REVERT: E 128 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6806 (pttm) REVERT: F 116 PHE cc_start: 0.6479 (m-80) cc_final: 0.6000 (m-10) outliers start: 118 outliers final: 55 residues processed: 316 average time/residue: 0.4190 time to fit residues: 214.2449 Evaluate side-chains 256 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 187 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 674 ASN Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 761 TYR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 315 TRP Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 221 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 0.1980 chunk 110 optimal weight: 8.9990 chunk 295 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 355 optimal weight: 10.0000 chunk 384 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 352 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 285 optimal weight: 20.0000 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN B 363 GLN B 375 ASN ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 31706 Z= 0.256 Angle : 0.578 10.385 43039 Z= 0.292 Chirality : 0.043 0.267 4920 Planarity : 0.004 0.049 5433 Dihedral : 6.672 115.111 4661 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.67 % Favored : 94.10 % Rotamer: Outliers : 3.54 % Allowed : 11.78 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3896 helix: 1.72 (0.15), residues: 1280 sheet: 0.04 (0.19), residues: 815 loop : -0.77 (0.16), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 198 HIS 0.012 0.001 HIS F 189 PHE 0.023 0.002 PHE C 183 TYR 0.041 0.002 TYR C 230 ARG 0.006 0.001 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 201 time to evaluate : 3.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8849 (pp) REVERT: A 561 MET cc_start: 0.1614 (pmm) cc_final: 0.0286 (mmt) REVERT: A 677 SER cc_start: 0.8587 (OUTLIER) cc_final: 0.8222 (p) REVERT: B 74 MET cc_start: 0.8670 (tmm) cc_final: 0.8261 (tmm) REVERT: B 195 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8878 (pt) REVERT: B 379 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8851 (mt) REVERT: B 834 GLU cc_start: 0.3728 (OUTLIER) cc_final: 0.2725 (tp30) REVERT: C 69 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8637 (t) REVERT: C 74 MET cc_start: 0.8011 (pmm) cc_final: 0.7796 (pmm) REVERT: D 209 MET cc_start: 0.8238 (tpp) cc_final: 0.7894 (tpp) REVERT: D 311 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7909 (p0) REVERT: D 315 TRP cc_start: 0.7840 (OUTLIER) cc_final: 0.6349 (t60) REVERT: D 354 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7738 (mpp) REVERT: D 470 MET cc_start: 0.8743 (mtm) cc_final: 0.8509 (mtm) REVERT: D 548 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.4742 (tmt170) REVERT: D 634 MET cc_start: 0.6708 (mmm) cc_final: 0.6410 (mmm) REVERT: D 695 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8030 (tpp80) REVERT: D 818 MET cc_start: -0.1861 (mmm) cc_final: -0.2860 (mtm) REVERT: E 128 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7320 (pttm) REVERT: F 116 PHE cc_start: 0.6539 (m-80) cc_final: 0.6033 (m-10) outliers start: 119 outliers final: 68 residues processed: 307 average time/residue: 0.4128 time to fit residues: 210.7247 Evaluate side-chains 266 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 186 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 674 ASN Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 315 TRP Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 351 optimal weight: 8.9990 chunk 267 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 238 optimal weight: 0.6980 chunk 356 optimal weight: 8.9990 chunk 377 optimal weight: 6.9990 chunk 186 optimal weight: 0.0470 chunk 338 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN B 363 GLN B 375 ASN B 494 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31706 Z= 0.149 Angle : 0.529 10.483 43039 Z= 0.265 Chirality : 0.042 0.244 4920 Planarity : 0.003 0.048 5433 Dihedral : 6.426 112.653 4656 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.65 % Favored : 94.12 % Rotamer: Outliers : 3.18 % Allowed : 12.50 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3896 helix: 1.75 (0.15), residues: 1278 sheet: 0.16 (0.19), residues: 804 loop : -0.81 (0.16), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 55 HIS 0.007 0.001 HIS C 119 PHE 0.018 0.001 PHE C 183 TYR 0.033 0.001 TYR D 703 ARG 0.005 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 196 time to evaluate : 3.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8857 (pp) REVERT: A 561 MET cc_start: 0.1804 (pmm) cc_final: 0.0501 (mmt) REVERT: A 677 SER cc_start: 0.8566 (OUTLIER) cc_final: 0.8199 (p) REVERT: A 823 MET cc_start: 0.5539 (mpp) cc_final: 0.4772 (tmm) REVERT: B 74 MET cc_start: 0.8717 (tmm) cc_final: 0.8234 (tmm) REVERT: B 470 MET cc_start: 0.8700 (mtm) cc_final: 0.8323 (ptp) REVERT: B 702 MET cc_start: 0.7815 (tmm) cc_final: 0.7581 (tmm) REVERT: B 785 MET cc_start: 0.9285 (mmm) cc_final: 0.8636 (mpp) REVERT: B 818 MET cc_start: -0.1626 (tpp) cc_final: -0.2029 (mpp) REVERT: B 834 GLU cc_start: 0.3792 (OUTLIER) cc_final: 0.2773 (tp30) REVERT: C 69 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8543 (t) REVERT: C 439 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7727 (t80) REVERT: D 209 MET cc_start: 0.8226 (tpp) cc_final: 0.7874 (tpp) REVERT: D 311 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7833 (p0) REVERT: D 315 TRP cc_start: 0.7735 (OUTLIER) cc_final: 0.6239 (t60) REVERT: D 354 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7706 (mpp) REVERT: D 548 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.4762 (tmt170) REVERT: D 634 MET cc_start: 0.6618 (mmm) cc_final: 0.6367 (mmm) REVERT: D 695 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7990 (tpp80) REVERT: D 818 MET cc_start: -0.1865 (mmm) cc_final: -0.2845 (mtm) REVERT: E 128 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7282 (pttm) REVERT: F 116 PHE cc_start: 0.6568 (m-80) cc_final: 0.6108 (m-10) outliers start: 107 outliers final: 68 residues processed: 290 average time/residue: 0.4068 time to fit residues: 194.9807 Evaluate side-chains 268 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 189 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 674 ASN Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 315 TRP Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 48 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 314 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 281 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 322 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 0.2980 chunk 339 optimal weight: 20.0000 chunk 95 optimal weight: 0.6980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN B 375 ASN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31706 Z= 0.251 Angle : 0.568 10.414 43039 Z= 0.287 Chirality : 0.043 0.347 4920 Planarity : 0.004 0.049 5433 Dihedral : 6.456 113.854 4650 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.42 % Favored : 93.35 % Rotamer: Outliers : 3.90 % Allowed : 12.38 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3896 helix: 1.68 (0.15), residues: 1277 sheet: -0.02 (0.19), residues: 808 loop : -0.87 (0.16), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 198 HIS 0.007 0.001 HIS C 119 PHE 0.018 0.001 PHE C 183 TYR 0.036 0.002 TYR D 703 ARG 0.007 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 187 time to evaluate : 4.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8915 (pp) REVERT: A 561 MET cc_start: 0.1744 (pmm) cc_final: 0.0442 (mmt) REVERT: A 677 SER cc_start: 0.8588 (OUTLIER) cc_final: 0.8207 (p) REVERT: A 823 MET cc_start: 0.5871 (mpp) cc_final: 0.5559 (ptp) REVERT: B 195 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8972 (pt) REVERT: B 785 MET cc_start: 0.9311 (mmm) cc_final: 0.9050 (tpp) REVERT: B 818 MET cc_start: -0.1603 (tpp) cc_final: -0.2005 (mpp) REVERT: B 834 GLU cc_start: 0.3714 (OUTLIER) cc_final: 0.2738 (tp30) REVERT: C 69 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8627 (t) REVERT: C 74 MET cc_start: 0.7934 (pmm) cc_final: 0.7692 (pmm) REVERT: C 439 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7801 (t80) REVERT: D 115 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.6836 (tpp80) REVERT: D 209 MET cc_start: 0.8215 (tpp) cc_final: 0.7852 (tpp) REVERT: D 311 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7923 (p0) REVERT: D 470 MET cc_start: 0.8650 (mtm) cc_final: 0.7891 (ptp) REVERT: D 472 PHE cc_start: 0.7364 (m-10) cc_final: 0.7064 (m-10) REVERT: D 548 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.4625 (tmt170) REVERT: D 657 LEU cc_start: 0.2338 (OUTLIER) cc_final: 0.1725 (pp) REVERT: D 695 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8043 (tpp80) REVERT: D 706 MET cc_start: 0.8762 (tpp) cc_final: 0.8377 (tpp) REVERT: E 128 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7469 (pttm) REVERT: F 116 PHE cc_start: 0.6545 (m-80) cc_final: 0.6072 (m-10) REVERT: G 221 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6819 (tpp-160) outliers start: 131 outliers final: 80 residues processed: 303 average time/residue: 0.4027 time to fit residues: 201.0241 Evaluate side-chains 270 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 177 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 674 ASN Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 CYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 315 TRP Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain H residue 187 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 127 optimal weight: 4.9990 chunk 340 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 378 optimal weight: 0.5980 chunk 314 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 0.0370 chunk 198 optimal weight: 0.9980 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN C 490 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31706 Z= 0.154 Angle : 0.544 9.852 43039 Z= 0.271 Chirality : 0.042 0.298 4920 Planarity : 0.003 0.049 5433 Dihedral : 6.273 111.408 4648 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.85 % Favored : 93.92 % Rotamer: Outliers : 3.18 % Allowed : 13.24 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3896 helix: 1.73 (0.15), residues: 1277 sheet: 0.01 (0.19), residues: 808 loop : -0.85 (0.16), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 198 HIS 0.006 0.001 HIS C 119 PHE 0.018 0.001 PHE D 197 TYR 0.034 0.001 TYR D 703 ARG 0.008 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 188 time to evaluate : 3.451 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: A 512 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8961 (pp) REVERT: A 561 MET cc_start: 0.1637 (pmm) cc_final: 0.0352 (mmt) REVERT: A 677 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.8178 (p) REVERT: A 823 MET cc_start: 0.5839 (mpp) cc_final: 0.5456 (ptp) REVERT: B 614 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7749 (pp) REVERT: B 785 MET cc_start: 0.9259 (mmm) cc_final: 0.9017 (tpp) REVERT: B 818 MET cc_start: -0.1592 (tpp) cc_final: -0.2001 (mpp) REVERT: B 834 GLU cc_start: 0.3604 (OUTLIER) cc_final: 0.2587 (tp30) REVERT: C 74 MET cc_start: 0.7927 (pmm) cc_final: 0.7677 (pmm) REVERT: C 439 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7705 (t80) REVERT: D 115 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.6911 (tpp80) REVERT: D 209 MET cc_start: 0.8183 (tpp) cc_final: 0.7805 (tpp) REVERT: D 311 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7911 (p0) REVERT: D 470 MET cc_start: 0.8798 (mtm) cc_final: 0.8015 (ptp) REVERT: D 472 PHE cc_start: 0.7316 (m-10) cc_final: 0.6912 (m-10) REVERT: D 548 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.4624 (tmt170) REVERT: D 695 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8004 (tpp80) REVERT: D 706 MET cc_start: 0.8734 (tpp) cc_final: 0.8479 (tpp) REVERT: E 128 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7492 (pttm) REVERT: F 116 PHE cc_start: 0.6648 (m-80) cc_final: 0.6227 (m-10) outliers start: 107 outliers final: 71 residues processed: 279 average time/residue: 0.4018 time to fit residues: 185.3774 Evaluate side-chains 263 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 182 time to evaluate : 3.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 490 ASN Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 CYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 187 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 364 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 215 optimal weight: 0.3980 chunk 276 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 376 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31706 Z= 0.206 Angle : 0.553 9.645 43039 Z= 0.276 Chirality : 0.042 0.295 4920 Planarity : 0.003 0.049 5433 Dihedral : 6.177 111.682 4642 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.19 % Favored : 93.58 % Rotamer: Outliers : 3.24 % Allowed : 13.86 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3896 helix: 1.69 (0.15), residues: 1283 sheet: -0.03 (0.19), residues: 804 loop : -0.88 (0.16), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 198 HIS 0.007 0.001 HIS C 119 PHE 0.030 0.001 PHE A 183 TYR 0.045 0.001 TYR C 230 ARG 0.010 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 185 time to evaluate : 3.791 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: A 283 ASP cc_start: 0.6463 (OUTLIER) cc_final: 0.5993 (m-30) REVERT: A 507 MET cc_start: 0.8637 (ttm) cc_final: 0.8434 (ttm) REVERT: A 561 MET cc_start: 0.1638 (pmm) cc_final: 0.0423 (mmt) REVERT: A 677 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8202 (p) REVERT: A 823 MET cc_start: 0.5895 (mpp) cc_final: 0.5469 (ptp) REVERT: B 614 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7356 (tt) REVERT: B 785 MET cc_start: 0.9276 (mmm) cc_final: 0.9032 (tpp) REVERT: B 818 MET cc_start: -0.1529 (tpp) cc_final: -0.1927 (mpp) REVERT: B 834 GLU cc_start: 0.3777 (OUTLIER) cc_final: 0.2779 (tp30) REVERT: C 90 MET cc_start: 0.7770 (ptt) cc_final: 0.7566 (ptt) REVERT: C 439 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7739 (t80) REVERT: C 490 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7723 (p0) REVERT: C 630 MET cc_start: 0.2600 (ptm) cc_final: 0.2348 (ppp) REVERT: D 115 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.6844 (tpp80) REVERT: D 209 MET cc_start: 0.8210 (tpp) cc_final: 0.7829 (tpp) REVERT: D 311 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7918 (p0) REVERT: D 470 MET cc_start: 0.8819 (mtm) cc_final: 0.8336 (ptp) REVERT: D 472 PHE cc_start: 0.7346 (m-10) cc_final: 0.6972 (m-10) REVERT: D 548 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.4617 (tmt170) REVERT: D 657 LEU cc_start: 0.2306 (OUTLIER) cc_final: 0.1713 (pp) REVERT: D 695 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8038 (tpp80) REVERT: D 706 MET cc_start: 0.8678 (tpp) cc_final: 0.8458 (tpp) REVERT: D 762 MET cc_start: 0.7773 (mtp) cc_final: 0.7514 (mtm) REVERT: E 128 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7534 (pttm) REVERT: F 116 PHE cc_start: 0.6659 (m-80) cc_final: 0.6248 (m-10) REVERT: F 143 GLU cc_start: 0.7648 (tp30) cc_final: 0.7446 (tp30) REVERT: G 221 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6832 (tpp-160) outliers start: 109 outliers final: 84 residues processed: 277 average time/residue: 0.4166 time to fit residues: 188.2939 Evaluate side-chains 278 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 181 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 674 ASN Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 490 ASN Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 CYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain H residue 187 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 233 optimal weight: 1.9990 chunk 150 optimal weight: 0.4980 chunk 225 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 239 optimal weight: 0.8980 chunk 256 optimal weight: 8.9990 chunk 186 optimal weight: 0.2980 chunk 35 optimal weight: 0.1980 chunk 296 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 490 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31706 Z= 0.140 Angle : 0.538 11.031 43039 Z= 0.267 Chirality : 0.042 0.286 4920 Planarity : 0.003 0.049 5433 Dihedral : 6.035 109.217 4638 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.70 % Favored : 94.10 % Rotamer: Outliers : 2.92 % Allowed : 14.25 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3896 helix: 1.73 (0.15), residues: 1283 sheet: 0.15 (0.20), residues: 780 loop : -0.89 (0.16), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 198 HIS 0.005 0.001 HIS C 119 PHE 0.026 0.001 PHE A 396 TYR 0.038 0.001 TYR D 703 ARG 0.004 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 195 time to evaluate : 3.692 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: A 283 ASP cc_start: 0.6302 (OUTLIER) cc_final: 0.5906 (m-30) REVERT: A 561 MET cc_start: 0.1796 (pmm) cc_final: 0.0592 (mmt) REVERT: A 677 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8192 (p) REVERT: A 823 MET cc_start: 0.5936 (mpp) cc_final: 0.5516 (ptp) REVERT: B 74 MET cc_start: 0.8885 (tpp) cc_final: 0.8429 (tpp) REVERT: B 502 MET cc_start: 0.8043 (mmt) cc_final: 0.7680 (tpt) REVERT: B 614 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7821 (pp) REVERT: B 785 MET cc_start: 0.9240 (mmm) cc_final: 0.9021 (tpp) REVERT: B 818 MET cc_start: -0.1536 (tpp) cc_final: -0.1933 (mpp) REVERT: B 834 GLU cc_start: 0.3730 (OUTLIER) cc_final: 0.2724 (tp30) REVERT: C 439 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7699 (t80) REVERT: C 630 MET cc_start: 0.2570 (ptm) cc_final: 0.2324 (ppp) REVERT: D 115 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7023 (tpp80) REVERT: D 209 MET cc_start: 0.8178 (tpp) cc_final: 0.7797 (tpp) REVERT: D 311 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7809 (p0) REVERT: D 470 MET cc_start: 0.8793 (mtm) cc_final: 0.8482 (ptp) REVERT: D 472 PHE cc_start: 0.7180 (m-10) cc_final: 0.6768 (m-10) REVERT: D 548 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.4628 (tmt170) REVERT: D 695 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7987 (tpp80) REVERT: D 706 MET cc_start: 0.8664 (tpp) cc_final: 0.8441 (tpp) REVERT: D 762 MET cc_start: 0.7617 (mtp) cc_final: 0.7317 (mtm) REVERT: E 128 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7475 (pttm) REVERT: F 116 PHE cc_start: 0.6704 (m-80) cc_final: 0.6301 (m-10) REVERT: G 221 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6807 (tpp-160) outliers start: 98 outliers final: 73 residues processed: 276 average time/residue: 0.4254 time to fit residues: 190.8379 Evaluate side-chains 269 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 185 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 CYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain H residue 187 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 342 optimal weight: 10.0000 chunk 361 optimal weight: 30.0000 chunk 329 optimal weight: 20.0000 chunk 351 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 317 optimal weight: 0.7980 chunk 332 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 154 GLN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31706 Z= 0.293 Angle : 0.607 11.511 43039 Z= 0.304 Chirality : 0.044 0.284 4920 Planarity : 0.004 0.047 5433 Dihedral : 6.288 112.560 4638 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.96 % Favored : 92.79 % Rotamer: Outliers : 2.95 % Allowed : 14.49 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3896 helix: 1.63 (0.15), residues: 1282 sheet: -0.06 (0.20), residues: 799 loop : -0.93 (0.16), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 198 HIS 0.008 0.001 HIS C 119 PHE 0.026 0.002 PHE C 183 TYR 0.054 0.002 TYR C 230 ARG 0.006 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 179 time to evaluate : 3.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.6292 (OUTLIER) cc_final: 0.5914 (m-30) REVERT: A 561 MET cc_start: 0.1843 (pmm) cc_final: 0.0638 (mmt) REVERT: A 677 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8327 (p) REVERT: A 701 MET cc_start: 0.7866 (mmt) cc_final: 0.7420 (mmt) REVERT: A 823 MET cc_start: 0.6274 (mpp) cc_final: 0.5637 (ptp) REVERT: B 785 MET cc_start: 0.9248 (mmm) cc_final: 0.8979 (tpp) REVERT: B 818 MET cc_start: -0.1516 (tpp) cc_final: -0.1911 (mpp) REVERT: B 834 GLU cc_start: 0.4017 (OUTLIER) cc_final: 0.2941 (tp30) REVERT: C 439 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7726 (t80) REVERT: C 630 MET cc_start: 0.2774 (ptm) cc_final: 0.2527 (ppp) REVERT: D 115 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.6515 (tpp80) REVERT: D 209 MET cc_start: 0.8215 (tpp) cc_final: 0.7841 (tpp) REVERT: D 311 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.7918 (p0) REVERT: D 470 MET cc_start: 0.8872 (mtm) cc_final: 0.8431 (ptp) REVERT: D 472 PHE cc_start: 0.7488 (m-10) cc_final: 0.7113 (m-10) REVERT: D 548 ARG cc_start: 0.6599 (OUTLIER) cc_final: 0.4650 (tmt170) REVERT: D 657 LEU cc_start: 0.2128 (OUTLIER) cc_final: 0.1522 (pp) REVERT: D 695 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8055 (tpp80) REVERT: D 706 MET cc_start: 0.8748 (tpp) cc_final: 0.8471 (tpp) REVERT: D 762 MET cc_start: 0.7806 (mtp) cc_final: 0.7524 (mtm) REVERT: E 128 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7623 (pttm) REVERT: F 116 PHE cc_start: 0.6634 (m-80) cc_final: 0.6210 (m-10) REVERT: G 221 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6833 (tpp-160) outliers start: 99 outliers final: 79 residues processed: 263 average time/residue: 0.4110 time to fit residues: 180.3044 Evaluate side-chains 270 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 180 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 CYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain H residue 187 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 349 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 371 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 258 optimal weight: 0.0470 chunk 389 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 chunk 310 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31706 Z= 0.206 Angle : 0.582 12.404 43039 Z= 0.289 Chirality : 0.043 0.287 4920 Planarity : 0.003 0.049 5433 Dihedral : 6.262 110.836 4638 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.37 % Favored : 93.40 % Rotamer: Outliers : 2.62 % Allowed : 15.08 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3896 helix: 1.60 (0.15), residues: 1283 sheet: -0.00 (0.20), residues: 768 loop : -0.96 (0.16), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 198 HIS 0.007 0.001 HIS C 119 PHE 0.041 0.001 PHE A 183 TYR 0.042 0.001 TYR C 230 ARG 0.006 0.000 ARG E 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 186 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TRP cc_start: 0.6961 (p-90) cc_final: 0.6580 (p-90) REVERT: A 200 MET cc_start: 0.5109 (mmp) cc_final: 0.4609 (mmp) REVERT: A 283 ASP cc_start: 0.6195 (OUTLIER) cc_final: 0.5903 (m-30) REVERT: A 450 MET cc_start: 0.7734 (pmm) cc_final: 0.7502 (pmm) REVERT: A 561 MET cc_start: 0.1827 (pmm) cc_final: 0.0618 (mmt) REVERT: A 677 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8255 (p) REVERT: A 701 MET cc_start: 0.7923 (mmt) cc_final: 0.7447 (mmt) REVERT: A 823 MET cc_start: 0.6330 (mpp) cc_final: 0.5701 (ptp) REVERT: B 74 MET cc_start: 0.9068 (tpp) cc_final: 0.8574 (tpp) REVERT: B 576 MET cc_start: 0.3989 (tmt) cc_final: 0.3766 (tmt) REVERT: B 785 MET cc_start: 0.9237 (mmm) cc_final: 0.8992 (tpp) REVERT: B 818 MET cc_start: -0.1439 (tpp) cc_final: -0.1836 (mpp) REVERT: B 834 GLU cc_start: 0.3921 (OUTLIER) cc_final: 0.2850 (tp30) REVERT: C 439 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7726 (t80) REVERT: C 630 MET cc_start: 0.2765 (ptm) cc_final: 0.2522 (ppp) REVERT: D 115 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.6556 (tpp80) REVERT: D 209 MET cc_start: 0.8204 (tpp) cc_final: 0.7827 (tpp) REVERT: D 311 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7916 (p0) REVERT: D 394 MET cc_start: 0.8616 (mmm) cc_final: 0.8400 (mmp) REVERT: D 470 MET cc_start: 0.8826 (mtm) cc_final: 0.8552 (ptp) REVERT: D 472 PHE cc_start: 0.7533 (m-10) cc_final: 0.7137 (m-10) REVERT: D 548 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.4701 (tmt170) REVERT: D 657 LEU cc_start: 0.2338 (OUTLIER) cc_final: 0.1746 (pp) REVERT: D 695 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.8017 (tpp80) REVERT: D 706 MET cc_start: 0.8705 (tpp) cc_final: 0.8447 (tpp) REVERT: D 762 MET cc_start: 0.7613 (mtp) cc_final: 0.7371 (mtm) REVERT: E 128 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7623 (pttm) REVERT: F 116 PHE cc_start: 0.6729 (m-80) cc_final: 0.6406 (m-10) REVERT: G 221 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6848 (tpp-160) outliers start: 88 outliers final: 74 residues processed: 258 average time/residue: 0.4004 time to fit residues: 170.4502 Evaluate side-chains 269 residues out of total 3428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 184 time to evaluate : 3.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 CYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain H residue 187 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 190 optimal weight: 0.6980 chunk 246 optimal weight: 2.9990 chunk 330 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 310 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 319 optimal weight: 30.0000 chunk 39 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.063859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.046375 restraints weight = 194345.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.047380 restraints weight = 125915.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.047930 restraints weight = 87364.984| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 31706 Z= 0.307 Angle : 0.630 12.221 43039 Z= 0.317 Chirality : 0.044 0.282 4920 Planarity : 0.004 0.047 5433 Dihedral : 6.496 113.341 4638 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.44 % Favored : 92.30 % Rotamer: Outliers : 2.86 % Allowed : 14.85 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.03 (0.14), residues: 3896 helix: 1.49 (0.15), residues: 1284 sheet: -0.18 (0.20), residues: 788 loop : -1.04 (0.16), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 198 HIS 0.008 0.001 HIS C 119 PHE 0.038 0.002 PHE A 183 TYR 0.055 0.002 TYR C 230 ARG 0.005 0.000 ARG C 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5738.88 seconds wall clock time: 104 minutes 35.14 seconds (6275.14 seconds total)