Starting phenix.real_space_refine on Sun Jul 5 09:43:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iht_35455/07_2026/8iht_35455.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iht_35455/07_2026/8iht_35455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iht_35455/07_2026/8iht_35455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iht_35455/07_2026/8iht_35455.map" model { file = "/net/cci-nas-00/data/ceres_data/8iht_35455/07_2026/8iht_35455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iht_35455/07_2026/8iht_35455.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.006 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Zn 1 6.06 5 P 317 5.49 5 S 77 5.16 5 C 16409 2.51 5 N 4944 2.21 5 O 5796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27545 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 925 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 607 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 801 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 711 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 779 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ML3:plan-1': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 609 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 760 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 639 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3216 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3280 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2844 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 5 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 3, 'TYR:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "N" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2212 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 2, 'ASP:plan': 8, 'GLN:plan1': 3, 'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 113 Chain: "K" Number of atoms: 4668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4668 Classifications: {'peptide': 598} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 88} Link IDs: {'PTRANS': 14, 'TRANS': 583} Chain breaks: 3 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 453 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 13, 'GLN:plan1': 3, 'ASP:plan': 9, 'ASN:plan1': 9, 'PHE:plan': 6, 'HIS:plan': 2, 'ARG:plan': 4, 'TYR:plan': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 230 Chain: "L" Number of atoms: 3047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3047 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'TYR:plan': 6, 'HIS:plan': 3, 'ASN:plan1': 4, 'ARG:plan': 2, 'ASP:plan': 9, 'GLN:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 134 Chain: "O" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1125 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'ASP:plan': 3, 'TRP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "P" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1320 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 5, 'GLU:plan': 5, 'GLN:plan1': 3, 'HIS:plan': 1, 'TRP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 87 Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 5.51, per 1000 atoms: 0.20 Number of scatterers: 27545 At special positions: 0 Unit cell: (132.68, 148.73, 200.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Ca 1 19.99 S 77 16.00 P 317 15.00 O 5796 8.00 N 4944 7.00 C 16409 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 882.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 501 " pdb="ZN ZN L 501 " - pdb=" ND1 HIS L 188 " 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5296 Finding SS restraints... Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 20 Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 23 Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 20 Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 23 Secondary structure from input PDB file: 119 helices and 21 sheets defined 58.6% alpha, 4.5% beta 150 base pairs and 238 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.569A pdb=" N ARG A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 115 removed outlier: 3.861A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.650A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.228A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.776A pdb=" N TYR B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.771A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 71 removed outlier: 4.651A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.560A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.561A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.553A pdb=" N TYR D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 74 removed outlier: 3.963A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 71 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 81 Processing helix chain 'D' and resid 88 through 99 removed outlier: 3.830A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.769A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.710A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.581A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.673A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.656A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.621A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.692A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.738A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 54 through 81 removed outlier: 3.778A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.533A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU H 97 " --> pdb=" O THR H 93 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.568A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 303 through 313 Processing helix chain 'M' and resid 318 through 330 removed outlier: 3.524A pdb=" N ILE M 322 " --> pdb=" O THR M 318 " (cutoff:3.500A) Processing helix chain 'M' and resid 333 through 335 No H-bonds generated for 'chain 'M' and resid 333 through 335' Processing helix chain 'M' and resid 336 through 343 Processing helix chain 'M' and resid 354 through 359 Processing helix chain 'M' and resid 382 through 388 Processing helix chain 'M' and resid 402 through 406 removed outlier: 3.732A pdb=" N THR M 405 " --> pdb=" O ASN M 402 " (cutoff:3.500A) Processing helix chain 'M' and resid 430 through 434 removed outlier: 3.685A pdb=" N ASN M 433 " --> pdb=" O HIS M 430 " (cutoff:3.500A) Processing helix chain 'M' and resid 544 through 577 removed outlier: 3.702A pdb=" N ILE M 574 " --> pdb=" O GLN M 570 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 74 removed outlier: 4.358A pdb=" N GLY N 74 " --> pdb=" O GLU N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 131 removed outlier: 3.570A pdb=" N LYS N 108 " --> pdb=" O ASN N 104 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS N 119 " --> pdb=" O ALA N 115 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS N 120 " --> pdb=" O LYS N 116 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN N 125 " --> pdb=" O SER N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 241 removed outlier: 3.724A pdb=" N VAL N 233 " --> pdb=" O LYS N 229 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR N 240 " --> pdb=" O TRP N 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 269 removed outlier: 3.965A pdb=" N GLN N 267 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU N 268 " --> pdb=" O GLU N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 297 removed outlier: 3.527A pdb=" N GLN N 275 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN N 277 " --> pdb=" O GLY N 273 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY N 294 " --> pdb=" O ASP N 290 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN N 295 " --> pdb=" O LYS N 291 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU N 297 " --> pdb=" O LEU N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 299 through 301 No H-bonds generated for 'chain 'N' and resid 299 through 301' Processing helix chain 'N' and resid 302 through 317 removed outlier: 3.653A pdb=" N LYS N 315 " --> pdb=" O LYS N 311 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 326 removed outlier: 3.546A pdb=" N ILE N 325 " --> pdb=" O VAL N 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 327 through 337 removed outlier: 3.586A pdb=" N LEU N 331 " --> pdb=" O GLY N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 345 removed outlier: 3.628A pdb=" N THR N 345 " --> pdb=" O LEU N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 348 through 369 Processing helix chain 'N' and resid 369 through 374 removed outlier: 3.601A pdb=" N TYR N 373 " --> pdb=" O HIS N 369 " (cutoff:3.500A) Processing helix chain 'N' and resid 391 through 400 removed outlier: 3.534A pdb=" N GLY N 396 " --> pdb=" O SER N 392 " (cutoff:3.500A) Processing helix chain 'K' and resid 661 through 666 removed outlier: 3.775A pdb=" N GLU K 665 " --> pdb=" O SER K 661 " (cutoff:3.500A) Processing helix chain 'K' and resid 667 through 677 Processing helix chain 'K' and resid 678 through 694 removed outlier: 3.773A pdb=" N GLU K 684 " --> pdb=" O HIS K 680 " (cutoff:3.500A) Processing helix chain 'K' and resid 698 through 711 removed outlier: 3.868A pdb=" N PHE K 708 " --> pdb=" O GLU K 704 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR K 709 " --> pdb=" O LYS K 705 " (cutoff:3.500A) Processing helix chain 'K' and resid 713 through 725 removed outlier: 3.605A pdb=" N TRP K 719 " --> pdb=" O GLU K 715 " (cutoff:3.500A) Processing helix chain 'K' and resid 760 through 765 removed outlier: 3.852A pdb=" N MET K 765 " --> pdb=" O ASP K 762 " (cutoff:3.500A) Processing helix chain 'K' and resid 771 through 778 removed outlier: 3.538A pdb=" N TRP K 775 " --> pdb=" O ASP K 771 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU K 776 " --> pdb=" O ASP K 772 " (cutoff:3.500A) Processing helix chain 'K' and resid 785 through 790 Processing helix chain 'K' and resid 805 through 841 removed outlier: 3.507A pdb=" N TYR K 820 " --> pdb=" O GLU K 816 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR K 827 " --> pdb=" O SER K 823 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE K 834 " --> pdb=" O CYS K 830 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS K 837 " --> pdb=" O THR K 833 " (cutoff:3.500A) Processing helix chain 'K' and resid 842 through 848 removed outlier: 3.896A pdb=" N ASN K 848 " --> pdb=" O ASN K 844 " (cutoff:3.500A) Processing helix chain 'K' and resid 852 through 857 removed outlier: 4.021A pdb=" N GLY K 856 " --> pdb=" O PRO K 853 " (cutoff:3.500A) Processing helix chain 'K' and resid 861 through 871 removed outlier: 3.702A pdb=" N ILE K 867 " --> pdb=" O TYR K 863 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS K 869 " --> pdb=" O LYS K 865 " (cutoff:3.500A) Processing helix chain 'K' and resid 874 through 886 removed outlier: 4.282A pdb=" N GLU K 878 " --> pdb=" O GLU K 874 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE K 879 " --> pdb=" O ARG K 875 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE K 880 " --> pdb=" O GLY K 876 " (cutoff:3.500A) Processing helix chain 'K' and resid 886 through 929 Proline residue: K 892 - end of helix removed outlier: 3.529A pdb=" N GLU K 911 " --> pdb=" O ARG K 907 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS K 914 " --> pdb=" O ARG K 910 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL K 915 " --> pdb=" O GLU K 911 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N PHE K 925 " --> pdb=" O GLN K 921 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LYS K 926 " --> pdb=" O LYS K 922 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER K 927 " --> pdb=" O VAL K 923 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU K 928 " --> pdb=" O PHE K 924 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP K 929 " --> pdb=" O PHE K 925 " (cutoff:3.500A) Processing helix chain 'K' and resid 929 through 934 removed outlier: 3.796A pdb=" N LEU K 933 " --> pdb=" O ASP K 929 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR K 934 " --> pdb=" O HIS K 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 929 through 934' Processing helix chain 'K' and resid 934 through 943 removed outlier: 3.962A pdb=" N LYS K 940 " --> pdb=" O LYS K 936 " (cutoff:3.500A) Processing helix chain 'K' and resid 946 through 965 removed outlier: 3.727A pdb=" N ILE K 952 " --> pdb=" O LEU K 948 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE K 955 " --> pdb=" O GLU K 951 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS K 963 " --> pdb=" O GLN K 959 " (cutoff:3.500A) Processing helix chain 'K' and resid 982 through 999 removed outlier: 4.153A pdb=" N TYR K 986 " --> pdb=" O LYS K 982 " (cutoff:3.500A) Processing helix chain 'K' and resid 1003 through 1022 removed outlier: 3.780A pdb=" N GLU K1008 " --> pdb=" O ASN K1004 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG K1009 " --> pdb=" O PRO K1005 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU K1014 " --> pdb=" O LEU K1010 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS K1015 " --> pdb=" O LYS K1011 " (cutoff:3.500A) Processing helix chain 'K' and resid 1025 through 1040 Processing helix chain 'K' and resid 1064 through 1069 Processing helix chain 'K' and resid 1070 through 1080 removed outlier: 4.345A pdb=" N LYS K1076 " --> pdb=" O SER K1072 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU K1077 " --> pdb=" O ARG K1073 " (cutoff:3.500A) Processing helix chain 'K' and resid 1141 through 1175 removed outlier: 3.669A pdb=" N PHE K1147 " --> pdb=" O ASN K1143 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE K1154 " --> pdb=" O HIS K1150 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE K1161 " --> pdb=" O ARG K1157 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET K1164 " --> pdb=" O GLU K1160 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU K1166 " --> pdb=" O LYS K1162 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ARG K1167 " --> pdb=" O GLN K1163 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS K1170 " --> pdb=" O GLU K1166 " (cutoff:3.500A) Processing helix chain 'K' and resid 1178 through 1183 Processing helix chain 'K' and resid 1189 through 1195 Processing helix chain 'K' and resid 1202 through 1216 removed outlier: 3.801A pdb=" N ARG K1213 " --> pdb=" O ARG K1209 " (cutoff:3.500A) Processing helix chain 'K' and resid 1220 through 1233 removed outlier: 3.547A pdb=" N LEU K1228 " --> pdb=" O PHE K1224 " (cutoff:3.500A) Processing helix chain 'K' and resid 1241 through 1258 removed outlier: 3.593A pdb=" N LEU K1256 " --> pdb=" O HIS K1252 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET K1257 " --> pdb=" O ALA K1253 " (cutoff:3.500A) Processing helix chain 'K' and resid 1259 through 1275 removed outlier: 3.786A pdb=" N LYS K1271 " --> pdb=" O ALA K1267 " (cutoff:3.500A) Processing helix chain 'K' and resid 1279 through 1294 removed outlier: 3.559A pdb=" N ILE K1284 " --> pdb=" O ALA K1280 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS K1293 " --> pdb=" O GLN K1289 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET K1294 " --> pdb=" O VAL K1290 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 32 removed outlier: 3.939A pdb=" N GLY L 30 " --> pdb=" O ALA L 27 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR L 32 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 55 removed outlier: 4.223A pdb=" N ARG L 46 " --> pdb=" O PRO L 42 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE L 52 " --> pdb=" O ALA L 48 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN L 54 " --> pdb=" O SER L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'L' and resid 72 through 77 removed outlier: 3.932A pdb=" N PHE L 77 " --> pdb=" O MET L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 89 removed outlier: 3.682A pdb=" N ARG L 88 " --> pdb=" O ASP L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 94 removed outlier: 3.652A pdb=" N LEU L 94 " --> pdb=" O PRO L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 104 Processing helix chain 'L' and resid 115 through 136 removed outlier: 3.802A pdb=" N GLY L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY L 130 " --> pdb=" O GLY L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 174 removed outlier: 3.605A pdb=" N LEU L 168 " --> pdb=" O ASN L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 195 Processing helix chain 'L' and resid 226 through 230 removed outlier: 3.587A pdb=" N LYS L 230 " --> pdb=" O GLY L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 262 Proline residue: L 253 - end of helix Processing helix chain 'L' and resid 287 through 300 removed outlier: 4.330A pdb=" N CYS L 294 " --> pdb=" O GLY L 290 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL L 295 " --> pdb=" O HIS L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 330 removed outlier: 3.642A pdb=" N ARG L 320 " --> pdb=" O ARG L 316 " (cutoff:3.500A) Processing helix chain 'L' and resid 365 through 381 removed outlier: 3.585A pdb=" N LYS L 371 " --> pdb=" O GLU L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 409 through 414 Processing helix chain 'O' and resid 303 through 313 Processing helix chain 'O' and resid 315 through 330 Processing helix chain 'O' and resid 337 through 344 removed outlier: 4.118A pdb=" N ASP O 344 " --> pdb=" O LEU O 340 " (cutoff:3.500A) Processing helix chain 'O' and resid 354 through 361 removed outlier: 4.070A pdb=" N PHE O 361 " --> pdb=" O ILE O 357 " (cutoff:3.500A) Processing helix chain 'O' and resid 544 through 577 removed outlier: 3.918A pdb=" N LYS O 554 " --> pdb=" O ASP O 550 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET O 560 " --> pdb=" O TYR O 556 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL O 561 " --> pdb=" O LYS O 557 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU O 577 " --> pdb=" O LEU O 573 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 242 Processing helix chain 'P' and resid 253 through 265 Processing helix chain 'P' and resid 266 through 268 No H-bonds generated for 'chain 'P' and resid 266 through 268' Processing helix chain 'P' and resid 271 through 296 removed outlier: 3.861A pdb=" N ASP P 290 " --> pdb=" O LYS P 286 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS P 291 " --> pdb=" O LEU P 287 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY P 294 " --> pdb=" O ASP P 290 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN P 295 " --> pdb=" O LYS P 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 299 through 317 removed outlier: 3.595A pdb=" N LEU P 304 " --> pdb=" O ARG P 300 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN P 305 " --> pdb=" O LEU P 301 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU P 308 " --> pdb=" O LEU P 304 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU P 309 " --> pdb=" O GLN P 305 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU P 310 " --> pdb=" O TYR P 306 " (cutoff:3.500A) Processing helix chain 'P' and resid 321 through 326 removed outlier: 3.730A pdb=" N ILE P 325 " --> pdb=" O VAL P 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 327 through 345 removed outlier: 3.805A pdb=" N LEU P 331 " --> pdb=" O GLY P 327 " (cutoff:3.500A) Proline residue: P 339 - end of helix removed outlier: 3.639A pdb=" N SER P 343 " --> pdb=" O PRO P 339 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER P 344 " --> pdb=" O GLU P 340 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR P 345 " --> pdb=" O LEU P 341 " (cutoff:3.500A) Processing helix chain 'P' and resid 348 through 370 removed outlier: 3.509A pdb=" N THR P 359 " --> pdb=" O LEU P 355 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET P 368 " --> pdb=" O VAL P 364 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS P 369 " --> pdb=" O TRP P 365 " (cutoff:3.500A) Processing helix chain 'P' and resid 391 through 400 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.052A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.051A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.177A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.440A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.589A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'M' and resid 272 through 274 Processing sheet with id=AA9, first strand: chain 'M' and resid 365 through 366 Processing sheet with id=AB1, first strand: chain 'M' and resid 437 through 439 Processing sheet with id=AB2, first strand: chain 'M' and resid 473 through 477 Processing sheet with id=AB3, first strand: chain 'M' and resid 504 through 506 removed outlier: 6.870A pdb=" N LEU M 504 " --> pdb=" O ILE M 539 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLN M 541 " --> pdb=" O LEU M 504 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR M 506 " --> pdb=" O GLN M 541 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASP M 543 " --> pdb=" O TYR M 506 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 79 through 81 removed outlier: 3.588A pdb=" N LEU N 21 " --> pdb=" O HIS N 18 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA N 16 " --> pdb=" O TYR N 23 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS N 14 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU N 15 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 29 through 32 removed outlier: 4.445A pdb=" N ASP N 32 " --> pdb=" O MET N 37 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET N 37 " --> pdb=" O ASP N 32 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 244 through 246 Processing sheet with id=AB7, first strand: chain 'K' and resid 756 through 757 Processing sheet with id=AB8, first strand: chain 'K' and resid 975 through 978 Processing sheet with id=AB9, first strand: chain 'L' and resid 63 through 64 removed outlier: 7.942A pdb=" N TYR L 64 " --> pdb=" O VAL L 21 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N TYR L 23 " --> pdb=" O TYR L 64 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA L 142 " --> pdb=" O VAL L 307 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL L 267 " --> pdb=" O MET L 306 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL L 308 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU L 269 " --> pdb=" O VAL L 308 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU L 181 " --> pdb=" O VAL L 268 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLN L 270 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE L 183 " --> pdb=" O GLN L 270 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL L 234 " --> pdb=" O VAL L 203 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR L 205 " --> pdb=" O VAL L 234 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL L 236 " --> pdb=" O THR L 205 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER L 207 " --> pdb=" O VAL L 236 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU L 238 " --> pdb=" O SER L 207 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N HIS L 209 " --> pdb=" O LEU L 238 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 262 through 263 Processing sheet with id=AC2, first strand: chain 'O' and resid 272 through 274 Processing sheet with id=AC3, first strand: chain 'P' and resid 245 through 246 1037 hydrogen bonds defined for protein. 3030 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 388 hydrogen bonds 776 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 238 stacking parallelities Total time for adding SS restraints: 6.24 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3991 1.31 - 1.44: 9051 1.44 - 1.56: 14923 1.56 - 1.69: 634 1.69 - 1.81: 120 Bond restraints: 28719 Sorted by residual: bond pdb=" CA VAL M 452 " pdb=" C VAL M 452 " ideal model delta sigma weight residual 1.525 1.455 0.070 8.10e-03 1.52e+04 7.49e+01 bond pdb=" CA ASP L 403 " pdb=" C ASP L 403 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.32e-02 5.74e+03 2.39e+01 bond pdb=" CA CYS M 466 " pdb=" C CYS M 466 " ideal model delta sigma weight residual 1.528 1.471 0.057 1.18e-02 7.18e+03 2.33e+01 bond pdb=" CA LEU L 401 " pdb=" C LEU L 401 " ideal model delta sigma weight residual 1.522 1.476 0.047 1.20e-02 6.94e+03 1.52e+01 bond pdb=" C3' DC I 8 " pdb=" O3' DC I 8 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.50e+01 ... (remaining 28714 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 39958 3.52 - 7.03: 234 7.03 - 10.55: 32 10.55 - 14.07: 9 14.07 - 17.59: 1 Bond angle restraints: 40234 Sorted by residual: angle pdb=" N VAL M 452 " pdb=" CA VAL M 452 " pdb=" C VAL M 452 " ideal model delta sigma weight residual 107.77 90.18 17.59 1.12e+00 7.97e-01 2.47e+02 angle pdb=" N VAL E 46 " pdb=" CA VAL E 46 " pdb=" C VAL E 46 " ideal model delta sigma weight residual 111.81 102.06 9.75 8.60e-01 1.35e+00 1.29e+02 angle pdb=" N PRO O 289 " pdb=" CA PRO O 289 " pdb=" C PRO O 289 " ideal model delta sigma weight residual 110.70 98.40 12.30 1.22e+00 6.72e-01 1.02e+02 angle pdb=" N ALA A 21 " pdb=" CA ALA A 21 " pdb=" C ALA A 21 " ideal model delta sigma weight residual 112.45 99.54 12.91 1.39e+00 5.18e-01 8.63e+01 angle pdb=" C VAL M 452 " pdb=" N PRO M 453 " pdb=" CA PRO M 453 " ideal model delta sigma weight residual 119.76 110.38 9.38 1.03e+00 9.43e-01 8.30e+01 ... (remaining 40229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 14728 35.51 - 71.01: 1647 71.01 - 106.52: 59 106.52 - 142.02: 4 142.02 - 177.53: 3 Dihedral angle restraints: 16441 sinusoidal: 8273 harmonic: 8168 Sorted by residual: dihedral pdb=" C VAL M 452 " pdb=" N VAL M 452 " pdb=" CA VAL M 452 " pdb=" CB VAL M 452 " ideal model delta harmonic sigma weight residual -122.00 -104.42 -17.58 0 2.50e+00 1.60e-01 4.94e+01 dihedral pdb=" C ASN K1081 " pdb=" N ASN K1081 " pdb=" CA ASN K1081 " pdb=" CB ASN K1081 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.03e+01 dihedral pdb=" CA MET K 765 " pdb=" C MET K 765 " pdb=" N PRO K 766 " pdb=" CA PRO K 766 " ideal model delta harmonic sigma weight residual -180.00 -155.17 -24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 16438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4182 0.089 - 0.178: 331 0.178 - 0.267: 9 0.267 - 0.357: 1 0.357 - 0.446: 2 Chirality restraints: 4525 Sorted by residual: chirality pdb=" CA ASN K1081 " pdb=" N ASN K1081 " pdb=" C ASN K1081 " pdb=" CB ASN K1081 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA VAL M 452 " pdb=" N VAL M 452 " pdb=" C VAL M 452 " pdb=" CB VAL M 452 " both_signs ideal model delta sigma weight residual False 2.44 2.81 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA ASP L 407 " pdb=" N ASP L 407 " pdb=" C ASP L 407 " pdb=" CB ASP L 407 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 4522 not shown) Planarity restraints: 4082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS M 107 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C LYS M 107 " 0.064 2.00e-02 2.50e+03 pdb=" O LYS M 107 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL M 108 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP O 288 " -0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO O 289 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO O 289 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO O 289 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP M 105 " 0.014 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C ASP M 105 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP M 105 " 0.017 2.00e-02 2.50e+03 pdb=" N SER M 106 " 0.016 2.00e-02 2.50e+03 ... (remaining 4079 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 138 2.54 - 3.13: 22569 3.13 - 3.72: 46412 3.72 - 4.31: 61515 4.31 - 4.90: 93024 Nonbonded interactions: 223658 Sorted by model distance: nonbonded pdb=" OD2 ASP L 186 " pdb="ZN ZN L 501 " model vdw 1.954 2.230 nonbonded pdb=" OD2 ASP L 274 " pdb="ZN ZN L 501 " model vdw 1.981 2.230 nonbonded pdb=" OD1 ASP L 186 " pdb="ZN ZN L 501 " model vdw 2.232 2.230 nonbonded pdb=" O ILE M 54 " pdb=" OG1 THR M 55 " model vdw 2.297 3.040 nonbonded pdb=" O LYS A 9 " pdb=" OG SER A 10 " model vdw 2.301 3.040 ... (remaining 223653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 22 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 29 or (resid 30 through 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 35 or (res \ id 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ gh 50 or (resid 51 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 52 th \ rough 61 or (resid 62 and (name N or name CA or name C or name O or name CB )) o \ r resid 63 through 64 or (resid 65 through 67 and (name N or name CA or name C o \ r name O or name CB )) or resid 68 through 77 or (resid 78 through 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 or (resid 82 through \ 83 and (name N or name CA or name C or name O or name CB )) or resid 84 or (resi \ d 85 and (name N or name CA or name C or name O or name CB )) or resid 86 throug \ h 101)) selection = (chain 'F' and (resid 22 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 34 or (resid 35 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1)) or resid 36 through 44 or (resid 45 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 70 or (resid 71 and (n \ ame N or name CA or name C or name O or name CB )) or resid 72 or (resid 73 and \ (name N or name CA or name C or name O or name CB )) or resid 74 through 90 or ( \ resid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 th \ rough 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) o \ r resid 98 through 99 or (resid 100 and (name N or name CA or name C or name O o \ r name CB )) or resid 101)) } ncs_group { reference = (chain 'C' and (resid 12 through 15 or (resid 16 and (name N or name CA or name \ C or name O )) or resid 17 through 24 or (resid 25 and (name N or name CA or nam \ e C or name O or name CB )) or resid 26 through 35 or (resid 36 and (name N or n \ ame CA or name C or name O or name CB )) or resid 37 through 40 or (resid 41 and \ (name N or name CA or name C or name O or name CB )) or resid 42 through 55 or \ (resid 56 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1)) or resid 57 or (resid 58 through 60 and (name N or name CA o \ r name C or name O or name CB )) or resid 61 through 62 or (resid 63 and (name N \ or name CA or name C or name O or name CB )) or resid 64 through 76 or (resid 7 \ 7 through 78 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 9 through 80 or (resid 81 and (name N or name CA or name C or name O or name CB \ )) or resid 82 through 84 or (resid 85 through 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 89 or (resid 90 and (name N or na \ me CA or name C or name O or name CB )) or resid 91 through 94 or (resid 95 and \ (name N or name CA or name C or name O or name CB )) or resid 96 through 114 or \ (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 116 \ through 117)) selection = (chain 'G' and (resid 12 through 32 or (resid 33 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 48 or (resid 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 58 or (res \ id 59 through 60 and (name N or name CA or name C or name O or name CB )) or res \ id 61 through 77 or (resid 78 and (name N or name CA or name C or name O or name \ CB )) or resid 79 through 86 or (resid 87 and (name N or name CA or name C or n \ ame O or name CB )) or resid 88 through 100 or (resid 101 and (name N or name CA \ or name C or name O or name CB )) or resid 102 through 117)) } ncs_group { reference = (chain 'D' and ((resid 33 through 40 and (name N or name CA or name C or name O \ or name CB )) or resid 41 through 53 or (resid 54 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 or (resid 57 through 61 and (n \ ame N or name CA or name C or name O or name CB )) or resid 62 through 84 or (re \ sid 85 and (name N or name CA or name C or name O or name CB )) or resid 86 or ( \ resid 87 through 90 and (name N or name CA or name C or name O or name CB )) or \ resid 91 through 121)) selection = (chain 'H' and (resid 33 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 59 or (resid 60 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 64 or (res \ id 65 and (name N or name CA or name C or name O or name CB )) or resid 66 throu \ gh 83 or (resid 84 through 85 and (name N or name CA or name C or name O or name \ CB )) or resid 86 through 87 or (resid 88 through 90 and (name N or name CA or \ name C or name O or name CB )) or resid 91 through 111 or (resid 112 and (name N \ or name CA or name C or name O or name CB )) or resid 113 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 29.080 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 28720 Z= 0.522 Angle : 0.892 17.587 40234 Z= 0.678 Chirality : 0.048 0.446 4525 Planarity : 0.005 0.080 4082 Dihedral : 23.521 177.526 11145 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.94 % Favored : 95.98 % Rotamer: Outliers : 0.20 % Allowed : 2.06 % Favored : 97.74 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.15), residues: 2738 helix: -1.46 (0.13), residues: 1453 sheet: -0.57 (0.50), residues: 117 loop : -1.29 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 564 TYR 0.030 0.002 TYR N 373 PHE 0.038 0.002 PHE P 374 TRP 0.012 0.001 TRP K 719 HIS 0.006 0.001 HIS P 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.52 (28719) covalent geometry : angle 0.89153 / 0.68 (40234) hydrogen bonds : bond 0.24122 / 16.40 ( 1425) hydrogen bonds : angle 8.34807 / 5.97 ( 3806) metal coordination : bond 0.00389 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 458 time to evaluate : 0.916 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: M 366 THR cc_start: 0.8405 (m) cc_final: 0.8163 (p) REVERT: N 107 MET cc_start: 0.5370 (ppp) cc_final: 0.4609 (tmm) REVERT: N 346 THR cc_start: 0.6769 (p) cc_final: 0.6407 (p) REVERT: L 207 SER cc_start: 0.9271 (t) cc_final: 0.9056 (p) REVERT: O 300 ASP cc_start: 0.6787 (m-30) cc_final: 0.6428 (t70) REVERT: P 348 ASP cc_start: 0.6625 (p0) cc_final: 0.6391 (t0) REVERT: P 401 MET cc_start: 0.6483 (mmm) cc_final: 0.6145 (mtm) outliers start: 4 outliers final: 2 residues processed: 459 average time/residue: 0.1913 time to fit residues: 133.1935 Evaluate side-chains 230 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 228 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 23 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 0.0670 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0470 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.0970 overall best weight: 1.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN F 25 ASN F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 79 HIS M 388 ASN ** M 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 277 GLN N 358 GLN K 961 ASN ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.094454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.070288 restraints weight = 122754.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.071221 restraints weight = 66876.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.071342 restraints weight = 44574.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.071508 restraints weight = 41760.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.071569 restraints weight = 37578.587| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 28720 Z= 0.178 Angle : 0.705 10.730 40234 Z= 0.398 Chirality : 0.046 0.336 4525 Planarity : 0.005 0.053 4082 Dihedral : 26.935 169.527 6447 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.52 % Rotamer: Outliers : 2.06 % Allowed : 10.65 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.15), residues: 2738 helix: -0.08 (0.13), residues: 1521 sheet: -0.65 (0.49), residues: 117 loop : -1.20 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 95 TYR 0.030 0.002 TYR P 261 PHE 0.030 0.002 PHE K1026 TRP 0.013 0.001 TRP N 31 HIS 0.009 0.001 HIS O 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (28719) covalent geometry : angle 0.70457 / 0.40 (40234) hydrogen bonds : bond 0.06564 / 4.38 ( 1425) hydrogen bonds : angle 4.80752 / 3.39 ( 3806) metal coordination : bond 0.00163 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 255 time to evaluate : 0.919 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7151 (mmtt) cc_final: 0.6781 (mmtt) REVERT: B 95 ARG cc_start: 0.6995 (ttt180) cc_final: 0.6768 (ttt180) REVERT: B 96 THR cc_start: 0.7650 (m) cc_final: 0.7181 (p) REVERT: C 89 ASN cc_start: 0.8017 (p0) cc_final: 0.7759 (p0) REVERT: G 99 ARG cc_start: 0.7355 (mtm180) cc_final: 0.7092 (mtp-110) REVERT: H 69 ARG cc_start: 0.7875 (ttt-90) cc_final: 0.7432 (mtp85) REVERT: H 70 ILE cc_start: 0.9104 (mm) cc_final: 0.8761 (tt) REVERT: N 123 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7185 (mt) REVERT: N 262 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8201 (pp20) REVERT: L 74 MET cc_start: 0.9043 (mtp) cc_final: 0.8639 (mtp) REVERT: L 288 MET cc_start: 0.8341 (ttp) cc_final: 0.8049 (tmm) REVERT: O 300 ASP cc_start: 0.7120 (m-30) cc_final: 0.6675 (t70) REVERT: O 327 ILE cc_start: 0.9068 (mp) cc_final: 0.8846 (mm) REVERT: P 357 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8639 (tptt) outliers start: 42 outliers final: 17 residues processed: 282 average time/residue: 0.1861 time to fit residues: 81.1633 Evaluate side-chains 230 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 262 GLU Chi-restraints excluded: chain N residue 276 SER Chi-restraints excluded: chain K residue 702 LEU Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain O residue 575 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 195 optimal weight: 4.9990 chunk 88 optimal weight: 50.0000 chunk 175 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 98 optimal weight: 30.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN H 106 HIS M 67 HIS ** M 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 510 GLN K 930 HIS K1221 HIS O 583 GLN ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.090552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.065568 restraints weight = 122208.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.066257 restraints weight = 69937.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.066173 restraints weight = 51453.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.066358 restraints weight = 46558.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066416 restraints weight = 41209.510| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 28720 Z= 0.257 Angle : 0.732 11.487 40234 Z= 0.404 Chirality : 0.047 0.296 4525 Planarity : 0.005 0.051 4082 Dihedral : 27.020 168.842 6443 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.36 % Allowed : 13.35 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.15), residues: 2738 helix: 0.38 (0.13), residues: 1524 sheet: -0.78 (0.48), residues: 116 loop : -1.11 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 110 TYR 0.037 0.003 TYR D 80 PHE 0.022 0.002 PHE O 336 TRP 0.010 0.002 TRP M 464 HIS 0.010 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.26 (28719) covalent geometry : angle 0.73163 / 0.40 (40234) hydrogen bonds : bond 0.06366 / 4.25 ( 1425) hydrogen bonds : angle 4.43474 / 3.11 ( 3806) metal coordination : bond 0.01562 / 0.82 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 0.865 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 9 LYS cc_start: 0.7011 (mmtt) cc_final: 0.6811 (mmtt) REVERT: A 18 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8221 (pttm) REVERT: A 81 ASP cc_start: 0.7204 (t0) cc_final: 0.6986 (t0) REVERT: B 59 LYS cc_start: 0.9161 (tppt) cc_final: 0.8899 (mmtm) REVERT: B 67 ARG cc_start: 0.8875 (ttp80) cc_final: 0.8531 (ttp80) REVERT: B 96 THR cc_start: 0.7601 (m) cc_final: 0.7166 (p) REVERT: G 38 ASN cc_start: 0.6435 (t0) cc_final: 0.5417 (p0) REVERT: G 104 GLN cc_start: 0.8102 (mt0) cc_final: 0.7457 (tm-30) REVERT: H 69 ARG cc_start: 0.7878 (ttt-90) cc_final: 0.7461 (mtp85) REVERT: N 262 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8366 (pp20) REVERT: K 860 MET cc_start: 0.8511 (mmt) cc_final: 0.8227 (mmt) REVERT: L 74 MET cc_start: 0.9196 (mtp) cc_final: 0.8824 (mtp) REVERT: L 288 MET cc_start: 0.8707 (ttp) cc_final: 0.8171 (tmm) outliers start: 48 outliers final: 24 residues processed: 250 average time/residue: 0.1969 time to fit residues: 76.2010 Evaluate side-chains 216 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 262 GLU Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain K residue 1256 LEU Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain O residue 364 VAL Chi-restraints excluded: chain P residue 264 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 63 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 chunk 174 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 93 optimal weight: 50.0000 chunk 13 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN M 388 ASN M 444 GLN K 824 ASN L 177 HIS L 231 ASN O 346 HIS ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.089907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.064554 restraints weight = 122153.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.065302 restraints weight = 70915.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.065266 restraints weight = 49497.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.065492 restraints weight = 44566.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.065517 restraints weight = 40592.992| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28720 Z= 0.241 Angle : 0.686 10.636 40234 Z= 0.380 Chirality : 0.045 0.278 4525 Planarity : 0.004 0.052 4082 Dihedral : 27.000 170.807 6442 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.65 % Allowed : 16.05 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 2738 helix: 0.55 (0.13), residues: 1526 sheet: -0.88 (0.48), residues: 115 loop : -1.08 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 95 TYR 0.029 0.002 TYR D 80 PHE 0.025 0.002 PHE K1026 TRP 0.018 0.002 TRP M 464 HIS 0.013 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.24 (28719) covalent geometry : angle 0.68573 / 0.38 (40234) hydrogen bonds : bond 0.05517 / 3.67 ( 1425) hydrogen bonds : angle 4.27544 / 3.00 ( 3806) metal coordination : bond 0.00616 / 0.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 201 time to evaluate : 0.963 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 18 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8422 (pttm) REVERT: B 59 LYS cc_start: 0.9234 (tppt) cc_final: 0.9006 (tppt) REVERT: B 67 ARG cc_start: 0.8775 (ttp80) cc_final: 0.8460 (ttp80) REVERT: G 38 ASN cc_start: 0.6316 (t0) cc_final: 0.5460 (p0) REVERT: G 99 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.6570 (mtt-85) REVERT: G 104 GLN cc_start: 0.8198 (mt0) cc_final: 0.7431 (tm-30) REVERT: H 69 ARG cc_start: 0.7857 (ttt-90) cc_final: 0.7512 (mtp85) REVERT: N 123 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7275 (mt) REVERT: N 262 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8486 (pp20) REVERT: K 860 MET cc_start: 0.8632 (mmt) cc_final: 0.8403 (mmt) REVERT: L 74 MET cc_start: 0.9182 (mtp) cc_final: 0.8893 (mtp) REVERT: L 288 MET cc_start: 0.8702 (ttp) cc_final: 0.8173 (tmm) REVERT: O 327 ILE cc_start: 0.9119 (mp) cc_final: 0.8910 (mm) outliers start: 54 outliers final: 38 residues processed: 237 average time/residue: 0.1872 time to fit residues: 69.1993 Evaluate side-chains 226 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain M residue 379 ILE Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 262 GLU Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain K residue 824 ASN Chi-restraints excluded: chain K residue 861 THR Chi-restraints excluded: chain K residue 957 VAL Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain O residue 346 HIS Chi-restraints excluded: chain O residue 364 VAL Chi-restraints excluded: chain P residue 264 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 204 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 283 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 92 GLN M 388 ASN ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.089680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.063983 restraints weight = 121306.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.065439 restraints weight = 67174.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.065591 restraints weight = 41943.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.065932 restraints weight = 38176.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.065920 restraints weight = 35470.291| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28720 Z= 0.188 Angle : 0.641 10.747 40234 Z= 0.356 Chirality : 0.043 0.256 4525 Planarity : 0.004 0.047 4082 Dihedral : 26.946 172.004 6442 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.75 % Allowed : 16.99 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2738 helix: 0.77 (0.13), residues: 1531 sheet: -0.98 (0.46), residues: 115 loop : -1.03 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 110 TYR 0.026 0.002 TYR D 80 PHE 0.013 0.001 PHE O 361 TRP 0.011 0.001 TRP K 782 HIS 0.019 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (28719) covalent geometry : angle 0.64115 / 0.36 (40234) hydrogen bonds : bond 0.05135 / 3.43 ( 1425) hydrogen bonds : angle 4.07598 / 2.85 ( 3806) metal coordination : bond 0.00534 / 0.28 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 0.932 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 124 ILE cc_start: 0.9092 (mm) cc_final: 0.8820 (tp) REVERT: B 67 ARG cc_start: 0.8786 (ttp80) cc_final: 0.8462 (ttp80) REVERT: B 96 THR cc_start: 0.7455 (m) cc_final: 0.7070 (p) REVERT: F 53 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8507 (tm-30) REVERT: G 38 ASN cc_start: 0.6341 (t0) cc_final: 0.5641 (p0) REVERT: G 99 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.6718 (mtt-85) REVERT: G 104 GLN cc_start: 0.8171 (mt0) cc_final: 0.7406 (tm-30) REVERT: N 123 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7238 (mt) REVERT: N 262 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8464 (pp20) REVERT: N 304 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8467 (tt) REVERT: L 74 MET cc_start: 0.9212 (mtp) cc_final: 0.8948 (mtp) REVERT: L 288 MET cc_start: 0.8683 (ttp) cc_final: 0.8173 (tmm) REVERT: O 327 ILE cc_start: 0.9128 (mp) cc_final: 0.8889 (mm) outliers start: 56 outliers final: 35 residues processed: 239 average time/residue: 0.1907 time to fit residues: 70.9738 Evaluate side-chains 224 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain M residue 379 ILE Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 262 GLU Chi-restraints excluded: chain N residue 304 LEU Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain K residue 957 VAL Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain O residue 333 VAL Chi-restraints excluded: chain O residue 346 HIS Chi-restraints excluded: chain O residue 364 VAL Chi-restraints excluded: chain P residue 264 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 183 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 284 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 103 optimal weight: 30.0000 chunk 275 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 255 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** M 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 824 ASN L 144 ASN L 235 ASN O 346 HIS P 267 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.088963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.063797 restraints weight = 120972.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.063874 restraints weight = 74722.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.064210 restraints weight = 54064.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.064327 restraints weight = 47633.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.064393 restraints weight = 43412.141| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 28720 Z= 0.240 Angle : 0.678 10.717 40234 Z= 0.374 Chirality : 0.045 0.316 4525 Planarity : 0.004 0.047 4082 Dihedral : 26.979 172.867 6442 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.29 % Allowed : 17.62 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.16), residues: 2738 helix: 0.71 (0.13), residues: 1527 sheet: -1.27 (0.45), residues: 115 loop : -1.03 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 8 TYR 0.023 0.002 TYR D 80 PHE 0.016 0.002 PHE H 67 TRP 0.014 0.001 TRP M 464 HIS 0.014 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.24 (28719) covalent geometry : angle 0.67845 / 0.37 (40234) hydrogen bonds : bond 0.05435 / 3.62 ( 1425) hydrogen bonds : angle 4.18529 / 2.93 ( 3806) metal coordination : bond 0.00758 / 0.40 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 188 time to evaluate : 0.981 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 124 ILE cc_start: 0.9120 (mm) cc_final: 0.8894 (tp) REVERT: B 96 THR cc_start: 0.7521 (m) cc_final: 0.7130 (p) REVERT: D 56 MET cc_start: 0.8289 (tpp) cc_final: 0.8019 (tpp) REVERT: F 53 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8483 (tm-30) REVERT: G 38 ASN cc_start: 0.6194 (t0) cc_final: 0.5551 (p0) REVERT: G 99 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.6732 (mtt-85) REVERT: G 104 GLN cc_start: 0.8242 (mt0) cc_final: 0.7487 (tm-30) REVERT: H 69 ARG cc_start: 0.7775 (ttt-90) cc_final: 0.7495 (mtp85) REVERT: N 123 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7285 (mt) REVERT: N 262 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8450 (pp20) REVERT: N 304 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8530 (tt) REVERT: L 6 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.8942 (p) REVERT: L 74 MET cc_start: 0.9249 (mtp) cc_final: 0.8958 (mtp) REVERT: L 288 MET cc_start: 0.8721 (ttp) cc_final: 0.8142 (tmm) REVERT: O 327 ILE cc_start: 0.9194 (mp) cc_final: 0.8945 (mm) outliers start: 67 outliers final: 46 residues processed: 234 average time/residue: 0.1918 time to fit residues: 70.5782 Evaluate side-chains 228 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain M residue 379 ILE Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 262 GLU Chi-restraints excluded: chain N residue 304 LEU Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain K residue 861 THR Chi-restraints excluded: chain K residue 902 ASP Chi-restraints excluded: chain K residue 957 VAL Chi-restraints excluded: chain K residue 1130 ILE Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain K residue 1255 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain O residue 333 VAL Chi-restraints excluded: chain O residue 346 HIS Chi-restraints excluded: chain O residue 364 VAL Chi-restraints excluded: chain O residue 560 MET Chi-restraints excluded: chain P residue 264 GLU Chi-restraints excluded: chain P residue 356 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 175 optimal weight: 0.7980 chunk 145 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 69 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 93 optimal weight: 50.0000 chunk 270 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 92 GLN ** M 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 346 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.089004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.063746 restraints weight = 121349.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.064289 restraints weight = 70474.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.064316 restraints weight = 50954.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.064414 restraints weight = 46581.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.064529 restraints weight = 42791.752| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28720 Z= 0.201 Angle : 0.641 11.307 40234 Z= 0.356 Chirality : 0.043 0.241 4525 Planarity : 0.004 0.046 4082 Dihedral : 26.948 173.751 6442 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.60 % Allowed : 18.56 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.16), residues: 2738 helix: 0.84 (0.13), residues: 1524 sheet: -1.43 (0.45), residues: 116 loop : -1.07 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 32 TYR 0.021 0.002 TYR K 675 PHE 0.016 0.002 PHE P 362 TRP 0.010 0.001 TRP K1223 HIS 0.027 0.001 HIS O 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (28719) covalent geometry : angle 0.64119 / 0.36 (40234) hydrogen bonds : bond 0.05050 / 3.38 ( 1425) hydrogen bonds : angle 4.04721 / 2.83 ( 3806) metal coordination : bond 0.00555 / 0.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 0.984 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 124 ILE cc_start: 0.9059 (mm) cc_final: 0.8856 (tp) REVERT: B 96 THR cc_start: 0.7453 (m) cc_final: 0.7036 (p) REVERT: D 56 MET cc_start: 0.8065 (tpp) cc_final: 0.7764 (tpp) REVERT: D 102 GLU cc_start: 0.7416 (tm-30) cc_final: 0.7187 (tm-30) REVERT: E 120 MET cc_start: 0.8062 (mtp) cc_final: 0.7787 (mtm) REVERT: F 23 ARG cc_start: 0.6086 (tpt170) cc_final: 0.5850 (tpt90) REVERT: F 53 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8422 (tm-30) REVERT: G 35 ARG cc_start: 0.8171 (tpp80) cc_final: 0.7916 (ttm-80) REVERT: G 38 ASN cc_start: 0.6131 (t0) cc_final: 0.5728 (p0) REVERT: G 99 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6795 (mtt-85) REVERT: G 104 GLN cc_start: 0.8147 (mt0) cc_final: 0.7405 (tm-30) REVERT: H 69 ARG cc_start: 0.7802 (ttt-90) cc_final: 0.7492 (mtp85) REVERT: N 304 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8553 (tt) REVERT: K 1194 MET cc_start: 0.8976 (mtp) cc_final: 0.8726 (mtm) REVERT: L 74 MET cc_start: 0.9213 (mtp) cc_final: 0.8935 (mtp) REVERT: L 288 MET cc_start: 0.8699 (ttp) cc_final: 0.8152 (tmm) REVERT: O 327 ILE cc_start: 0.9186 (mp) cc_final: 0.8934 (mm) outliers start: 53 outliers final: 39 residues processed: 219 average time/residue: 0.2083 time to fit residues: 70.2885 Evaluate side-chains 227 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain M residue 379 ILE Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain N residue 304 LEU Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain K residue 902 ASP Chi-restraints excluded: chain K residue 957 VAL Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain O residue 333 VAL Chi-restraints excluded: chain O residue 364 VAL Chi-restraints excluded: chain O residue 560 MET Chi-restraints excluded: chain P residue 356 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 79 optimal weight: 30.0000 chunk 150 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 49 optimal weight: 0.1980 chunk 270 optimal weight: 3.9990 chunk 273 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** M 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 295 ASN K1132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.088523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.063170 restraints weight = 121413.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.063881 restraints weight = 69828.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.064032 restraints weight = 49232.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.064079 restraints weight = 45961.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.064107 restraints weight = 40259.857| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28720 Z= 0.224 Angle : 0.666 10.788 40234 Z= 0.367 Chirality : 0.044 0.251 4525 Planarity : 0.004 0.047 4082 Dihedral : 26.945 174.427 6442 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.36 % Allowed : 19.29 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.16), residues: 2738 helix: 0.86 (0.13), residues: 1522 sheet: -1.52 (0.45), residues: 116 loop : -1.07 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 32 TYR 0.021 0.002 TYR P 238 PHE 0.017 0.002 PHE H 67 TRP 0.012 0.001 TRP K1223 HIS 0.012 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 (28719) covalent geometry : angle 0.66557 / 0.37 (40234) hydrogen bonds : bond 0.05214 / 3.49 ( 1425) hydrogen bonds : angle 4.09458 / 2.86 ( 3806) metal coordination : bond 0.00705 / 0.37 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.900 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: A 100 LEU cc_start: 0.9393 (mm) cc_final: 0.9189 (mp) REVERT: A 122 LYS cc_start: 0.8817 (tptp) cc_final: 0.8604 (ptpp) REVERT: B 96 THR cc_start: 0.7538 (m) cc_final: 0.6966 (t) REVERT: D 56 MET cc_start: 0.7795 (tpp) cc_final: 0.7497 (tpp) REVERT: D 102 GLU cc_start: 0.7448 (tm-30) cc_final: 0.6745 (tm-30) REVERT: E 120 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7781 (mtm) REVERT: F 53 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8418 (tm-30) REVERT: G 38 ASN cc_start: 0.6117 (t0) cc_final: 0.5733 (p0) REVERT: G 99 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.6826 (mtt-85) REVERT: G 104 GLN cc_start: 0.8216 (mt0) cc_final: 0.7435 (tm-30) REVERT: H 69 ARG cc_start: 0.7939 (ttt-90) cc_final: 0.7590 (mtp85) REVERT: N 88 TRP cc_start: 0.4442 (t-100) cc_final: 0.4214 (t-100) REVERT: N 304 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8538 (tt) REVERT: K 1194 MET cc_start: 0.9056 (mtp) cc_final: 0.8818 (mtm) REVERT: L 6 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.8953 (p) REVERT: L 74 MET cc_start: 0.9245 (mtp) cc_final: 0.8963 (mtp) REVERT: L 288 MET cc_start: 0.8739 (ttp) cc_final: 0.8155 (tmm) outliers start: 48 outliers final: 38 residues processed: 221 average time/residue: 0.1970 time to fit residues: 68.3030 Evaluate side-chains 228 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain M residue 379 ILE Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain N residue 304 LEU Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain K residue 861 THR Chi-restraints excluded: chain K residue 902 ASP Chi-restraints excluded: chain K residue 957 VAL Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain O residue 333 VAL Chi-restraints excluded: chain O residue 364 VAL Chi-restraints excluded: chain O residue 560 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 246 optimal weight: 0.8980 chunk 90 optimal weight: 50.0000 chunk 174 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 chunk 79 optimal weight: 30.0000 chunk 15 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 271 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 265 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS E 108 ASN G 94 ASN H 92 GLN ** M 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.089529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.065224 restraints weight = 122510.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.065100 restraints weight = 70758.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.065563 restraints weight = 52911.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.065549 restraints weight = 47713.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.065591 restraints weight = 42339.058| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28720 Z= 0.136 Angle : 0.617 11.001 40234 Z= 0.341 Chirality : 0.042 0.335 4525 Planarity : 0.004 0.044 4082 Dihedral : 26.845 175.436 6442 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.96 % Allowed : 19.54 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.16), residues: 2738 helix: 1.05 (0.13), residues: 1514 sheet: -1.37 (0.45), residues: 116 loop : -0.93 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 32 TYR 0.023 0.001 TYR P 238 PHE 0.019 0.001 PHE P 362 TRP 0.012 0.001 TRP K 782 HIS 0.011 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (28719) covalent geometry : angle 0.61687 / 0.34 (40234) hydrogen bonds : bond 0.04591 / 3.11 ( 1425) hydrogen bonds : angle 3.87056 / 2.69 ( 3806) metal coordination : bond 0.00186 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 0.977 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 100 LEU cc_start: 0.9386 (mm) cc_final: 0.9139 (mp) REVERT: B 96 THR cc_start: 0.7179 (m) cc_final: 0.6812 (p) REVERT: D 56 MET cc_start: 0.7695 (tpp) cc_final: 0.7439 (tpp) REVERT: D 68 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8264 (tm-30) REVERT: F 23 ARG cc_start: 0.6165 (tpt170) cc_final: 0.5937 (tpt90) REVERT: F 53 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8367 (tm-30) REVERT: G 35 ARG cc_start: 0.7888 (ttm-80) cc_final: 0.7552 (ttm-80) REVERT: G 99 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.6751 (mtt-85) REVERT: G 104 GLN cc_start: 0.8178 (mt0) cc_final: 0.7423 (tm-30) REVERT: H 69 ARG cc_start: 0.7930 (ttt-90) cc_final: 0.7570 (mtp85) REVERT: L 74 MET cc_start: 0.9049 (mtp) cc_final: 0.8843 (mtp) REVERT: L 288 MET cc_start: 0.8611 (ttp) cc_final: 0.8116 (tmm) REVERT: O 305 GLU cc_start: 0.8643 (tp30) cc_final: 0.8207 (tm-30) REVERT: O 327 ILE cc_start: 0.9214 (mp) cc_final: 0.8963 (mm) outliers start: 40 outliers final: 29 residues processed: 224 average time/residue: 0.1969 time to fit residues: 68.9988 Evaluate side-chains 214 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain M residue 379 ILE Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain K residue 860 MET Chi-restraints excluded: chain K residue 902 ASP Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain O residue 364 VAL Chi-restraints excluded: chain O residue 560 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 235 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 257 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN G 38 ASN ** M 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.089384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.064347 restraints weight = 121886.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.065190 restraints weight = 69508.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.065701 restraints weight = 45508.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.065596 restraints weight = 40012.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.065690 restraints weight = 36936.405| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28720 Z= 0.142 Angle : 0.618 11.337 40234 Z= 0.340 Chirality : 0.042 0.259 4525 Planarity : 0.004 0.058 4082 Dihedral : 26.787 175.677 6442 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.91 % Allowed : 20.08 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.16), residues: 2738 helix: 1.13 (0.13), residues: 1520 sheet: -1.27 (0.48), residues: 107 loop : -0.93 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 32 TYR 0.023 0.001 TYR P 238 PHE 0.020 0.001 PHE H 67 TRP 0.010 0.001 TRP K 782 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (28719) covalent geometry : angle 0.61799 / 0.34 (40234) hydrogen bonds : bond 0.04588 / 3.11 ( 1425) hydrogen bonds : angle 3.82643 / 2.66 ( 3806) metal coordination : bond 0.00287 / 0.15 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.969 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 100 LEU cc_start: 0.9367 (mm) cc_final: 0.9144 (mp) REVERT: B 96 THR cc_start: 0.7181 (m) cc_final: 0.6833 (p) REVERT: D 56 MET cc_start: 0.7828 (tpp) cc_final: 0.7569 (tpp) REVERT: D 68 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8214 (tm-30) REVERT: F 23 ARG cc_start: 0.6140 (tpt170) cc_final: 0.5923 (tpt90) REVERT: F 53 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8373 (tm-30) REVERT: G 99 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.6624 (mtt-85) REVERT: G 104 GLN cc_start: 0.8206 (mt0) cc_final: 0.7402 (tm-30) REVERT: H 69 ARG cc_start: 0.7892 (ttt-90) cc_final: 0.7529 (mtp85) REVERT: K 757 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8439 (ttm170) REVERT: K 1194 MET cc_start: 0.9070 (mtp) cc_final: 0.8822 (mtm) REVERT: L 6 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8890 (p) REVERT: L 74 MET cc_start: 0.9080 (mtp) cc_final: 0.8865 (mtp) REVERT: L 288 MET cc_start: 0.8627 (ttp) cc_final: 0.8107 (tmm) REVERT: O 327 ILE cc_start: 0.9206 (mp) cc_final: 0.8973 (mm) outliers start: 39 outliers final: 28 residues processed: 215 average time/residue: 0.2005 time to fit residues: 67.7021 Evaluate side-chains 211 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain M residue 379 ILE Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain K residue 757 ARG Chi-restraints excluded: chain K residue 902 ASP Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain O residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 200 optimal weight: 0.9990 chunk 283 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 179 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.089710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064759 restraints weight = 121007.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.065575 restraints weight = 69880.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.065805 restraints weight = 46200.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.065899 restraints weight = 41261.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.065945 restraints weight = 37251.803| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28720 Z= 0.133 Angle : 0.608 10.811 40234 Z= 0.334 Chirality : 0.042 0.244 4525 Planarity : 0.004 0.043 4082 Dihedral : 26.707 175.882 6442 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.42 % Allowed : 20.52 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.16), residues: 2738 helix: 1.23 (0.13), residues: 1530 sheet: -1.15 (0.48), residues: 107 loop : -0.85 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 92 TYR 0.026 0.001 TYR G 39 PHE 0.018 0.001 PHE P 362 TRP 0.010 0.001 TRP M 464 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (28719) covalent geometry : angle 0.60795 / 0.33 (40234) hydrogen bonds : bond 0.04428 / 3.01 ( 1425) hydrogen bonds : angle 3.74000 / 2.60 ( 3806) metal coordination : bond 0.00236 / 0.12 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4267.36 seconds wall clock time: 74 minutes 46.61 seconds (4486.61 seconds total)