Starting phenix.real_space_refine on Sat Aug 8 08:39:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iht_35455/08_2026/8iht_35455.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iht_35455/08_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_35455/08_2026/8iht_35455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iht_35455/08_2026/8iht_35455.map" model { file = "/net/cci-nas-00/data/ceres_data/8iht_35455/08_2026/8iht_35455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iht_35455/08_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-2.2rc3-6140/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, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.55, per 1000 atoms: 0.17 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: 1.67 Conformation dependent library (CDL) restraints added in 685.2 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: 3.03 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: 6.32 Time building geometry restraints manager: 2.21 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: 39955 3.52 - 7.03: 237 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: 2.280 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 25.930 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: 29.880 ------------------------------------------------------------------------------- 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 : 0.895 17.587 40234 Z= 0.682 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 0.89463 / 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 : 0.818 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: M 366 THR cc_start: 0.8405 (m) cc_final: 0.8162 (p) REVERT: N 346 THR cc_start: 0.6769 (p) cc_final: 0.6409 (p) REVERT: L 207 SER cc_start: 0.9271 (t) cc_final: 0.9055 (p) REVERT: O 300 ASP cc_start: 0.6787 (m-30) cc_final: 0.6430 (t70) REVERT: P 348 ASP cc_start: 0.6625 (p0) cc_final: 0.6389 (t0) REVERT: P 401 MET cc_start: 0.6483 (mmm) cc_final: 0.6144 (mtm) outliers start: 4 outliers final: 2 residues processed: 459 average time/residue: 0.1979 time to fit residues: 137.2311 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 : 0.807 ------------------------------------------------------------------------------- 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 H 60 ASN H 79 HIS M 388 ASN M 421 ASN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 961 ASN ** 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 = 0.3980 r_free = 0.3980 target = 0.094492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.070526 restraints weight = 123498.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.071283 restraints weight = 68625.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.071623 restraints weight = 45661.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.071721 restraints weight = 39384.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.071774 restraints weight = 36480.767| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28720 Z= 0.183 Angle : 0.707 10.352 40234 Z= 0.399 Chirality : 0.046 0.347 4525 Planarity : 0.005 0.046 4082 Dihedral : 26.884 170.912 6447 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.48 % Favored : 97.48 % Rotamer: Outliers : 1.91 % Allowed : 10.70 % Favored : 87.38 % 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: -0.09 (0.13), residues: 1524 sheet: -0.64 (0.49), residues: 117 loop : -1.20 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 95 TYR 0.028 0.002 TYR P 261 PHE 0.029 0.002 PHE K1026 TRP 0.012 0.001 TRP N 31 HIS 0.008 0.001 HIS O 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (28719) covalent geometry : angle 0.70695 / 0.40 (40234) hydrogen bonds : bond 0.06918 / 4.62 ( 1425) hydrogen bonds : angle 4.90791 / 3.46 ( 3806) metal coordination : bond 0.00156 / 0.08 ( 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 295 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 0.624 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: A 9 LYS cc_start: 0.7134 (mmtt) cc_final: 0.6771 (mmtt) REVERT: B 96 THR cc_start: 0.7663 (m) cc_final: 0.7227 (p) REVERT: C 89 ASN cc_start: 0.7875 (p0) cc_final: 0.7600 (p0) REVERT: D 83 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8516 (mtt90) REVERT: D 102 GLU cc_start: 0.7476 (tp30) cc_final: 0.7115 (tp30) REVERT: D 106 HIS cc_start: 0.8044 (m-70) cc_final: 0.7228 (m170) REVERT: H 69 ARG cc_start: 0.7955 (ttt-90) cc_final: 0.7502 (mtp85) REVERT: H 70 ILE cc_start: 0.9164 (mm) cc_final: 0.8818 (tt) REVERT: N 107 MET cc_start: 0.4949 (tmm) cc_final: 0.3828 (tmm) REVERT: N 110 ARG cc_start: 0.8632 (tmm160) cc_final: 0.8224 (tmm160) REVERT: N 123 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7165 (mt) REVERT: N 262 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8186 (pp20) REVERT: L 74 MET cc_start: 0.9050 (mtp) cc_final: 0.8693 (mtp) REVERT: L 288 MET cc_start: 0.8397 (ttp) cc_final: 0.8041 (tmm) REVERT: O 300 ASP cc_start: 0.7052 (m-30) cc_final: 0.6621 (t70) REVERT: P 357 LYS cc_start: 0.8944 (ttpp) cc_final: 0.8697 (tptt) outliers start: 39 outliers final: 15 residues processed: 283 average time/residue: 0.1568 time to fit residues: 69.2074 Evaluate side-chains 234 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 83 ARG 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 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: 0.7980 chunk 88 optimal weight: 50.0000 chunk 175 optimal weight: 4.9990 chunk 110 optimal weight: 0.4980 chunk 162 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 HIS ** K 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 346 HIS O 583 GLN ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.091667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.067269 restraints weight = 122865.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.067435 restraints weight = 73482.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.067867 restraints weight = 52061.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.067929 restraints weight = 46850.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.068050 restraints weight = 41742.290| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 28720 Z= 0.227 Angle : 0.706 10.340 40234 Z= 0.390 Chirality : 0.046 0.328 4525 Planarity : 0.005 0.051 4082 Dihedral : 26.897 168.282 6443 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.36 % Allowed : 12.81 % Favored : 84.83 % 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: -0.35 (0.15), residues: 2738 helix: 0.44 (0.13), residues: 1522 sheet: -0.73 (0.48), residues: 117 loop : -1.05 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.001 ARG C 20 TYR 0.027 0.002 TYR K 675 PHE 0.024 0.002 PHE P 374 TRP 0.011 0.002 TRP K 966 HIS 0.008 0.001 HIS O 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.23 (28719) covalent geometry : angle 0.70642 / 0.39 (40234) hydrogen bonds : bond 0.06055 / 4.05 ( 1425) hydrogen bonds : angle 4.36613 / 3.06 ( 3806) metal coordination : bond 0.01316 / 0.69 ( 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 263 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9313 (tp) cc_final: 0.9103 (tp) REVERT: B 27 GLN cc_start: 0.8254 (pp30) cc_final: 0.7941 (pp30) REVERT: B 59 LYS cc_start: 0.9226 (tppt) cc_final: 0.8889 (mmtp) REVERT: B 67 ARG cc_start: 0.8877 (ttp80) cc_final: 0.8538 (ttp80) REVERT: B 95 ARG cc_start: 0.6992 (mtt180) cc_final: 0.6756 (ttt180) REVERT: B 96 THR cc_start: 0.7971 (m) cc_final: 0.7551 (p) REVERT: D 68 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8163 (tm-30) REVERT: G 38 ASN cc_start: 0.6448 (t0) cc_final: 0.5397 (p0) REVERT: G 99 ARG cc_start: 0.7728 (mtp85) cc_final: 0.7233 (mtp-110) REVERT: G 104 GLN cc_start: 0.7962 (mt0) cc_final: 0.7380 (tm-30) REVERT: N 123 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7214 (mt) REVERT: N 262 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8330 (pp20) REVERT: K 860 MET cc_start: 0.8283 (mmt) cc_final: 0.8082 (mmt) REVERT: L 74 MET cc_start: 0.9145 (mtp) cc_final: 0.8774 (mtp) REVERT: L 288 MET cc_start: 0.8618 (ttp) cc_final: 0.8118 (tmm) outliers start: 48 outliers final: 24 residues processed: 248 average time/residue: 0.1710 time to fit residues: 66.0636 Evaluate side-chains 221 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 11 THR 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 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 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 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 L residue 276 LEU Chi-restraints excluded: chain L residue 383 THR 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: 10.0000 chunk 131 optimal weight: 0.5980 chunk 103 optimal weight: 30.0000 chunk 174 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 93 optimal weight: 50.0000 chunk 13 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 92 GLN H 106 HIS M 388 ASN K 824 ASN K1221 HIS L 231 ASN P 267 GLN ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.090536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.065180 restraints weight = 121090.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.066200 restraints weight = 68889.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.066301 restraints weight = 45753.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.066349 restraints weight = 42095.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.066452 restraints weight = 39099.320| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 28720 Z= 0.223 Angle : 0.688 15.487 40234 Z= 0.378 Chirality : 0.046 0.365 4525 Planarity : 0.004 0.050 4082 Dihedral : 26.886 170.222 6442 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.60 % Allowed : 15.46 % Favored : 81.93 % 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: -0.17 (0.16), residues: 2738 helix: 0.65 (0.13), residues: 1526 sheet: -0.81 (0.48), residues: 115 loop : -1.04 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 23 TYR 0.043 0.002 TYR D 80 PHE 0.029 0.002 PHE K1026 TRP 0.021 0.002 TRP M 464 HIS 0.006 0.001 HIS P 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.22 (28719) covalent geometry : angle 0.68793 / 0.38 (40234) hydrogen bonds : bond 0.05350 / 3.56 ( 1425) hydrogen bonds : angle 4.16470 / 2.92 ( 3806) metal coordination : bond 0.00471 / 0.25 ( 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 267 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 214 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8128 (pttm) REVERT: A 65 LEU cc_start: 0.9244 (tp) cc_final: 0.9029 (tp) REVERT: A 124 ILE cc_start: 0.9109 (mm) cc_final: 0.8884 (tp) REVERT: B 27 GLN cc_start: 0.8371 (pp30) cc_final: 0.8111 (pp30) REVERT: B 59 LYS cc_start: 0.9265 (tppt) cc_final: 0.8978 (tppt) REVERT: B 67 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8418 (ttp80) REVERT: B 74 GLU cc_start: 0.8678 (tt0) cc_final: 0.8419 (tm-30) REVERT: B 96 THR cc_start: 0.7807 (m) cc_final: 0.7382 (p) REVERT: F 53 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8553 (tm-30) REVERT: G 20 ARG cc_start: 0.5516 (ptm-80) cc_final: 0.5310 (ptm-80) REVERT: G 99 ARG cc_start: 0.7654 (mtp85) cc_final: 0.6207 (mtt-85) REVERT: G 104 GLN cc_start: 0.8113 (mt0) cc_final: 0.7437 (tm-30) REVERT: H 69 ARG cc_start: 0.7826 (ttt-90) cc_final: 0.7373 (ttp80) REVERT: N 81 TYR cc_start: 0.7366 (m-80) cc_final: 0.7165 (t80) REVERT: N 123 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7168 (mt) REVERT: N 262 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8465 (pp20) REVERT: K 860 MET cc_start: 0.8579 (mmt) cc_final: 0.8332 (mmt) REVERT: L 53 MET cc_start: 0.8948 (mmm) cc_final: 0.8674 (mmm) REVERT: L 74 MET cc_start: 0.9160 (mtp) cc_final: 0.8819 (mtp) REVERT: L 288 MET cc_start: 0.8658 (ttp) cc_final: 0.8186 (tmm) outliers start: 53 outliers final: 32 residues processed: 250 average time/residue: 0.1952 time to fit residues: 76.2681 Evaluate side-chains 223 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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 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 105 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 42 LEU 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 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 276 LEU Chi-restraints excluded: chain L residue 383 THR 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: 8.9990 chunk 228 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 283 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 92 GLN M 388 ASN M 444 GLN L 144 ASN L 177 HIS ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 369 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.090455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065224 restraints weight = 121791.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.065993 restraints weight = 69812.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.066027 restraints weight = 50056.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.066167 restraints weight = 44546.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.066116 restraints weight = 39685.283| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28720 Z= 0.178 Angle : 0.643 10.866 40234 Z= 0.354 Chirality : 0.044 0.355 4525 Planarity : 0.004 0.048 4082 Dihedral : 26.820 171.436 6442 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.31 % Allowed : 17.28 % Favored : 80.41 % 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: 0.01 (0.16), residues: 2738 helix: 0.83 (0.13), residues: 1531 sheet: -0.99 (0.47), residues: 117 loop : -0.99 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 29 TYR 0.023 0.002 TYR D 80 PHE 0.016 0.001 PHE H 67 TRP 0.010 0.001 TRP K 782 HIS 0.012 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (28719) covalent geometry : angle 0.64296 / 0.35 (40234) hydrogen bonds : bond 0.05034 / 3.37 ( 1425) hydrogen bonds : angle 4.01785 / 2.81 ( 3806) metal coordination : bond 0.00508 / 0.27 ( 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 255 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 1.024 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 18 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8268 (pttm) REVERT: A 65 LEU cc_start: 0.9252 (tp) cc_final: 0.9028 (tp) REVERT: A 124 ILE cc_start: 0.9066 (mm) cc_final: 0.8830 (tp) REVERT: B 27 GLN cc_start: 0.8350 (pp30) cc_final: 0.8068 (pp30) REVERT: B 67 ARG cc_start: 0.8774 (ttp80) cc_final: 0.8431 (ttp80) REVERT: B 74 GLU cc_start: 0.8656 (tt0) cc_final: 0.8422 (tm-30) REVERT: B 96 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7376 (p) REVERT: F 53 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8463 (tm-30) REVERT: G 38 ASN cc_start: 0.6363 (t0) cc_final: 0.5251 (p0) REVERT: G 99 ARG cc_start: 0.7670 (mtp85) cc_final: 0.6227 (mtt-85) REVERT: G 104 GLN cc_start: 0.8158 (mt0) cc_final: 0.7426 (tm-30) REVERT: H 69 ARG cc_start: 0.7820 (ttt-90) cc_final: 0.7424 (mtp85) REVERT: H 92 GLN cc_start: 0.8851 (pt0) cc_final: 0.8583 (pt0) REVERT: N 123 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7230 (mt) REVERT: N 262 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8460 (pp20) REVERT: L 74 MET cc_start: 0.9181 (mtp) cc_final: 0.8923 (mtp) REVERT: L 288 MET cc_start: 0.8612 (ttp) cc_final: 0.8127 (tmm) outliers start: 47 outliers final: 33 residues processed: 236 average time/residue: 0.1993 time to fit residues: 73.4376 Evaluate side-chains 239 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 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 48 LEU Chi-restraints excluded: chain A residue 77 ASP 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 B residue 96 THR 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 G residue 56 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 94 ASN 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 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 371 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 101 SER 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 O residue 560 MET 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: 0.0770 chunk 150 optimal weight: 10.0000 chunk 284 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 103 optimal weight: 30.0000 chunk 275 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 255 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- 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** K 824 ASN L 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.089770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.064702 restraints weight = 121422.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.064925 restraints weight = 71570.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.065215 restraints weight = 52379.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.065284 restraints weight = 46070.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.065378 restraints weight = 41070.586| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4297 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= 0.196 Angle : 0.648 10.820 40234 Z= 0.356 Chirality : 0.044 0.289 4525 Planarity : 0.004 0.044 4082 Dihedral : 26.810 172.203 6442 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.95 % Allowed : 17.57 % Favored : 79.48 % 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: 0.87 (0.13), residues: 1537 sheet: -1.06 (0.46), residues: 117 loop : -1.00 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 32 TYR 0.029 0.002 TYR N 81 PHE 0.012 0.001 PHE B 61 TRP 0.010 0.001 TRP M 464 HIS 0.023 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.20 (28719) covalent geometry : angle 0.64825 / 0.36 (40234) hydrogen bonds : bond 0.05063 / 3.39 ( 1425) hydrogen bonds : angle 4.03730 / 2.82 ( 3806) metal coordination : bond 0.00558 / 0.29 ( 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 267 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 207 time to evaluate : 0.989 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: 0.8627 (OUTLIER) cc_final: 0.8395 (pttm) REVERT: A 65 LEU cc_start: 0.9245 (tp) cc_final: 0.9010 (tp) REVERT: A 122 LYS cc_start: 0.8881 (tptp) cc_final: 0.8620 (tppt) REVERT: B 27 GLN cc_start: 0.8362 (pp30) cc_final: 0.8080 (pp30) REVERT: B 74 GLU cc_start: 0.8669 (tt0) cc_final: 0.8467 (tm-30) REVERT: B 96 THR cc_start: 0.7872 (m) cc_final: 0.7449 (p) REVERT: D 56 MET cc_start: 0.8241 (tpp) cc_final: 0.8003 (tpp) REVERT: F 53 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8406 (tm-30) REVERT: G 38 ASN cc_start: 0.6400 (t0) cc_final: 0.5502 (p0) REVERT: G 99 ARG cc_start: 0.7751 (mtp85) cc_final: 0.6303 (mtt-85) REVERT: G 104 GLN cc_start: 0.8232 (mt0) cc_final: 0.7466 (tm-30) REVERT: H 69 ARG cc_start: 0.7830 (ttt-90) cc_final: 0.7447 (mtp85) REVERT: N 123 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7257 (mt) REVERT: N 262 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8461 (pp20) REVERT: N 304 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8472 (tt) REVERT: L 74 MET cc_start: 0.9198 (mtp) cc_final: 0.8938 (mtp) REVERT: L 288 MET cc_start: 0.8646 (ttp) cc_final: 0.8138 (tmm) outliers start: 60 outliers final: 38 residues processed: 248 average time/residue: 0.1984 time to fit residues: 76.9752 Evaluate side-chains 237 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 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 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 H residue 42 LEU 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 81 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 253 THR 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 175 optimal weight: 2.9990 chunk 145 optimal weight: 50.0000 chunk 77 optimal weight: 30.0000 chunk 69 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 93 optimal weight: 50.0000 chunk 270 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN H 92 GLN K 815 HIS ** K 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1132 ASN ** 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 = 0.3864 r_free = 0.3864 target = 0.088481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.063203 restraints weight = 121769.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.063575 restraints weight = 71512.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.063750 restraints weight = 52328.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.063829 restraints weight = 48493.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.063859 restraints weight = 42433.517| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28720 Z= 0.250 Angle : 0.703 13.178 40234 Z= 0.383 Chirality : 0.046 0.372 4525 Planarity : 0.005 0.125 4082 Dihedral : 26.876 173.025 6442 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.09 % Allowed : 18.75 % Favored : 78.15 % 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: -0.11 (0.16), residues: 2738 helix: 0.72 (0.13), residues: 1530 sheet: -1.29 (0.46), residues: 115 loop : -1.01 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 8 TYR 0.022 0.002 TYR N 394 PHE 0.017 0.002 PHE K 669 TRP 0.010 0.002 TRP K1223 HIS 0.011 0.001 HIS P 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.25 (28719) covalent geometry : angle 0.70349 / 0.38 (40234) hydrogen bonds : bond 0.05581 / 3.72 ( 1425) hydrogen bonds : angle 4.18771 / 2.93 ( 3806) metal coordination : bond 0.00768 / 0.40 ( 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 259 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 196 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.5627 (OUTLIER) cc_final: 0.5357 (ttt180) REVERT: A 65 LEU cc_start: 0.9228 (tp) cc_final: 0.8962 (tp) REVERT: B 96 THR cc_start: 0.7986 (m) cc_final: 0.7596 (p) REVERT: D 56 MET cc_start: 0.8072 (tpp) cc_final: 0.7771 (tpp) REVERT: E 120 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7821 (mtm) REVERT: F 53 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8442 (tm-30) REVERT: G 38 ASN cc_start: 0.6509 (t0) cc_final: 0.5513 (p0) REVERT: G 99 ARG cc_start: 0.7665 (mtp85) cc_final: 0.6121 (mtt-85) REVERT: G 100 VAL cc_start: 0.7808 (p) cc_final: 0.7586 (p) REVERT: G 104 GLN cc_start: 0.8224 (mt0) cc_final: 0.7457 (tm-30) REVERT: G 116 LEU cc_start: 0.8026 (tt) cc_final: 0.6852 (mm) REVERT: H 69 ARG cc_start: 0.7818 (ttt-90) cc_final: 0.7423 (mtp85) REVERT: N 88 TRP cc_start: 0.4506 (t-100) cc_final: 0.4296 (t-100) REVERT: N 262 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8454 (pp20) REVERT: N 304 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8587 (tt) REVERT: L 6 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8967 (p) REVERT: L 74 MET cc_start: 0.9204 (mtp) cc_final: 0.8958 (mtp) REVERT: L 259 MET cc_start: 0.8366 (ptt) cc_final: 0.7985 (ptt) REVERT: L 288 MET cc_start: 0.8747 (ttp) cc_final: 0.8138 (tmm) outliers start: 63 outliers final: 41 residues processed: 238 average time/residue: 0.1935 time to fit residues: 72.6307 Evaluate side-chains 235 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG 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 57 VAL 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 108 ASN 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 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 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 1134 SER Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain K residue 1215 ILE Chi-restraints excluded: chain L residue 6 THR 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 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 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: 20.0000 chunk 279 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 chunk 273 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** K 930 HIS ** 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 = 0.3900 r_free = 0.3900 target = 0.089667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.064629 restraints weight = 121781.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064647 restraints weight = 74168.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.064817 restraints weight = 55667.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.064868 restraints weight = 54061.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.064915 restraints weight = 46770.896| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28720 Z= 0.170 Angle : 0.641 11.345 40234 Z= 0.352 Chirality : 0.043 0.356 4525 Planarity : 0.004 0.082 4082 Dihedral : 26.800 174.117 6442 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.21 % Allowed : 19.69 % Favored : 78.11 % 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: 0.10 (0.16), residues: 2738 helix: 0.94 (0.13), residues: 1518 sheet: -1.32 (0.45), residues: 115 loop : -0.96 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG N 110 TYR 0.020 0.002 TYR K 675 PHE 0.012 0.001 PHE B 61 TRP 0.011 0.001 TRP K 782 HIS 0.009 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (28719) covalent geometry : angle 0.64067 / 0.35 (40234) hydrogen bonds : bond 0.04856 / 3.27 ( 1425) hydrogen bonds : angle 3.98555 / 2.78 ( 3806) metal coordination : bond 0.00414 / 0.22 ( 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 242 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 1.043 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 65 LEU cc_start: 0.9227 (tp) cc_final: 0.8973 (tp) REVERT: A 122 LYS cc_start: 0.9037 (tptp) cc_final: 0.8778 (ptpp) REVERT: B 96 THR cc_start: 0.7996 (m) cc_final: 0.7546 (p) REVERT: D 56 MET cc_start: 0.7725 (tpp) cc_final: 0.7439 (tpp) REVERT: D 68 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8295 (tm-30) REVERT: F 53 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8368 (tm-30) REVERT: G 35 ARG cc_start: 0.8354 (tpp80) cc_final: 0.7824 (ttm-80) REVERT: G 38 ASN cc_start: 0.6437 (t0) cc_final: 0.5538 (p0) REVERT: G 99 ARG cc_start: 0.7691 (mtp85) cc_final: 0.6302 (mtt-85) REVERT: G 104 GLN cc_start: 0.8241 (mt0) cc_final: 0.7458 (tm-30) REVERT: H 69 ARG cc_start: 0.7820 (ttt-90) cc_final: 0.7371 (mtp85) REVERT: N 304 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8529 (tt) REVERT: K 1194 MET cc_start: 0.9036 (mtp) cc_final: 0.8802 (mtm) REVERT: L 74 MET cc_start: 0.9131 (mtp) cc_final: 0.8887 (mtp) REVERT: L 259 MET cc_start: 0.8246 (ptt) cc_final: 0.8007 (ptt) REVERT: L 288 MET cc_start: 0.8586 (ttp) cc_final: 0.8111 (tmm) outliers start: 45 outliers final: 33 residues processed: 227 average time/residue: 0.2014 time to fit residues: 71.9476 Evaluate side-chains 220 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 14 LYS 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 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 H residue 42 LEU 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 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 90 THR Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain O residue 327 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 246 optimal weight: 0.7980 chunk 90 optimal weight: 40.0000 chunk 174 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 chunk 15 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 271 optimal weight: 30.0000 chunk 28 optimal weight: 1.9990 chunk 265 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** 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 = 0.3914 r_free = 0.3914 target = 0.090322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.065563 restraints weight = 122471.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.065437 restraints weight = 73863.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.065635 restraints weight = 59325.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.065706 restraints weight = 54893.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.065792 restraints weight = 46414.372| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28720 Z= 0.139 Angle : 0.630 12.920 40234 Z= 0.344 Chirality : 0.042 0.353 4525 Planarity : 0.004 0.044 4082 Dihedral : 26.683 175.031 6442 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.82 % Allowed : 19.93 % Favored : 78.25 % 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: 0.31 (0.16), residues: 2738 helix: 1.10 (0.13), residues: 1519 sheet: -1.16 (0.46), residues: 117 loop : -0.85 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 32 TYR 0.021 0.001 TYR P 238 PHE 0.021 0.001 PHE H 67 TRP 0.011 0.001 TRP K 782 HIS 0.008 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (28719) covalent geometry : angle 0.62960 / 0.34 (40234) hydrogen bonds : bond 0.04570 / 3.10 ( 1425) hydrogen bonds : angle 3.85014 / 2.68 ( 3806) metal coordination : bond 0.00219 / 0.12 ( 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 232 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.7923 (mt0) cc_final: 0.7590 (tt0) REVERT: A 65 LEU cc_start: 0.9238 (tp) cc_final: 0.8987 (tp) REVERT: B 96 THR cc_start: 0.8137 (m) cc_final: 0.7746 (p) REVERT: C 56 GLU cc_start: 0.7772 (tt0) cc_final: 0.7531 (mt-10) REVERT: D 56 MET cc_start: 0.7771 (tpp) cc_final: 0.7535 (tpp) REVERT: D 68 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8175 (tm-30) REVERT: E 120 MET cc_start: 0.7094 (mtm) cc_final: 0.6753 (mpp) REVERT: G 38 ASN cc_start: 0.6378 (t0) cc_final: 0.5712 (p0) REVERT: G 99 ARG cc_start: 0.7841 (mtp85) cc_final: 0.6438 (mtt-85) REVERT: G 100 VAL cc_start: 0.7826 (p) cc_final: 0.7592 (p) REVERT: G 104 GLN cc_start: 0.8241 (mt0) cc_final: 0.7429 (tm-30) REVERT: H 69 ARG cc_start: 0.7802 (ttt-90) cc_final: 0.7402 (mtp85) REVERT: K 1194 MET cc_start: 0.9046 (mtp) cc_final: 0.8839 (mtm) REVERT: L 259 MET cc_start: 0.8159 (ptt) cc_final: 0.7951 (ptt) REVERT: L 288 MET cc_start: 0.8510 (ttp) cc_final: 0.8073 (tmm) outliers start: 37 outliers final: 33 residues processed: 219 average time/residue: 0.2039 time to fit residues: 70.1095 Evaluate side-chains 215 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 14 LYS 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 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU 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 346 THR 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 1134 SER Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain L residue 12 THR 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 327 ILE 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 O residue 575 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 235 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 169 optimal weight: 0.0980 chunk 197 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.090231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.065716 restraints weight = 122442.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.065444 restraints weight = 76822.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.065578 restraints weight = 60766.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.065929 restraints weight = 51370.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.065923 restraints weight = 46203.515| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5107 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= 0.143 Angle : 0.622 11.596 40234 Z= 0.339 Chirality : 0.042 0.349 4525 Planarity : 0.004 0.043 4082 Dihedral : 26.633 175.092 6442 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.96 % Allowed : 20.03 % 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: 0.40 (0.16), residues: 2738 helix: 1.18 (0.13), residues: 1526 sheet: -1.15 (0.46), residues: 116 loop : -0.83 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 32 TYR 0.022 0.001 TYR P 238 PHE 0.011 0.001 PHE E 67 TRP 0.010 0.001 TRP K 782 HIS 0.009 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (28719) covalent geometry : angle 0.62202 / 0.34 (40234) hydrogen bonds : bond 0.04545 / 3.09 ( 1425) hydrogen bonds : angle 3.80965 / 2.65 ( 3806) metal coordination : bond 0.00326 / 0.17 ( 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 225 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.7932 (mt0) cc_final: 0.7606 (tt0) REVERT: A 65 LEU cc_start: 0.9250 (tp) cc_final: 0.8995 (tp) REVERT: B 96 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7719 (p) REVERT: C 24 GLN cc_start: 0.6504 (tt0) cc_final: 0.6226 (mp10) REVERT: C 56 GLU cc_start: 0.7778 (tt0) cc_final: 0.7052 (mt-10) REVERT: D 56 MET cc_start: 0.7746 (tpp) cc_final: 0.7519 (tpp) REVERT: D 68 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8211 (tm-30) REVERT: E 120 MET cc_start: 0.7167 (mtm) cc_final: 0.6937 (mpp) REVERT: G 38 ASN cc_start: 0.6381 (t0) cc_final: 0.5971 (p0) REVERT: G 99 ARG cc_start: 0.7790 (mtp85) cc_final: 0.6563 (mtt-85) REVERT: G 104 GLN cc_start: 0.8207 (mt0) cc_final: 0.7440 (tm-30) REVERT: H 69 ARG cc_start: 0.7928 (ttt-90) cc_final: 0.7445 (mtp85) REVERT: K 1194 MET cc_start: 0.9079 (mtp) cc_final: 0.8866 (mtm) REVERT: L 288 MET cc_start: 0.8567 (ttp) cc_final: 0.8110 (tmm) REVERT: O 544 GLU cc_start: 0.8422 (pm20) cc_final: 0.7628 (tm-30) outliers start: 40 outliers final: 32 residues processed: 211 average time/residue: 0.2045 time to fit residues: 67.7855 Evaluate side-chains 208 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 14 LYS 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 B residue 96 THR 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 80 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU 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 371 ASP Chi-restraints excluded: chain K residue 861 THR 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 12 THR 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 327 ILE 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 O residue 575 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 200 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 179 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 246 optimal weight: 0.0170 chunk 125 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 186 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.090379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.065638 restraints weight = 122093.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.065670 restraints weight = 73491.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.065712 restraints weight = 56026.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.065875 restraints weight = 54537.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.065988 restraints weight = 47668.567| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5214 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= 0.138 Angle : 0.622 14.024 40234 Z= 0.338 Chirality : 0.042 0.386 4525 Planarity : 0.004 0.053 4082 Dihedral : 26.588 175.348 6442 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.77 % Allowed : 20.13 % Favored : 78.11 % 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: 0.52 (0.16), residues: 2738 helix: 1.28 (0.13), residues: 1525 sheet: -1.07 (0.47), residues: 116 loop : -0.77 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 32 TYR 0.044 0.001 TYR P 261 PHE 0.020 0.001 PHE H 67 TRP 0.010 0.001 TRP K 782 HIS 0.009 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (28719) covalent geometry : angle 0.62206 / 0.34 (40234) hydrogen bonds : bond 0.04429 / 3.01 ( 1425) hydrogen bonds : angle 3.74226 / 2.60 ( 3806) metal coordination : bond 0.00265 / 0.14 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4261.36 seconds wall clock time: 74 minutes 43.13 seconds (4483.13 seconds total)