Starting phenix.real_space_refine on Mon Jun 23 10:09:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iht_35455/06_2025/8iht_35455.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iht_35455/06_2025/8iht_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_35455/06_2025/8iht_35455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iht_35455/06_2025/8iht_35455.map" model { file = "/net/cci-nas-00/data/ceres_data/8iht_35455/06_2025/8iht_35455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iht_35455/06_2025/8iht_35455.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 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: {'PHE:plan': 1, 'ARG: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: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS: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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ML3:plan-1': 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: {'GLN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 5, '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: {'GLN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 9, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 13, 'ASP:plan': 9} 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: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 2} 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: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} 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: 14.41, per 1000 atoms: 0.52 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: 6.22 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 9.40 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: 14.92 Time building geometry restraints manager: 7.40 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=" CA SER B 47 " pdb=" C SER B 47 " ideal model delta sigma weight residual 1.524 1.476 0.047 1.30e-02 5.92e+03 1.32e+01 ... (remaining 28714 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 39980 3.52 - 7.03: 212 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: 4297 0.089 - 0.178: 217 0.178 - 0.267: 8 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: 2.510 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: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 71.360 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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 : 0.006 0.128 28720 Z= 0.337 Angle : 0.828 17.587 40234 Z= 0.535 Chirality : 0.043 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 : 8.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (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 TRP 0.012 0.001 TRP K 719 HIS 0.006 0.001 HIS P 369 PHE 0.038 0.002 PHE P 374 TYR 0.030 0.002 TYR N 373 ARG 0.011 0.001 ARG O 564 Details of bonding type rmsd hydrogen bonds : bond 0.24122 ( 1425) hydrogen bonds : angle 8.34807 ( 3806) metal coordination : bond 0.00389 ( 1) covalent geometry : bond 0.00632 (28719) covalent geometry : angle 0.82772 (40234) *********************** 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 : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 366 THR cc_start: 0.8406 (m) cc_final: 0.8163 (p) REVERT: N 107 MET cc_start: 0.5370 (ppp) cc_final: 0.4609 (tmm) REVERT: N 346 THR cc_start: 0.6769 (p) cc_final: 0.6407 (p) REVERT: L 207 SER cc_start: 0.9271 (t) cc_final: 0.9056 (p) REVERT: O 300 ASP cc_start: 0.6787 (m-30) cc_final: 0.6428 (t70) REVERT: P 348 ASP cc_start: 0.6625 (p0) cc_final: 0.6391 (t0) REVERT: P 401 MET cc_start: 0.6483 (mmm) cc_final: 0.6145 (mtm) outliers start: 4 outliers final: 2 residues processed: 459 average time/residue: 0.4733 time to fit residues: 324.4022 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 : 2.626 ------------------------------------------------------------------------------- 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 256 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 123 optimal weight: 0.0970 chunk 238 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 276 optimal weight: 20.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 79 HIS ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 961 ASN K 965 HIS O 583 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 = 0.3964 r_free = 0.3964 target = 0.093641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.069064 restraints weight = 122709.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.070119 restraints weight = 67032.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.070173 restraints weight = 44489.405| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 28720 Z= 0.177 Angle : 0.636 10.272 40234 Z= 0.358 Chirality : 0.039 0.208 4525 Planarity : 0.005 0.046 4082 Dihedral : 26.686 172.429 6447 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.48 % Favored : 97.48 % Rotamer: Outliers : 1.87 % Allowed : 10.11 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 2738 helix: 0.15 (0.13), residues: 1517 sheet: -0.62 (0.48), residues: 117 loop : -1.17 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 31 HIS 0.007 0.001 HIS O 346 PHE 0.035 0.002 PHE K1026 TYR 0.033 0.002 TYR P 238 ARG 0.023 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.05490 ( 1425) hydrogen bonds : angle 4.36316 ( 3806) metal coordination : bond 0.00133 ( 1) covalent geometry : bond 0.00388 (28719) covalent geometry : angle 0.63631 (40234) *********************** 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 294 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7133 (mmtt) cc_final: 0.6737 (mmtt) REVERT: B 44 LYS cc_start: 0.8391 (mmmt) cc_final: 0.8108 (mmmt) REVERT: B 67 ARG cc_start: 0.8786 (ttp80) cc_final: 0.8519 (ttp80) REVERT: B 93 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7514 (tm-30) REVERT: B 96 THR cc_start: 0.7730 (m) cc_final: 0.7310 (p) REVERT: C 89 ASN cc_start: 0.8059 (p0) cc_final: 0.7826 (p0) REVERT: D 59 MET cc_start: 0.8527 (mmt) cc_final: 0.8264 (mmt) REVERT: D 83 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7935 (mmt180) REVERT: G 42 ARG cc_start: 0.3038 (mtt-85) cc_final: 0.2831 (mtt-85) REVERT: H 69 ARG cc_start: 0.7818 (ttt-90) cc_final: 0.7446 (mtp85) REVERT: N 123 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7314 (mt) REVERT: N 262 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8269 (pp20) REVERT: K 860 MET cc_start: 0.7715 (mmt) cc_final: 0.7513 (mmt) REVERT: L 74 MET cc_start: 0.8994 (mtp) cc_final: 0.8722 (mtp) REVERT: L 288 MET cc_start: 0.8383 (ttp) cc_final: 0.7984 (tmm) REVERT: O 327 ILE cc_start: 0.9066 (mp) cc_final: 0.8862 (mm) REVERT: P 357 LYS cc_start: 0.9042 (ttpp) cc_final: 0.8751 (tptt) outliers start: 38 outliers final: 17 residues processed: 279 average time/residue: 0.4544 time to fit residues: 192.7800 Evaluate side-chains 223 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR 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 E residue 60 LEU 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 262 GLU Chi-restraints excluded: chain K residue 702 LEU Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain K residue 1256 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain O residue 364 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 97 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 196 optimal weight: 6.9990 chunk 227 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN H 106 HIS M 421 ASN K 961 ASN O 346 HIS P 267 GLN ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.093662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.068992 restraints weight = 123265.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.069804 restraints weight = 70342.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.069969 restraints weight = 48297.804| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28720 Z= 0.144 Angle : 0.576 10.939 40234 Z= 0.323 Chirality : 0.038 0.199 4525 Planarity : 0.004 0.044 4082 Dihedral : 26.526 169.168 6443 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.91 % Allowed : 12.71 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2738 helix: 0.88 (0.13), residues: 1523 sheet: -0.50 (0.47), residues: 117 loop : -0.85 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 447 HIS 0.005 0.001 HIS B 75 PHE 0.019 0.001 PHE H 67 TYR 0.022 0.001 TYR P 238 ARG 0.013 0.001 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 1425) hydrogen bonds : angle 3.89010 ( 3806) metal coordination : bond 0.00312 ( 1) covalent geometry : bond 0.00314 (28719) covalent geometry : angle 0.57571 (40234) *********************** 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 268 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 2.694 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 9 LYS cc_start: 0.6816 (mmtt) cc_final: 0.6436 (mmmt) REVERT: A 81 ASP cc_start: 0.6919 (t0) cc_final: 0.6607 (t0) REVERT: B 63 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8315 (tm-30) REVERT: B 67 ARG cc_start: 0.8772 (ttp80) cc_final: 0.8379 (ttp80) REVERT: B 93 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7762 (tm-30) REVERT: B 96 THR cc_start: 0.7710 (m) cc_final: 0.7336 (p) REVERT: D 68 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8111 (tm-30) REVERT: G 38 ASN cc_start: 0.6018 (t0) cc_final: 0.5685 (t0) REVERT: G 42 ARG cc_start: 0.3088 (mtt-85) cc_final: 0.2877 (mtt-85) REVERT: G 104 GLN cc_start: 0.8161 (mt0) cc_final: 0.7421 (tm-30) REVERT: N 123 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7282 (mt) REVERT: N 262 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8318 (pp20) REVERT: K 860 MET cc_start: 0.7815 (mmt) cc_final: 0.7564 (mmt) REVERT: K 965 HIS cc_start: 0.7714 (OUTLIER) cc_final: 0.6701 (m90) REVERT: L 288 MET cc_start: 0.8324 (ttp) cc_final: 0.7789 (tmm) REVERT: P 262 GLU cc_start: 0.9168 (tt0) cc_final: 0.8887 (tp30) outliers start: 39 outliers final: 14 residues processed: 254 average time/residue: 0.4969 time to fit residues: 195.2688 Evaluate side-chains 212 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 92 LEU 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 E residue 60 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 42 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 K residue 965 HIS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 47 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 125 optimal weight: 0.4980 chunk 22 optimal weight: 0.2980 chunk 222 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 41 optimal weight: 0.0870 chunk 4 optimal weight: 10.0000 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN M 421 ASN L 177 HIS ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 277 GLN ** P 369 HIS ** 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 = 0.3983 r_free = 0.3983 target = 0.093850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.069338 restraints weight = 123540.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.069760 restraints weight = 72413.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.070103 restraints weight = 51937.284| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3734 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= 0.130 Angle : 0.557 11.100 40234 Z= 0.311 Chirality : 0.037 0.199 4525 Planarity : 0.003 0.044 4082 Dihedral : 26.382 169.158 6442 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.91 % Allowed : 14.38 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 2738 helix: 1.16 (0.13), residues: 1521 sheet: -0.24 (0.49), residues: 117 loop : -0.73 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 966 HIS 0.004 0.001 HIS B 75 PHE 0.030 0.001 PHE K1026 TYR 0.019 0.001 TYR D 80 ARG 0.009 0.000 ARG N 110 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 1425) hydrogen bonds : angle 3.68001 ( 3806) metal coordination : bond 0.00138 ( 1) covalent geometry : bond 0.00280 (28719) covalent geometry : angle 0.55741 (40234) *********************** 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 253 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 6.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.6625 (mmtt) cc_final: 0.6334 (mmmt) REVERT: B 59 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8703 (tppt) REVERT: B 67 ARG cc_start: 0.8777 (ttp80) cc_final: 0.8515 (ttp80) REVERT: B 74 GLU cc_start: 0.8557 (tt0) cc_final: 0.8211 (tm-30) REVERT: B 93 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7786 (tm-30) REVERT: B 96 THR cc_start: 0.7624 (m) cc_final: 0.7292 (p) REVERT: D 68 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8126 (tm-30) REVERT: D 80 TYR cc_start: 0.8123 (m-10) cc_final: 0.7536 (m-80) REVERT: G 35 ARG cc_start: 0.8023 (tpp80) cc_final: 0.7818 (tpp80) REVERT: G 104 GLN cc_start: 0.8310 (mt0) cc_final: 0.7544 (tm-30) REVERT: H 92 GLN cc_start: 0.8784 (pt0) cc_final: 0.8566 (pt0) REVERT: K 860 MET cc_start: 0.7894 (mmt) cc_final: 0.7634 (mmt) REVERT: K 963 LYS cc_start: 0.7062 (tptt) cc_final: 0.6788 (tptp) REVERT: L 288 MET cc_start: 0.8286 (ttp) cc_final: 0.7603 (tmm) REVERT: P 262 GLU cc_start: 0.9232 (tt0) cc_final: 0.8927 (tp30) REVERT: P 347 MET cc_start: 0.8475 (ptp) cc_final: 0.8184 (ptp) outliers start: 39 outliers final: 20 residues processed: 238 average time/residue: 0.7808 time to fit residues: 288.1841 Evaluate side-chains 219 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 5.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 92 LEU 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 E residue 60 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 83 LEU 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 546 SER Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain P residue 323 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 228 optimal weight: 0.0980 chunk 286 optimal weight: 0.4980 chunk 146 optimal weight: 40.0000 chunk 237 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 285 optimal weight: 50.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 HIS ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 930 HIS K1132 ASN K1221 HIS ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 369 HIS ** 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 = 0.3926 r_free = 0.3926 target = 0.090898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.066087 restraints weight = 124251.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066078 restraints weight = 73628.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066390 restraints weight = 55300.940| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 28720 Z= 0.207 Angle : 0.614 10.011 40234 Z= 0.341 Chirality : 0.039 0.188 4525 Planarity : 0.004 0.041 4082 Dihedral : 26.482 170.559 6442 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.91 % Allowed : 14.97 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2738 helix: 1.07 (0.13), residues: 1529 sheet: -0.41 (0.48), residues: 117 loop : -0.84 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 966 HIS 0.006 0.001 HIS L 150 PHE 0.020 0.002 PHE C 25 TYR 0.021 0.002 TYR K 675 ARG 0.010 0.001 ARG N 110 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 1425) hydrogen bonds : angle 3.85763 ( 3806) metal coordination : bond 0.00505 ( 1) covalent geometry : bond 0.00461 (28719) covalent geometry : angle 0.61389 (40234) *********************** 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 234 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9130 (mmtt) cc_final: 0.8753 (tppt) REVERT: B 93 GLN cc_start: 0.8335 (mm-40) cc_final: 0.8049 (tm-30) REVERT: B 96 THR cc_start: 0.7967 (m) cc_final: 0.7617 (t) REVERT: B 98 TYR cc_start: 0.8259 (m-10) cc_final: 0.8014 (m-80) REVERT: D 56 MET cc_start: 0.8042 (tpp) cc_final: 0.7750 (tpp) REVERT: G 99 ARG cc_start: 0.7947 (mtp-110) cc_final: 0.6507 (mtt-85) REVERT: G 104 GLN cc_start: 0.8072 (mt0) cc_final: 0.7358 (tm-30) REVERT: H 79 HIS cc_start: 0.7987 (t70) cc_final: 0.7600 (t70) REVERT: N 262 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8453 (pp20) REVERT: K 965 HIS cc_start: 0.7202 (OUTLIER) cc_final: 0.6754 (m90) REVERT: L 288 MET cc_start: 0.8561 (ttp) cc_final: 0.7892 (tmm) REVERT: P 262 GLU cc_start: 0.9190 (tt0) cc_final: 0.8967 (tp30) REVERT: P 347 MET cc_start: 0.8839 (ptp) cc_final: 0.8467 (ptp) outliers start: 39 outliers final: 26 residues processed: 219 average time/residue: 0.4334 time to fit residues: 148.0976 Evaluate side-chains 200 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 3.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 105 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 262 GLU Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain K residue 861 THR Chi-restraints excluded: chain K residue 965 HIS 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 O residue 364 VAL Chi-restraints excluded: chain O residue 575 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 258 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 262 optimal weight: 0.6980 chunk 144 optimal weight: 40.0000 chunk 134 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 33 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN H 92 GLN N 126 GLN L 144 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 = 0.3946 r_free = 0.3946 target = 0.091814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.067259 restraints weight = 124311.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.067319 restraints weight = 72807.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.067485 restraints weight = 54902.666| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28720 Z= 0.140 Angle : 0.562 10.733 40234 Z= 0.312 Chirality : 0.037 0.211 4525 Planarity : 0.004 0.041 4082 Dihedral : 26.331 174.153 6442 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.91 % Allowed : 16.35 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 2738 helix: 1.32 (0.13), residues: 1518 sheet: -0.37 (0.48), residues: 117 loop : -0.71 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 966 HIS 0.004 0.001 HIS B 75 PHE 0.031 0.001 PHE K1026 TYR 0.029 0.001 TYR D 80 ARG 0.009 0.000 ARG N 110 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 1425) hydrogen bonds : angle 3.60743 ( 3806) metal coordination : bond 0.00263 ( 1) covalent geometry : bond 0.00309 (28719) covalent geometry : angle 0.56215 (40234) *********************** 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 230 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9419 (mm) cc_final: 0.9025 (mp) REVERT: A 122 LYS cc_start: 0.9086 (tppt) cc_final: 0.8852 (ptpp) REVERT: B 59 LYS cc_start: 0.9144 (mmtt) cc_final: 0.8714 (tppt) REVERT: B 93 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7899 (tm-30) REVERT: B 96 THR cc_start: 0.7851 (m) cc_final: 0.7398 (t) REVERT: B 98 TYR cc_start: 0.8297 (m-10) cc_final: 0.8008 (m-10) REVERT: G 35 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7966 (tpp80) REVERT: G 99 ARG cc_start: 0.7912 (mtp-110) cc_final: 0.6521 (mtt-85) REVERT: G 104 GLN cc_start: 0.8108 (mt0) cc_final: 0.7363 (tm-30) REVERT: H 79 HIS cc_start: 0.7902 (t70) cc_final: 0.7478 (t70) REVERT: H 92 GLN cc_start: 0.8896 (pt0) cc_final: 0.8276 (pm20) REVERT: N 110 ARG cc_start: 0.8754 (ttp80) cc_final: 0.8514 (ttp80) REVERT: N 126 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8168 (mm-40) REVERT: K 965 HIS cc_start: 0.7122 (OUTLIER) cc_final: 0.6628 (m90) REVERT: L 373 MET cc_start: 0.8819 (mmm) cc_final: 0.8577 (mmm) REVERT: O 544 GLU cc_start: 0.8395 (pm20) cc_final: 0.7602 (tm-30) REVERT: P 241 LYS cc_start: 0.8904 (mptt) cc_final: 0.8559 (mptt) REVERT: P 347 MET cc_start: 0.8841 (ptp) cc_final: 0.8520 (ptp) outliers start: 39 outliers final: 19 residues processed: 215 average time/residue: 0.4452 time to fit residues: 148.0055 Evaluate side-chains 206 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR 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 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 94 ASN Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain N residue 126 GLN Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain K residue 861 THR Chi-restraints excluded: chain K residue 965 HIS Chi-restraints excluded: chain K residue 1130 ILE Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 258 ILE Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain O residue 364 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 204 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 210 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 94 ASN M 388 ASN L 235 ASN L 419 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.090118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.065348 restraints weight = 123445.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.065729 restraints weight = 70512.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.065972 restraints weight = 52360.754| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 28720 Z= 0.204 Angle : 0.604 10.512 40234 Z= 0.334 Chirality : 0.039 0.231 4525 Planarity : 0.004 0.042 4082 Dihedral : 26.366 174.128 6442 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.31 % Allowed : 16.84 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.16), residues: 2738 helix: 1.28 (0.13), residues: 1519 sheet: -0.61 (0.47), residues: 118 loop : -0.77 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 966 HIS 0.010 0.001 HIS D 106 PHE 0.019 0.002 PHE H 67 TYR 0.022 0.002 TYR P 238 ARG 0.010 0.001 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 1425) hydrogen bonds : angle 3.77586 ( 3806) metal coordination : bond 0.00466 ( 1) covalent geometry : bond 0.00455 (28719) covalent geometry : angle 0.60400 (40234) *********************** 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 230 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9062 (tppt) cc_final: 0.8839 (ptpp) REVERT: B 59 LYS cc_start: 0.9154 (mmtt) cc_final: 0.8764 (tppt) REVERT: B 93 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7905 (tm-30) REVERT: B 96 THR cc_start: 0.8049 (m) cc_final: 0.7712 (t) REVERT: B 98 TYR cc_start: 0.8385 (m-10) cc_final: 0.8067 (m-10) REVERT: D 56 MET cc_start: 0.7711 (tpp) cc_final: 0.7422 (tpp) REVERT: G 99 ARG cc_start: 0.7995 (mtp-110) cc_final: 0.6591 (mtt-85) REVERT: G 104 GLN cc_start: 0.8088 (mt0) cc_final: 0.7316 (tm-30) REVERT: H 79 HIS cc_start: 0.7854 (t70) cc_final: 0.7500 (t70) REVERT: N 88 TRP cc_start: 0.4432 (t-100) cc_final: 0.4171 (t-100) REVERT: N 110 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8501 (ttp80) REVERT: N 126 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8131 (mm-40) REVERT: K 860 MET cc_start: 0.8608 (mmt) cc_final: 0.8349 (mmt) REVERT: K 965 HIS cc_start: 0.7124 (OUTLIER) cc_final: 0.6716 (m90) REVERT: L 288 MET cc_start: 0.8600 (tmm) cc_final: 0.7939 (tmm) REVERT: O 544 GLU cc_start: 0.8373 (pm20) cc_final: 0.7646 (tm-30) REVERT: P 262 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8783 (mm-30) REVERT: P 282 CYS cc_start: 0.6434 (t) cc_final: 0.6059 (t) REVERT: P 347 MET cc_start: 0.8886 (ptp) cc_final: 0.8522 (ptp) outliers start: 47 outliers final: 32 residues processed: 214 average time/residue: 0.4255 time to fit residues: 141.9481 Evaluate side-chains 208 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain 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 81 TYR Chi-restraints excluded: chain N residue 126 GLN 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 961 ASN Chi-restraints excluded: chain K residue 965 HIS Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain L residue 258 ILE Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain O residue 364 VAL Chi-restraints excluded: chain P residue 262 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 248 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 199 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 263 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 202 optimal weight: 4.9990 chunk 282 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN N 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.090596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.065757 restraints weight = 123668.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.066126 restraints weight = 70315.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.066332 restraints weight = 50697.170| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5130 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= 0.157 Angle : 0.578 10.756 40234 Z= 0.320 Chirality : 0.038 0.239 4525 Planarity : 0.004 0.086 4082 Dihedral : 26.323 176.047 6442 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.06 % Allowed : 17.08 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2738 helix: 1.38 (0.13), residues: 1523 sheet: -0.63 (0.48), residues: 116 loop : -0.74 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 966 HIS 0.021 0.001 HIS D 79 PHE 0.016 0.001 PHE P 362 TYR 0.019 0.001 TYR P 238 ARG 0.012 0.000 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 1425) hydrogen bonds : angle 3.66353 ( 3806) metal coordination : bond 0.00321 ( 1) covalent geometry : bond 0.00350 (28719) covalent geometry : angle 0.57812 (40234) *********************** 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 226 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8717 (mt) REVERT: B 59 LYS cc_start: 0.9134 (mmtt) cc_final: 0.8754 (tppt) REVERT: B 93 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7962 (tm-30) REVERT: B 96 THR cc_start: 0.7880 (m) cc_final: 0.7518 (t) REVERT: B 98 TYR cc_start: 0.8357 (m-10) cc_final: 0.8008 (m-10) REVERT: D 49 THR cc_start: 0.8263 (m) cc_final: 0.7939 (p) REVERT: G 99 ARG cc_start: 0.8040 (mtp-110) cc_final: 0.6610 (mtt-85) REVERT: G 104 GLN cc_start: 0.8106 (mt0) cc_final: 0.7275 (tm-30) REVERT: H 79 HIS cc_start: 0.7812 (t70) cc_final: 0.7423 (t70) REVERT: H 92 GLN cc_start: 0.8901 (pt0) cc_final: 0.8267 (pm20) REVERT: N 126 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8217 (mm-40) REVERT: N 304 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8501 (tt) REVERT: K 965 HIS cc_start: 0.7154 (OUTLIER) cc_final: 0.6751 (m90) REVERT: L 288 MET cc_start: 0.8596 (tmm) cc_final: 0.7977 (tmm) REVERT: O 544 GLU cc_start: 0.8370 (pm20) cc_final: 0.7668 (tm-30) REVERT: P 347 MET cc_start: 0.8910 (ptp) cc_final: 0.8548 (ptp) REVERT: P 373 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.7168 (p90) outliers start: 42 outliers final: 27 residues processed: 210 average time/residue: 0.4600 time to fit residues: 148.2004 Evaluate side-chains 207 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 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 126 GLN Chi-restraints excluded: chain N residue 304 LEU Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain K residue 902 ASP Chi-restraints excluded: chain K residue 961 ASN Chi-restraints excluded: chain K residue 965 HIS Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 258 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 O residue 575 ASP Chi-restraints excluded: chain P residue 373 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 267 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 249 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 252 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 305 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 = 0.3922 r_free = 0.3922 target = 0.090497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.065854 restraints weight = 123340.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066287 restraints weight = 69558.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.066552 restraints weight = 52661.052| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5326 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= 0.156 Angle : 0.579 10.960 40234 Z= 0.320 Chirality : 0.037 0.239 4525 Planarity : 0.004 0.086 4082 Dihedral : 26.263 176.921 6442 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.96 % Allowed : 17.33 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 2738 helix: 1.43 (0.13), residues: 1514 sheet: -0.67 (0.47), residues: 116 loop : -0.73 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 966 HIS 0.014 0.001 HIS D 106 PHE 0.021 0.001 PHE H 67 TYR 0.022 0.001 TYR P 238 ARG 0.013 0.000 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 1425) hydrogen bonds : angle 3.65883 ( 3806) metal coordination : bond 0.00313 ( 1) covalent geometry : bond 0.00348 (28719) covalent geometry : angle 0.57916 (40234) *********************** 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 228 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9134 (mmtt) cc_final: 0.8743 (tppt) REVERT: B 93 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7960 (tm-30) REVERT: B 96 THR cc_start: 0.7903 (m) cc_final: 0.7547 (t) REVERT: B 98 TYR cc_start: 0.8356 (m-10) cc_final: 0.7995 (m-10) REVERT: D 49 THR cc_start: 0.8279 (m) cc_final: 0.7977 (p) REVERT: E 120 MET cc_start: 0.7775 (mtp) cc_final: 0.6854 (mmm) REVERT: G 99 ARG cc_start: 0.8054 (mtp-110) cc_final: 0.6577 (mtt-85) REVERT: G 104 GLN cc_start: 0.8164 (mt0) cc_final: 0.7319 (tm-30) REVERT: H 79 HIS cc_start: 0.7785 (t70) cc_final: 0.7400 (t70) REVERT: N 88 TRP cc_start: 0.4464 (t-100) cc_final: 0.4255 (t-100) REVERT: N 126 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8214 (mm-40) REVERT: N 304 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8493 (tt) REVERT: K 965 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6763 (m90) REVERT: L 288 MET cc_start: 0.8575 (tmm) cc_final: 0.7951 (tmm) REVERT: O 544 GLU cc_start: 0.8364 (pm20) cc_final: 0.7703 (tm-30) REVERT: P 347 MET cc_start: 0.8898 (ptp) cc_final: 0.8512 (ptp) REVERT: P 357 LYS cc_start: 0.8829 (tptt) cc_final: 0.8336 (tppt) REVERT: P 373 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.7164 (p90) outliers start: 40 outliers final: 28 residues processed: 212 average time/residue: 0.4461 time to fit residues: 144.5822 Evaluate side-chains 211 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 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 81 ASP Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 96 THR 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 546 SER Chi-restraints excluded: chain N residue 126 GLN Chi-restraints excluded: chain N residue 304 LEU Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain K residue 902 ASP Chi-restraints excluded: chain K residue 961 ASN Chi-restraints excluded: chain K residue 965 HIS Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 258 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 O residue 575 ASP Chi-restraints excluded: chain P residue 373 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 48 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 294 optimal weight: 8.9990 chunk 131 optimal weight: 0.0000 chunk 151 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 92 GLN M 371 GLN N 126 GLN ** P 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.090205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.065560 restraints weight = 123144.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.065976 restraints weight = 70037.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066208 restraints weight = 52228.527| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28720 Z= 0.167 Angle : 0.590 10.653 40234 Z= 0.326 Chirality : 0.038 0.241 4525 Planarity : 0.004 0.060 4082 Dihedral : 26.255 177.419 6442 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.72 % Allowed : 17.72 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.16), residues: 2738 helix: 1.40 (0.13), residues: 1523 sheet: -0.74 (0.47), residues: 116 loop : -0.72 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 966 HIS 0.012 0.001 HIS D 106 PHE 0.017 0.001 PHE P 362 TYR 0.024 0.001 TYR P 238 ARG 0.014 0.001 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 1425) hydrogen bonds : angle 3.67207 ( 3806) metal coordination : bond 0.00368 ( 1) covalent geometry : bond 0.00374 (28719) covalent geometry : angle 0.59049 (40234) ********************** 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 218 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 5.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9132 (mmtt) cc_final: 0.8760 (tppt) REVERT: B 93 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8030 (tm-30) REVERT: B 96 THR cc_start: 0.7978 (m) cc_final: 0.7610 (t) REVERT: B 98 TYR cc_start: 0.8374 (m-10) cc_final: 0.7994 (m-10) REVERT: D 49 THR cc_start: 0.8285 (m) cc_final: 0.8031 (p) REVERT: E 120 MET cc_start: 0.7838 (mtp) cc_final: 0.6960 (mmm) REVERT: G 99 ARG cc_start: 0.8042 (mtp-110) cc_final: 0.6694 (mtt-85) REVERT: G 104 GLN cc_start: 0.8108 (mt0) cc_final: 0.7283 (tm-30) REVERT: H 76 ARG cc_start: 0.7479 (ptp-110) cc_final: 0.7092 (ttm170) REVERT: H 79 HIS cc_start: 0.7801 (t70) cc_final: 0.7403 (t70) REVERT: H 92 GLN cc_start: 0.8954 (pt0) cc_final: 0.8324 (pm20) REVERT: N 126 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8204 (mm-40) REVERT: N 304 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8528 (tt) REVERT: K 965 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6759 (m90) REVERT: L 288 MET cc_start: 0.8584 (tmm) cc_final: 0.7955 (tmm) REVERT: O 544 GLU cc_start: 0.8351 (pm20) cc_final: 0.7725 (tm-30) REVERT: P 347 MET cc_start: 0.8900 (ptp) cc_final: 0.8524 (ptp) REVERT: P 373 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.7197 (p90) outliers start: 35 outliers final: 28 residues processed: 206 average time/residue: 0.5731 time to fit residues: 185.7917 Evaluate side-chains 211 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 45 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 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 126 GLN Chi-restraints excluded: chain N residue 304 LEU Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain K residue 902 ASP Chi-restraints excluded: chain K residue 961 ASN Chi-restraints excluded: chain K residue 965 HIS Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1144 ILE Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 258 ILE Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain O residue 364 VAL Chi-restraints excluded: chain O residue 575 ASP Chi-restraints excluded: chain P residue 373 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 210 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 279 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 211 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 305 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 = 0.3901 r_free = 0.3901 target = 0.089457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.064657 restraints weight = 123945.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.064775 restraints weight = 71161.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.065042 restraints weight = 54322.666| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 28720 Z= 0.204 Angle : 0.618 10.864 40234 Z= 0.339 Chirality : 0.039 0.238 4525 Planarity : 0.004 0.068 4082 Dihedral : 26.292 177.933 6442 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.82 % Allowed : 18.11 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 2738 helix: 1.34 (0.13), residues: 1518 sheet: -0.95 (0.46), residues: 117 loop : -0.83 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP N 88 HIS 0.014 0.001 HIS D 79 PHE 0.019 0.002 PHE H 67 TYR 0.024 0.002 TYR P 238 ARG 0.014 0.001 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 1425) hydrogen bonds : angle 3.77677 ( 3806) metal coordination : bond 0.00580 ( 1) covalent geometry : bond 0.00458 (28719) covalent geometry : angle 0.61775 (40234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8954.77 seconds wall clock time: 161 minutes 33.76 seconds (9693.76 seconds total)