Starting phenix.real_space_refine on Sun May 3 21:38:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jy3_61886/05_2026/9jy3_61886.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jy3_61886/05_2026/9jy3_61886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jy3_61886/05_2026/9jy3_61886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jy3_61886/05_2026/9jy3_61886.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jy3_61886/05_2026/9jy3_61886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jy3_61886/05_2026/9jy3_61886.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 10039 2.51 5 N 2509 2.21 5 O 2986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15638 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "B" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 237 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "E" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "F" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "G" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 907 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "M" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 285 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "N" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 310 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "a" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "b" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 237 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 933 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "g" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 907 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "m" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 285 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "n" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 310 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "O" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1578 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 199} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "P" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1511 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 12, 'TRANS': 183} Chain breaks: 3 Chain: "Q" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1578 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "R" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1511 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 12, 'TRANS': 183} Chain breaks: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.89, per 1000 atoms: 0.25 Number of scatterers: 15638 At special positions: 0 Unit cell: (97.232, 131.84, 198.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 2986 8.00 N 2509 7.00 C 10039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 122 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 107 " distance=2.04 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 135 " - pdb=" SG CYS O 195 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 149 " - pdb=" SG CYS P 204 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 135 " - pdb=" SG CYS Q 195 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 149 " - pdb=" SG CYS R 204 " distance=2.03 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 Links applied NAG-ASN " NAG d 201 " - " ASN d 74 " " NAG d 202 " - " ASN d 38 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 689.9 milliseconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3732 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 36 sheets defined 27.9% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 28 through 31 removed outlier: 3.518A pdb=" N LEU A 31 " --> pdb=" O ASP A 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 31' Processing helix chain 'A' and resid 32 through 54 removed outlier: 4.376A pdb=" N ASP A 36 " --> pdb=" O CYS A 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 55 removed outlier: 3.592A pdb=" N PHE B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 126 Processing helix chain 'E' and resid 126 through 153 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 126 through 154 Processing helix chain 'G' and resid 76 through 80 Processing helix chain 'G' and resid 111 through 140 removed outlier: 3.774A pdb=" N ILE G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 289 removed outlier: 4.084A pdb=" N MET M 261 " --> pdb=" O GLU M 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 288 removed outlier: 3.583A pdb=" N CYS N 283 " --> pdb=" O ILE N 279 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 54 removed outlier: 3.524A pdb=" N LEU a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP a 36 " --> pdb=" O CYS a 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 55 Processing helix chain 'd' and resid 64 through 66 No H-bonds generated for 'chain 'd' and resid 64 through 66' Processing helix chain 'd' and resid 100 through 126 Processing helix chain 'e' and resid 88 through 93 removed outlier: 3.760A pdb=" N SER e 93 " --> pdb=" O GLU e 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 153 Processing helix chain 'f' and resid 126 through 154 removed outlier: 3.763A pdb=" N ASN f 154 " --> pdb=" O TYR f 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 80 removed outlier: 3.922A pdb=" N ASP g 80 " --> pdb=" O ASN g 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 140 Processing helix chain 'm' and resid 255 through 289 removed outlier: 4.664A pdb=" N VAL m 259 " --> pdb=" O HIS m 255 " (cutoff:3.500A) Processing helix chain 'n' and resid 252 through 288 Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.533A pdb=" N ASP O 82 " --> pdb=" O GLU O 79 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE O 83 " --> pdb=" O GLN O 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 79 through 83' Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 183 through 189 Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.621A pdb=" N TYR P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.673A pdb=" N ILE Q 83 " --> pdb=" O GLN Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 129 Processing helix chain 'Q' and resid 184 through 188 Processing helix chain 'R' and resid 28 through 30 No H-bonds generated for 'chain 'R' and resid 28 through 30' Processing helix chain 'R' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'D' and resid 27 through 28 removed outlier: 3.545A pdb=" N GLU D 27 " --> pdb=" O PHE D 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 42 through 45 removed outlier: 5.905A pdb=" N TRP D 43 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG D 72 " --> pdb=" O TRP D 43 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU D 45 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG E 115 " --> pdb=" O HIS D 89 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG D 91 " --> pdb=" O ARG E 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'E' and resid 38 through 41 removed outlier: 3.557A pdb=" N THR E 44 " --> pdb=" O SER E 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 37 through 41 removed outlier: 3.640A pdb=" N LEU F 47 " --> pdb=" O LEU F 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 removed outlier: 4.617A pdb=" N TRP F 59 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR F 99 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN F 60 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY F 94 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN G 98 " --> pdb=" O TYR F 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 122 through 124 removed outlier: 3.531A pdb=" N MET F 123 " --> pdb=" O ILE G 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 31 through 33 removed outlier: 7.099A pdb=" N VAL G 42 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU G 74 " --> pdb=" O VAL G 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 54 through 57 Processing sheet with id=AB1, first strand: chain 'd' and resid 26 through 29 removed outlier: 6.399A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU d 60 " --> pdb=" O VAL d 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP d 59 " --> pdb=" O THR d 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 42 through 46 removed outlier: 6.294A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY d 46 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG d 68 " --> pdb=" O GLY d 46 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'd' and resid 96 through 98 removed outlier: 3.507A pdb=" N MET e 123 " --> pdb=" O VAL d 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'e' and resid 37 through 41 removed outlier: 3.519A pdb=" N THR e 44 " --> pdb=" O SER e 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 37 through 41 Processing sheet with id=AB6, first strand: chain 'f' and resid 64 through 65 Processing sheet with id=AB7, first strand: chain 'f' and resid 112 through 116 removed outlier: 4.097A pdb=" N ARG f 115 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N CYS g 87 " --> pdb=" O SER g 94 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR g 85 " --> pdb=" O PRO g 96 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLN g 98 " --> pdb=" O GLY g 83 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLY g 83 " --> pdb=" O GLN g 98 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'g' and resid 31 through 34 removed outlier: 4.248A pdb=" N GLY g 75 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU g 44 " --> pdb=" O ASN g 73 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN g 73 " --> pdb=" O LEU g 44 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N CYS g 46 " --> pdb=" O LYS g 71 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYS g 71 " --> pdb=" O CYS g 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.715A pdb=" N ASP O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.634A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 118 through 119 removed outlier: 3.755A pdb=" N VAL O 134 " --> pdb=" O PHE O 119 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 154 through 155 removed outlier: 3.769A pdb=" N ASN O 146 " --> pdb=" O THR O 198 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.789A pdb=" N GLU P 10 " --> pdb=" O THR P 117 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR P 119 " --> pdb=" O GLU P 10 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N MET P 34 " --> pdb=" O LEU P 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.789A pdb=" N GLU P 10 " --> pdb=" O THR P 117 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR P 119 " --> pdb=" O GLU P 10 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL P 111 " --> pdb=" O ARG P 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 129 through 133 removed outlier: 3.721A pdb=" N GLY P 153 " --> pdb=" O TYR P 184 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR P 184 " --> pdb=" O GLY P 153 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 160 through 163 Processing sheet with id=AC9, first strand: chain 'Q' and resid 4 through 6 removed outlier: 3.611A pdb=" N ASP Q 70 " --> pdb=" O SER Q 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.753A pdb=" N LEU Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR Q 49 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 130 through 140 removed outlier: 5.823A pdb=" N TYR Q 174 " --> pdb=" O ASN Q 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 146 through 151 removed outlier: 3.642A pdb=" N ASN Q 146 " --> pdb=" O THR Q 198 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS Q 195 " --> pdb=" O LYS Q 208 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS Q 208 " --> pdb=" O CYS Q 195 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA Q 197 " --> pdb=" O ILE Q 206 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'R' and resid 10 through 12 removed outlier: 3.542A pdb=" N GLU R 10 " --> pdb=" O THR R 117 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR R 94 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N MET R 34 " --> pdb=" O LEU R 50 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU R 50 " --> pdb=" O MET R 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 129 through 130 Processing sheet with id=AD7, first strand: chain 'R' and resid 147 through 148 removed outlier: 3.543A pdb=" N SER R 189 " --> pdb=" O HIS R 173 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 160 through 163 removed outlier: 3.697A pdb=" N VAL R 215 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 178 through 179 removed outlier: 3.540A pdb=" N VAL R 178 " --> pdb=" O THR R 185 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR R 185 " --> pdb=" O VAL R 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 770 hydrogen bonds defined for protein. 2103 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 15815 1.57 - 1.93: 146 1.93 - 2.28: 0 2.28 - 2.64: 0 2.64 - 3.00: 1 Bond restraints: 15962 Sorted by residual: bond pdb=" C LYS Q 107 " pdb=" N ALA Q 110 " ideal model delta sigma weight residual 1.329 2.996 -1.667 1.40e-02 5.10e+03 1.42e+04 bond pdb=" N ALA Q 113 " pdb=" CA ALA Q 113 " ideal model delta sigma weight residual 1.453 1.493 -0.041 1.44e-02 4.82e+03 7.93e+00 bond pdb=" N ASP Q 111 " pdb=" CA ASP Q 111 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.22e-02 6.72e+03 7.11e+00 bond pdb=" C ALA Q 113 " pdb=" N PRO Q 114 " ideal model delta sigma weight residual 1.330 1.356 -0.026 1.22e-02 6.72e+03 4.70e+00 bond pdb=" N ALA Q 112 " pdb=" CA ALA Q 112 " ideal model delta sigma weight residual 1.455 1.480 -0.026 1.26e-02 6.30e+03 4.15e+00 ... (remaining 15957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.21: 21646 9.21 - 18.43: 8 18.43 - 27.64: 0 27.64 - 36.86: 0 36.86 - 46.07: 3 Bond angle restraints: 21657 Sorted by residual: angle pdb=" CA LYS Q 107 " pdb=" C LYS Q 107 " pdb=" N ALA Q 110 " ideal model delta sigma weight residual 115.63 158.07 -42.44 1.36e+00 5.41e-01 9.74e+02 angle pdb=" O LYS Q 107 " pdb=" C LYS Q 107 " pdb=" N ALA Q 110 " ideal model delta sigma weight residual 122.43 83.71 38.72 1.26e+00 6.30e-01 9.44e+02 angle pdb=" C LYS Q 107 " pdb=" N ALA Q 110 " pdb=" CA ALA Q 110 " ideal model delta sigma weight residual 121.70 75.63 46.07 1.80e+00 3.09e-01 6.55e+02 angle pdb=" N ALA Q 112 " pdb=" CA ALA Q 112 " pdb=" C ALA Q 112 " ideal model delta sigma weight residual 109.23 100.64 8.59 1.55e+00 4.16e-01 3.07e+01 angle pdb=" CB MET N 265 " pdb=" CG MET N 265 " pdb=" SD MET N 265 " ideal model delta sigma weight residual 112.70 99.44 13.26 3.00e+00 1.11e-01 1.95e+01 ... (remaining 21652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 8143 17.37 - 34.75: 1064 34.75 - 52.12: 272 52.12 - 69.50: 45 69.50 - 86.87: 21 Dihedral angle restraints: 9545 sinusoidal: 3731 harmonic: 5814 Sorted by residual: dihedral pdb=" CA LEU Q 94 " pdb=" C LEU Q 94 " pdb=" N PRO Q 95 " pdb=" CA PRO Q 95 " ideal model delta harmonic sigma weight residual -180.00 -116.22 -63.78 0 5.00e+00 4.00e-02 1.63e+02 dihedral pdb=" CB CYS Q 135 " pdb=" SG CYS Q 135 " pdb=" SG CYS Q 195 " pdb=" CB CYS Q 195 " ideal model delta sinusoidal sigma weight residual -86.00 -150.57 64.57 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CA ASN d 74 " pdb=" C ASN d 74 " pdb=" N GLY d 75 " pdb=" CA GLY d 75 " ideal model delta harmonic sigma weight residual -180.00 -149.31 -30.69 0 5.00e+00 4.00e-02 3.77e+01 ... (remaining 9542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2249 0.072 - 0.144: 246 0.144 - 0.216: 13 0.216 - 0.288: 3 0.288 - 0.360: 1 Chirality restraints: 2512 Sorted by residual: chirality pdb=" CA ASP Q 111 " pdb=" N ASP Q 111 " pdb=" C ASP Q 111 " pdb=" CB ASP Q 111 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C1 NAG d 202 " pdb=" ND2 ASN d 38 " pdb=" C2 NAG d 202 " pdb=" O5 NAG d 202 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB THR d 110 " pdb=" CA THR d 110 " pdb=" OG1 THR d 110 " pdb=" CG2 THR d 110 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2509 not shown) Planarity restraints: 2685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE Q 106 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C ILE Q 106 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE Q 106 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS Q 107 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS Q 107 " -0.031 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C LYS Q 107 " 0.059 2.00e-02 2.50e+03 pdb=" O LYS Q 107 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA Q 110 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU Q 94 " 0.052 5.00e-02 4.00e+02 7.85e-02 9.85e+00 pdb=" N PRO Q 95 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO Q 95 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO Q 95 " 0.043 5.00e-02 4.00e+02 ... (remaining 2682 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 653 2.71 - 3.26: 15504 3.26 - 3.80: 25372 3.80 - 4.35: 30688 4.35 - 4.90: 52117 Nonbonded interactions: 124334 Sorted by model distance: nonbonded pdb=" O GLY F 67 " pdb=" OH TYR R 102 " model vdw 2.162 3.040 nonbonded pdb=" OH TYR Q 36 " pdb=" OE1 GLN Q 89 " model vdw 2.175 3.040 nonbonded pdb=" OH TYR f 113 " pdb=" OD2 ASP g 35 " model vdw 2.192 3.040 nonbonded pdb=" NZ LYS O 61 " pdb=" OD2 ASP O 82 " model vdw 2.248 3.120 nonbonded pdb=" O GLN E 92 " pdb=" OH TYR E 96 " model vdw 2.249 3.040 ... (remaining 124329 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 'A' and resid 27 through 55) selection = chain 'B' selection = (chain 'a' and resid 27 through 55) selection = chain 'b' } ncs_group { reference = chain 'D' selection = (chain 'd' and resid 22 through 126) } ncs_group { reference = (chain 'E' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'F' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'e' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'f' and resid 33 through 153) } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'P' selection = chain 'R' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.770 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 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 : 0.014 1.667 15986 Z= 0.954 Angle : 0.908 46.074 21707 Z= 0.518 Chirality : 0.044 0.360 2512 Planarity : 0.004 0.078 2683 Dihedral : 16.636 86.872 5747 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.71 % Rotamer: Outliers : 4.34 % Allowed : 24.89 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 1936 helix: 2.17 (0.22), residues: 481 sheet: -0.23 (0.21), residues: 613 loop : -0.79 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 270 TYR 0.024 0.001 TYR b 33 PHE 0.024 0.001 PHE n 277 TRP 0.018 0.001 TRP Q 164 HIS 0.005 0.001 HIS R 208 Details of bonding type rmsd covalent geometry : bond 0.01358 (15962) covalent geometry : angle 0.90465 (21657) SS BOND : bond 0.00233 ( 22) SS BOND : angle 0.94109 ( 44) hydrogen bonds : bond 0.19650 ( 767) hydrogen bonds : angle 7.55124 ( 2103) link_NAG-ASN : bond 0.01293 ( 2) link_NAG-ASN : angle 4.87740 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 346 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 MET cc_start: 0.3402 (mpp) cc_final: 0.2875 (ptm) REVERT: E 123 MET cc_start: 0.2527 (ppp) cc_final: 0.2259 (ppp) REVERT: F 72 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6805 (t0) REVERT: F 121 ASN cc_start: 0.7266 (t0) cc_final: 0.6911 (p0) REVERT: F 124 GLU cc_start: 0.6372 (mt-10) cc_final: 0.5850 (mm-30) REVERT: b 46 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.5802 (mm) REVERT: d 98 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7167 (tm-30) REVERT: d 99 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6076 (mp) REVERT: e 44 THR cc_start: 0.8994 (m) cc_final: 0.8724 (p) REVERT: e 107 ASP cc_start: 0.8769 (p0) cc_final: 0.8452 (p0) REVERT: e 117 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7442 (tpt-90) REVERT: e 125 MET cc_start: 0.7612 (pmm) cc_final: 0.7155 (ptp) REVERT: e 135 ILE cc_start: 0.8136 (mm) cc_final: 0.7882 (tt) REVERT: f 123 MET cc_start: 0.0329 (ppp) cc_final: -0.0061 (ppp) REVERT: g 32 LYS cc_start: 0.5992 (tmtt) cc_final: 0.5250 (mptt) REVERT: g 51 LYS cc_start: 0.4686 (tttm) cc_final: 0.3458 (mmmt) REVERT: g 60 LYS cc_start: 0.3679 (pptt) cc_final: 0.3234 (pptt) REVERT: n 266 TYR cc_start: 0.6198 (m-10) cc_final: 0.5824 (m-80) REVERT: O 176 MET cc_start: 0.7840 (tpp) cc_final: 0.7442 (tpp) REVERT: O 207 VAL cc_start: 0.7697 (t) cc_final: 0.7463 (m) REVERT: P 84 LEU cc_start: 0.9064 (mt) cc_final: 0.8829 (mt) REVERT: Q 111 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.6535 (m-30) REVERT: Q 164 TRP cc_start: 0.7994 (m-90) cc_final: 0.7575 (m-90) REVERT: Q 168 ASP cc_start: 0.6514 (p0) cc_final: 0.6257 (p0) REVERT: Q 211 ASN cc_start: 0.5207 (p0) cc_final: 0.4287 (m-40) REVERT: R 144 MET cc_start: 0.2723 (OUTLIER) cc_final: 0.2293 (ptt) outliers start: 76 outliers final: 61 residues processed: 397 average time/residue: 0.1196 time to fit residues: 72.6211 Evaluate side-chains 356 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 290 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 119 CYS Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 81 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 111 ASP Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain g residue 33 VAL Chi-restraints excluded: chain m residue 260 ASN Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 254 LEU Chi-restraints excluded: chain n residue 263 TYR Chi-restraints excluded: chain n residue 277 PHE Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 199 HIS Chi-restraints excluded: chain P residue 66 ASP Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 34 ASN Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 56 SER Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 111 ASP Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 195 CYS Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 43 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 66 ASP Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 160 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN O 139 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 ASN Q 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.195299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120576 restraints weight = 24899.442| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.65 r_work: 0.3224 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 15986 Z= 0.333 Angle : 0.823 11.143 21707 Z= 0.418 Chirality : 0.049 0.217 2512 Planarity : 0.005 0.109 2683 Dihedral : 8.637 72.147 2282 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.64 % Favored : 95.20 % Rotamer: Outliers : 7.53 % Allowed : 21.97 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.05 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.19), residues: 1938 helix: 2.31 (0.22), residues: 486 sheet: -0.30 (0.21), residues: 638 loop : -1.01 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 156 TYR 0.029 0.002 TYR Q 174 PHE 0.025 0.002 PHE G 118 TRP 0.024 0.003 TRP R 112 HIS 0.006 0.002 HIS m 255 Details of bonding type rmsd covalent geometry : bond 0.00776 (15962) covalent geometry : angle 0.82134 (21657) SS BOND : bond 0.00392 ( 22) SS BOND : angle 1.16579 ( 44) hydrogen bonds : bond 0.04370 ( 767) hydrogen bonds : angle 5.67748 ( 2103) link_NAG-ASN : bond 0.00096 ( 2) link_NAG-ASN : angle 2.73816 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 296 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 23 LYS cc_start: 0.2903 (OUTLIER) cc_final: -0.1609 (pttt) REVERT: D 111 ASP cc_start: 0.6803 (t0) cc_final: 0.6392 (m-30) REVERT: E 123 MET cc_start: 0.6935 (ppp) cc_final: 0.6494 (ptt) REVERT: E 125 MET cc_start: 0.6039 (tpp) cc_final: 0.5778 (tpp) REVERT: F 114 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8728 (tt) REVERT: F 120 GLU cc_start: 0.7686 (pp20) cc_final: 0.7401 (pp20) REVERT: F 121 ASN cc_start: 0.7246 (t0) cc_final: 0.6799 (p0) REVERT: F 124 GLU cc_start: 0.6253 (mt-10) cc_final: 0.5893 (tm-30) REVERT: b 46 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6075 (mm) REVERT: d 36 ASN cc_start: 0.7617 (t0) cc_final: 0.6927 (p0) REVERT: d 56 THR cc_start: 0.7799 (p) cc_final: 0.7390 (p) REVERT: d 98 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7163 (tm-30) REVERT: d 99 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6553 (mp) REVERT: e 86 GLU cc_start: 0.9012 (mp0) cc_final: 0.8603 (mp0) REVERT: e 107 ASP cc_start: 0.8605 (p0) cc_final: 0.8221 (p0) REVERT: e 117 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7410 (tpt-90) REVERT: e 135 ILE cc_start: 0.8197 (mm) cc_final: 0.7949 (tt) REVERT: f 47 LEU cc_start: 0.8146 (mt) cc_final: 0.7817 (pp) REVERT: f 82 LEU cc_start: 0.6470 (tp) cc_final: 0.6027 (tp) REVERT: f 97 VAL cc_start: 0.3383 (t) cc_final: 0.2865 (t) REVERT: g 102 ARG cc_start: 0.5595 (tmm-80) cc_final: 0.5244 (tmm-80) REVERT: O 207 VAL cc_start: 0.7826 (t) cc_final: 0.7615 (m) REVERT: Q 18 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.6652 (ttp-170) REVERT: Q 46 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8739 (tp) REVERT: Q 135 CYS cc_start: 0.3386 (OUTLIER) cc_final: 0.3025 (m) REVERT: Q 164 TRP cc_start: 0.8150 (OUTLIER) cc_final: 0.7843 (m-90) REVERT: Q 168 ASP cc_start: 0.6659 (p0) cc_final: 0.6442 (p0) REVERT: Q 211 ASN cc_start: 0.5348 (p0) cc_final: 0.4504 (m-40) REVERT: R 18 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7669 (ttt) REVERT: R 144 MET cc_start: 0.2227 (OUTLIER) cc_final: 0.1893 (ptp) REVERT: R 203 THR cc_start: -0.0460 (OUTLIER) cc_final: -0.0687 (m) REVERT: R 216 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6688 (p0) outliers start: 132 outliers final: 89 residues processed: 401 average time/residue: 0.1115 time to fit residues: 70.2444 Evaluate side-chains 374 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 273 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 119 CYS Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 47 THR Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 74 ASN Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 126 ASP Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain g residue 58 ASP Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 199 HIS Chi-restraints excluded: chain P residue 48 MET Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 18 ARG Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 34 ASN Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 79 GLU Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 135 CYS Chi-restraints excluded: chain Q residue 151 ILE Chi-restraints excluded: chain Q residue 164 TRP Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 18 MET Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 205 ASN Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 216 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 74 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 137 optimal weight: 0.3980 chunk 164 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 GLN f 51 GLN f 60 GLN f 109 ASN ** g 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 ASN m 260 ASN ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN O 138 ASN P 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.200715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.126767 restraints weight = 26204.252| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.58 r_work: 0.3336 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15986 Z= 0.148 Angle : 0.692 13.029 21707 Z= 0.344 Chirality : 0.044 0.194 2512 Planarity : 0.004 0.091 2683 Dihedral : 7.442 64.596 2231 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.41 % Favored : 96.49 % Rotamer: Outliers : 6.22 % Allowed : 24.77 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.05 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.19), residues: 1938 helix: 2.26 (0.21), residues: 486 sheet: -0.23 (0.20), residues: 652 loop : -1.01 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 117 TYR 0.017 0.001 TYR Q 141 PHE 0.018 0.001 PHE n 277 TRP 0.019 0.002 TRP f 59 HIS 0.004 0.001 HIS m 255 Details of bonding type rmsd covalent geometry : bond 0.00330 (15962) covalent geometry : angle 0.69057 (21657) SS BOND : bond 0.00292 ( 22) SS BOND : angle 0.75949 ( 44) hydrogen bonds : bond 0.03889 ( 767) hydrogen bonds : angle 5.13713 ( 2103) link_NAG-ASN : bond 0.00408 ( 2) link_NAG-ASN : angle 2.95817 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 291 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 CYS cc_start: 0.6652 (OUTLIER) cc_final: 0.6294 (p) REVERT: D 111 ASP cc_start: 0.6835 (t0) cc_final: 0.6381 (m-30) REVERT: E 125 MET cc_start: 0.5998 (tpp) cc_final: 0.5650 (tpp) REVERT: F 72 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7254 (t0) REVERT: F 120 GLU cc_start: 0.7608 (pp20) cc_final: 0.7227 (pp20) REVERT: F 121 ASN cc_start: 0.7163 (t0) cc_final: 0.6755 (p0) REVERT: F 124 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5797 (tm-30) REVERT: G 41 SER cc_start: 0.9481 (m) cc_final: 0.9276 (m) REVERT: G 64 PHE cc_start: 0.7246 (t80) cc_final: 0.7041 (t80) REVERT: G 91 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7708 (tm-30) REVERT: M 262 MET cc_start: 0.7750 (tpp) cc_final: 0.6910 (tpp) REVERT: N 259 ASN cc_start: 0.8921 (t0) cc_final: 0.8182 (t0) REVERT: b 46 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6658 (pp) REVERT: d 36 ASN cc_start: 0.7526 (t0) cc_final: 0.6884 (p0) REVERT: e 83 SER cc_start: 0.8851 (t) cc_final: 0.8588 (p) REVERT: e 86 GLU cc_start: 0.8907 (mp0) cc_final: 0.8370 (mp0) REVERT: e 107 ASP cc_start: 0.8500 (p0) cc_final: 0.8239 (p0) REVERT: e 117 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7157 (tpt-90) REVERT: f 82 LEU cc_start: 0.6506 (tp) cc_final: 0.6204 (tp) REVERT: f 112 LEU cc_start: 0.4434 (tp) cc_final: 0.4224 (tp) REVERT: f 147 LEU cc_start: 0.6759 (tt) cc_final: 0.6445 (pp) REVERT: g 77 ASN cc_start: 0.7550 (p0) cc_final: 0.7246 (p0) REVERT: g 111 ASN cc_start: 0.6767 (OUTLIER) cc_final: 0.6441 (m110) REVERT: O 207 VAL cc_start: 0.7826 (t) cc_final: 0.7604 (m) REVERT: Q 135 CYS cc_start: 0.3829 (OUTLIER) cc_final: 0.3527 (m) REVERT: Q 164 TRP cc_start: 0.8024 (m-90) cc_final: 0.7712 (m-90) REVERT: Q 211 ASN cc_start: 0.5456 (p0) cc_final: 0.4756 (m-40) REVERT: R 18 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7843 (ttt) REVERT: R 144 MET cc_start: 0.2290 (OUTLIER) cc_final: 0.1991 (ptp) REVERT: R 216 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6855 (p0) outliers start: 109 outliers final: 70 residues processed: 367 average time/residue: 0.1104 time to fit residues: 63.5929 Evaluate side-chains 352 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 273 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 81 ASP Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 154 ASN Chi-restraints excluded: chain g residue 58 ASP Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain n residue 263 TYR Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 199 HIS Chi-restraints excluded: chain P residue 48 MET Chi-restraints excluded: chain P residue 66 ASP Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 135 CYS Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain R residue 18 MET Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 205 ASN Chi-restraints excluded: chain R residue 216 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 183 optimal weight: 6.9990 chunk 33 optimal weight: 0.4980 chunk 82 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 GLN f 51 GLN ** g 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN O 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.200753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123167 restraints weight = 26044.598| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.37 r_work: 0.3315 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15986 Z= 0.152 Angle : 0.685 10.519 21707 Z= 0.338 Chirality : 0.043 0.195 2512 Planarity : 0.004 0.090 2683 Dihedral : 7.043 63.898 2221 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.77 % Favored : 96.13 % Rotamer: Outliers : 6.79 % Allowed : 24.94 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.05 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.19), residues: 1938 helix: 2.35 (0.22), residues: 486 sheet: -0.21 (0.20), residues: 646 loop : -0.99 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG g 102 TYR 0.018 0.001 TYR Q 141 PHE 0.015 0.001 PHE n 277 TRP 0.023 0.002 TRP G 72 HIS 0.003 0.001 HIS m 255 Details of bonding type rmsd covalent geometry : bond 0.00346 (15962) covalent geometry : angle 0.68360 (21657) SS BOND : bond 0.00254 ( 22) SS BOND : angle 0.83057 ( 44) hydrogen bonds : bond 0.03625 ( 767) hydrogen bonds : angle 4.88307 ( 2103) link_NAG-ASN : bond 0.00325 ( 2) link_NAG-ASN : angle 2.43964 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 281 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 23 LYS cc_start: 0.2479 (OUTLIER) cc_final: -0.1817 (pttt) REVERT: D 93 CYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6585 (p) REVERT: D 111 ASP cc_start: 0.6920 (t0) cc_final: 0.6497 (m-30) REVERT: E 125 MET cc_start: 0.5984 (tpp) cc_final: 0.5711 (tpp) REVERT: F 48 THR cc_start: 0.8623 (m) cc_final: 0.8227 (p) REVERT: F 72 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7277 (t0) REVERT: F 124 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5756 (tm-30) REVERT: G 64 PHE cc_start: 0.7288 (t80) cc_final: 0.7052 (t80) REVERT: G 91 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7762 (tm-30) REVERT: M 262 MET cc_start: 0.7976 (tpp) cc_final: 0.7138 (tpp) REVERT: N 259 ASN cc_start: 0.8997 (t0) cc_final: 0.8208 (t0) REVERT: N 270 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8033 (mt) REVERT: d 56 THR cc_start: 0.7831 (p) cc_final: 0.7373 (p) REVERT: e 83 SER cc_start: 0.8821 (t) cc_final: 0.8577 (p) REVERT: e 86 GLU cc_start: 0.8865 (mp0) cc_final: 0.8606 (mp0) REVERT: e 107 ASP cc_start: 0.8485 (p0) cc_final: 0.8274 (p0) REVERT: e 117 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7061 (tpt-90) REVERT: f 82 LEU cc_start: 0.6473 (tp) cc_final: 0.6227 (tp) REVERT: f 147 LEU cc_start: 0.6683 (tt) cc_final: 0.6404 (pp) REVERT: g 32 LYS cc_start: 0.6803 (tmtt) cc_final: 0.5622 (pttp) REVERT: g 97 LEU cc_start: 0.3834 (OUTLIER) cc_final: 0.3188 (mp) REVERT: m 271 MET cc_start: 0.8437 (ttt) cc_final: 0.8027 (tpt) REVERT: O 176 MET cc_start: 0.7610 (ttt) cc_final: 0.7332 (ttt) REVERT: O 207 VAL cc_start: 0.7848 (t) cc_final: 0.7646 (m) REVERT: Q 46 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8592 (tp) REVERT: Q 96 TRP cc_start: 0.8760 (m100) cc_final: 0.8241 (m100) REVERT: Q 135 CYS cc_start: 0.3950 (OUTLIER) cc_final: 0.3678 (m) REVERT: Q 211 ASN cc_start: 0.5460 (p0) cc_final: 0.4943 (m-40) REVERT: R 18 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7661 (ttt) REVERT: R 144 MET cc_start: 0.2114 (OUTLIER) cc_final: 0.1785 (ptp) outliers start: 119 outliers final: 76 residues processed: 362 average time/residue: 0.1064 time to fit residues: 60.4906 Evaluate side-chains 352 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 266 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 265 MET Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 74 ASN Chi-restraints excluded: chain d residue 81 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain g residue 58 ASP Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain n residue 255 LEU Chi-restraints excluded: chain n residue 263 TYR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 48 MET Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 135 CYS Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 18 MET Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 144 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 128 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 chunk 126 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN R 52 ASN ** R 205 ASN ** 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 = 0.4548 r_free = 0.4548 target = 0.201284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125955 restraints weight = 26277.017| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.45 r_work: 0.3343 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15986 Z= 0.135 Angle : 0.670 10.567 21707 Z= 0.333 Chirality : 0.043 0.216 2512 Planarity : 0.004 0.110 2683 Dihedral : 6.564 60.894 2215 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 6.11 % Allowed : 25.51 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.05 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 1938 helix: 2.36 (0.22), residues: 486 sheet: -0.14 (0.20), residues: 650 loop : -0.91 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG g 102 TYR 0.017 0.001 TYR f 99 PHE 0.016 0.001 PHE n 277 TRP 0.029 0.002 TRP g 72 HIS 0.003 0.001 HIS m 255 Details of bonding type rmsd covalent geometry : bond 0.00302 (15962) covalent geometry : angle 0.66806 (21657) SS BOND : bond 0.00368 ( 22) SS BOND : angle 1.04894 ( 44) hydrogen bonds : bond 0.03455 ( 767) hydrogen bonds : angle 4.70315 ( 2103) link_NAG-ASN : bond 0.00369 ( 2) link_NAG-ASN : angle 2.38688 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 300 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 23 LYS cc_start: 0.1979 (OUTLIER) cc_final: -0.2358 (pttt) REVERT: D 93 CYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6607 (p) REVERT: D 111 ASP cc_start: 0.6871 (t0) cc_final: 0.6515 (m-30) REVERT: E 125 MET cc_start: 0.6059 (tpp) cc_final: 0.5596 (tpp) REVERT: F 48 THR cc_start: 0.8598 (m) cc_final: 0.8272 (p) REVERT: F 72 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7292 (t0) REVERT: F 120 GLU cc_start: 0.7232 (pp20) cc_final: 0.7008 (pp20) REVERT: F 121 ASN cc_start: 0.7358 (t0) cc_final: 0.7026 (p0) REVERT: F 124 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5797 (tm-30) REVERT: G 56 PHE cc_start: 0.7791 (m-80) cc_final: 0.7401 (m-10) REVERT: G 64 PHE cc_start: 0.7350 (t80) cc_final: 0.7067 (t80) REVERT: G 114 THR cc_start: 0.7358 (p) cc_final: 0.7072 (p) REVERT: M 262 MET cc_start: 0.8137 (tpp) cc_final: 0.7211 (tpp) REVERT: N 259 ASN cc_start: 0.9056 (t0) cc_final: 0.8282 (t0) REVERT: N 270 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8053 (mt) REVERT: b 46 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.5891 (mm) REVERT: e 83 SER cc_start: 0.8833 (t) cc_final: 0.8619 (p) REVERT: e 86 GLU cc_start: 0.8871 (mp0) cc_final: 0.8604 (mp0) REVERT: e 107 ASP cc_start: 0.8451 (p0) cc_final: 0.8244 (p0) REVERT: e 117 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7054 (ttp-110) REVERT: f 47 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7986 (mp) REVERT: f 52 TYR cc_start: 0.2661 (OUTLIER) cc_final: 0.1015 (p90) REVERT: f 147 LEU cc_start: 0.6695 (tt) cc_final: 0.6415 (pp) REVERT: g 44 LEU cc_start: 0.4635 (mm) cc_final: 0.4374 (mm) REVERT: g 97 LEU cc_start: 0.3733 (OUTLIER) cc_final: 0.3016 (mp) REVERT: m 260 ASN cc_start: 0.7827 (t0) cc_final: 0.7392 (t0) REVERT: n 253 LEU cc_start: 0.7856 (pt) cc_final: 0.7629 (mm) REVERT: O 176 MET cc_start: 0.7589 (ttt) cc_final: 0.7267 (ttt) REVERT: O 207 VAL cc_start: 0.7822 (t) cc_final: 0.7620 (m) REVERT: P 6 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: Q 46 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8601 (tp) REVERT: Q 96 TRP cc_start: 0.8714 (m100) cc_final: 0.8218 (m100) REVERT: Q 135 CYS cc_start: 0.3924 (OUTLIER) cc_final: 0.3702 (m) REVERT: Q 211 ASN cc_start: 0.5491 (p0) cc_final: 0.5153 (t0) outliers start: 107 outliers final: 74 residues processed: 374 average time/residue: 0.1031 time to fit residues: 60.5824 Evaluate side-chains 366 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 280 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 265 MET Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 74 ASN Chi-restraints excluded: chain d residue 81 ASP Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 135 ILE Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 154 ASN Chi-restraints excluded: chain g residue 58 ASP Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain n residue 255 LEU Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 48 MET Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 135 CYS Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 166 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 116 optimal weight: 0.0020 chunk 64 optimal weight: 0.0040 chunk 6 optimal weight: 8.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN P 35 ASN ** R 205 ASN ** 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 = 0.4553 r_free = 0.4553 target = 0.201527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.128926 restraints weight = 26130.669| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.47 r_work: 0.3366 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15986 Z= 0.125 Angle : 0.665 11.160 21707 Z= 0.330 Chirality : 0.042 0.246 2512 Planarity : 0.004 0.087 2683 Dihedral : 6.108 58.889 2205 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.77 % Favored : 96.13 % Rotamer: Outliers : 5.99 % Allowed : 24.94 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.05 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 1938 helix: 2.38 (0.21), residues: 486 sheet: -0.10 (0.21), residues: 650 loop : -0.83 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 270 TYR 0.022 0.001 TYR Q 141 PHE 0.038 0.001 PHE G 118 TRP 0.039 0.001 TRP g 72 HIS 0.002 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00279 (15962) covalent geometry : angle 0.66337 (21657) SS BOND : bond 0.00224 ( 22) SS BOND : angle 0.86827 ( 44) hydrogen bonds : bond 0.03356 ( 767) hydrogen bonds : angle 4.57547 ( 2103) link_NAG-ASN : bond 0.00366 ( 2) link_NAG-ASN : angle 2.25680 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 298 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 23 LYS cc_start: 0.1732 (OUTLIER) cc_final: -0.2493 (pttt) REVERT: D 93 CYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6769 (p) REVERT: E 125 MET cc_start: 0.6048 (tpp) cc_final: 0.5656 (tpp) REVERT: F 48 THR cc_start: 0.8614 (m) cc_final: 0.8337 (p) REVERT: F 124 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5754 (tm-30) REVERT: G 56 PHE cc_start: 0.7743 (m-80) cc_final: 0.7462 (m-10) REVERT: G 64 PHE cc_start: 0.7345 (t80) cc_final: 0.7058 (t80) REVERT: M 262 MET cc_start: 0.8265 (tpp) cc_final: 0.7529 (tpp) REVERT: N 256 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8525 (pt0) REVERT: N 259 ASN cc_start: 0.9067 (t0) cc_final: 0.8658 (t0) REVERT: N 270 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8008 (mt) REVERT: b 46 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.5836 (mm) REVERT: d 56 THR cc_start: 0.7678 (p) cc_final: 0.7291 (p) REVERT: e 83 SER cc_start: 0.8810 (t) cc_final: 0.8608 (p) REVERT: e 86 GLU cc_start: 0.8847 (mp0) cc_final: 0.8583 (mp0) REVERT: e 107 ASP cc_start: 0.8428 (p0) cc_final: 0.8226 (p0) REVERT: e 117 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7054 (tpt-90) REVERT: f 47 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7904 (mt) REVERT: g 44 LEU cc_start: 0.4817 (mm) cc_final: 0.4562 (mm) REVERT: g 97 LEU cc_start: 0.3784 (OUTLIER) cc_final: 0.3123 (mp) REVERT: m 260 ASN cc_start: 0.7867 (t0) cc_final: 0.7602 (t0) REVERT: n 253 LEU cc_start: 0.7862 (pt) cc_final: 0.7612 (mm) REVERT: O 176 MET cc_start: 0.7535 (ttt) cc_final: 0.7204 (ttt) REVERT: P 60 TYR cc_start: 0.9114 (m-80) cc_final: 0.8615 (m-80) REVERT: P 121 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: Q 46 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8578 (tp) REVERT: Q 96 TRP cc_start: 0.8642 (m100) cc_final: 0.6631 (m-90) outliers start: 105 outliers final: 78 residues processed: 370 average time/residue: 0.1164 time to fit residues: 67.1437 Evaluate side-chains 364 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 277 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 265 MET Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 74 ASN Chi-restraints excluded: chain d residue 81 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 135 ILE Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 107 CYS Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain n residue 255 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 48 MET Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 79 GLU Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 11 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 183 optimal weight: 0.0870 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 ASN O 77 ASN P 173 HIS R 6 GLN ** R 205 ASN ** 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 = 0.4511 r_free = 0.4511 target = 0.197765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120485 restraints weight = 25936.845| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.45 r_work: 0.3262 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15986 Z= 0.246 Angle : 0.743 10.827 21707 Z= 0.371 Chirality : 0.045 0.194 2512 Planarity : 0.004 0.106 2683 Dihedral : 6.442 68.223 2204 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.54 % Favored : 95.36 % Rotamer: Outliers : 6.68 % Allowed : 25.00 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.05 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 1938 helix: 2.36 (0.22), residues: 482 sheet: -0.21 (0.20), residues: 646 loop : -0.96 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG g 102 TYR 0.020 0.002 TYR P 108 PHE 0.040 0.002 PHE G 118 TRP 0.020 0.002 TRP g 72 HIS 0.004 0.001 HIS P 173 Details of bonding type rmsd covalent geometry : bond 0.00575 (15962) covalent geometry : angle 0.73935 (21657) SS BOND : bond 0.00286 ( 22) SS BOND : angle 1.63313 ( 44) hydrogen bonds : bond 0.03591 ( 767) hydrogen bonds : angle 4.78046 ( 2103) link_NAG-ASN : bond 0.00215 ( 2) link_NAG-ASN : angle 2.17027 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 277 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 23 LYS cc_start: 0.1922 (OUTLIER) cc_final: -0.2104 (pttt) REVERT: D 93 CYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6943 (p) REVERT: D 111 ASP cc_start: 0.6713 (t0) cc_final: 0.6284 (m-30) REVERT: E 125 MET cc_start: 0.6164 (tpp) cc_final: 0.5829 (tpp) REVERT: F 124 GLU cc_start: 0.5979 (OUTLIER) cc_final: 0.5766 (tm-30) REVERT: G 56 PHE cc_start: 0.7911 (m-80) cc_final: 0.7646 (m-10) REVERT: G 61 MET cc_start: 0.7891 (mtp) cc_final: 0.7639 (mtp) REVERT: M 262 MET cc_start: 0.8353 (tpp) cc_final: 0.7344 (tpp) REVERT: M 269 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8587 (tp) REVERT: N 256 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8548 (pt0) REVERT: N 259 ASN cc_start: 0.9152 (t0) cc_final: 0.8411 (t0) REVERT: d 98 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7028 (tm-30) REVERT: d 99 LEU cc_start: 0.7599 (mt) cc_final: 0.7276 (mt) REVERT: e 83 SER cc_start: 0.8865 (t) cc_final: 0.8623 (p) REVERT: e 86 GLU cc_start: 0.8894 (mp0) cc_final: 0.8313 (mp0) REVERT: e 107 ASP cc_start: 0.8451 (p0) cc_final: 0.8247 (p0) REVERT: e 117 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7151 (tpt-90) REVERT: f 47 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8049 (mt) REVERT: g 51 LYS cc_start: 0.4129 (tmtt) cc_final: 0.3083 (mmmt) REVERT: g 97 LEU cc_start: 0.4022 (OUTLIER) cc_final: 0.3557 (mp) REVERT: m 260 ASN cc_start: 0.8018 (t0) cc_final: 0.7552 (t0) REVERT: m 271 MET cc_start: 0.8378 (ttt) cc_final: 0.8072 (tpt) REVERT: n 266 TYR cc_start: 0.7963 (m-80) cc_final: 0.7663 (m-80) REVERT: P 6 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: Q 46 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8640 (tp) REVERT: Q 168 ASP cc_start: 0.7264 (p0) cc_final: 0.6709 (p0) outliers start: 117 outliers final: 93 residues processed: 361 average time/residue: 0.1104 time to fit residues: 63.1214 Evaluate side-chains 365 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 264 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 265 MET Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 47 THR Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 74 ASN Chi-restraints excluded: chain d residue 81 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 135 ILE Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 58 ASP Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 107 CYS Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain n residue 255 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 199 HIS Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 48 MET Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 9 SER Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 79 GLU Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 195 CYS Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 66 ASP Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 179 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 66 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 159 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN O 77 ASN R 6 GLN ** R 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.199746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.126098 restraints weight = 26154.266| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.47 r_work: 0.3317 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15986 Z= 0.154 Angle : 0.712 11.021 21707 Z= 0.351 Chirality : 0.044 0.238 2512 Planarity : 0.004 0.091 2683 Dihedral : 6.215 64.362 2202 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.87 % Rotamer: Outliers : 6.34 % Allowed : 25.46 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.05 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1938 helix: 2.39 (0.22), residues: 482 sheet: -0.18 (0.20), residues: 648 loop : -0.92 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 63 TYR 0.016 0.001 TYR f 99 PHE 0.034 0.001 PHE G 118 TRP 0.020 0.002 TRP g 72 HIS 0.003 0.001 HIS P 173 Details of bonding type rmsd covalent geometry : bond 0.00352 (15962) covalent geometry : angle 0.70914 (21657) SS BOND : bond 0.00276 ( 22) SS BOND : angle 1.37964 ( 44) hydrogen bonds : bond 0.03408 ( 767) hydrogen bonds : angle 4.62463 ( 2103) link_NAG-ASN : bond 0.00285 ( 2) link_NAG-ASN : angle 2.14742 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 276 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 23 LYS cc_start: 0.1618 (OUTLIER) cc_final: -0.2290 (pttt) REVERT: D 93 CYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6822 (p) REVERT: D 111 ASP cc_start: 0.6691 (t0) cc_final: 0.6293 (m-30) REVERT: E 125 MET cc_start: 0.6147 (tpp) cc_final: 0.5730 (tpp) REVERT: F 48 THR cc_start: 0.8636 (m) cc_final: 0.8249 (p) REVERT: F 124 GLU cc_start: 0.5840 (OUTLIER) cc_final: 0.5609 (tm-30) REVERT: G 56 PHE cc_start: 0.7869 (m-80) cc_final: 0.7636 (m-10) REVERT: G 61 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7628 (mtp) REVERT: M 262 MET cc_start: 0.8413 (tpp) cc_final: 0.7358 (tpp) REVERT: M 269 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8562 (tp) REVERT: N 259 ASN cc_start: 0.9113 (t0) cc_final: 0.8352 (t0) REVERT: d 56 THR cc_start: 0.7643 (p) cc_final: 0.7424 (p) REVERT: e 83 SER cc_start: 0.8856 (t) cc_final: 0.8626 (p) REVERT: e 86 GLU cc_start: 0.8865 (mp0) cc_final: 0.8281 (mp0) REVERT: e 117 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7208 (ttp-110) REVERT: f 47 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7861 (mt) REVERT: f 147 LEU cc_start: 0.6251 (tt) cc_final: 0.6043 (pp) REVERT: g 51 LYS cc_start: 0.4000 (tmtt) cc_final: 0.2966 (mmtt) REVERT: g 108 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7480 (pt) REVERT: m 260 ASN cc_start: 0.7890 (t0) cc_final: 0.7494 (t0) REVERT: n 253 LEU cc_start: 0.7903 (pt) cc_final: 0.7650 (mm) REVERT: n 266 TYR cc_start: 0.7933 (m-80) cc_final: 0.7686 (m-80) REVERT: P 6 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.7934 (mt0) REVERT: P 60 TYR cc_start: 0.9140 (m-80) cc_final: 0.8601 (m-80) REVERT: Q 46 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8573 (tp) REVERT: Q 211 ASN cc_start: 0.5138 (p0) cc_final: 0.4596 (m-40) outliers start: 111 outliers final: 88 residues processed: 355 average time/residue: 0.1137 time to fit residues: 63.4084 Evaluate side-chains 367 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 270 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 265 MET Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 81 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 135 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 154 ASN Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 58 ASP Chi-restraints excluded: chain g residue 77 ASN Chi-restraints excluded: chain g residue 107 CYS Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 265 THR Chi-restraints excluded: chain n residue 255 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 199 HIS Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 48 MET Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 9 SER Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 79 GLU Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 195 CYS Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 179 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 161 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 chunk 159 optimal weight: 0.0060 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 GLN ** f 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN R 6 GLN ** R 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.198946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121874 restraints weight = 26096.011| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.43 r_work: 0.3309 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15986 Z= 0.186 Angle : 0.736 11.543 21707 Z= 0.364 Chirality : 0.044 0.224 2512 Planarity : 0.004 0.095 2683 Dihedral : 6.346 64.919 2202 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.51 % Rotamer: Outliers : 5.88 % Allowed : 26.08 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.05 % Twisted Proline : 1.35 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.19), residues: 1938 helix: 2.36 (0.21), residues: 482 sheet: -0.25 (0.20), residues: 641 loop : -0.98 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 63 TYR 0.015 0.001 TYR P 108 PHE 0.033 0.002 PHE G 118 TRP 0.017 0.002 TRP g 72 HIS 0.003 0.001 HIS P 173 Details of bonding type rmsd covalent geometry : bond 0.00435 (15962) covalent geometry : angle 0.73329 (21657) SS BOND : bond 0.00338 ( 22) SS BOND : angle 1.31727 ( 44) hydrogen bonds : bond 0.03431 ( 767) hydrogen bonds : angle 4.63220 ( 2103) link_NAG-ASN : bond 0.00254 ( 2) link_NAG-ASN : angle 2.05328 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 272 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 23 LYS cc_start: 0.1501 (OUTLIER) cc_final: -0.2376 (pttt) REVERT: D 93 CYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6814 (p) REVERT: D 111 ASP cc_start: 0.6682 (t0) cc_final: 0.6292 (m-30) REVERT: E 125 MET cc_start: 0.6104 (tpp) cc_final: 0.5848 (tpp) REVERT: F 48 THR cc_start: 0.8653 (m) cc_final: 0.8242 (p) REVERT: F 121 ASN cc_start: 0.7004 (t0) cc_final: 0.6720 (t0) REVERT: G 56 PHE cc_start: 0.7855 (m-80) cc_final: 0.7625 (m-10) REVERT: G 61 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7640 (mtp) REVERT: M 262 MET cc_start: 0.8434 (tpp) cc_final: 0.7405 (tpp) REVERT: M 269 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8565 (tp) REVERT: N 259 ASN cc_start: 0.9122 (t0) cc_final: 0.8357 (t0) REVERT: b 35 LEU cc_start: 0.8993 (tt) cc_final: 0.8784 (pp) REVERT: d 98 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6821 (tm-30) REVERT: d 99 LEU cc_start: 0.7529 (mt) cc_final: 0.7225 (mp) REVERT: e 83 SER cc_start: 0.8825 (t) cc_final: 0.8601 (p) REVERT: e 86 GLU cc_start: 0.8842 (mp0) cc_final: 0.8236 (mp0) REVERT: e 117 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7092 (tpt-90) REVERT: f 47 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7864 (mt) REVERT: g 51 LYS cc_start: 0.4026 (tmtt) cc_final: 0.2990 (mmtt) REVERT: g 97 LEU cc_start: 0.3851 (OUTLIER) cc_final: 0.3426 (mp) REVERT: g 102 ARG cc_start: 0.6137 (ttp80) cc_final: 0.5930 (ttp80) REVERT: g 108 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7554 (pt) REVERT: m 260 ASN cc_start: 0.7923 (t0) cc_final: 0.7511 (t0) REVERT: m 271 MET cc_start: 0.8521 (ttt) cc_final: 0.8203 (tpt) REVERT: n 253 LEU cc_start: 0.7886 (pt) cc_final: 0.7602 (mm) REVERT: n 266 TYR cc_start: 0.7926 (m-80) cc_final: 0.7700 (m-80) REVERT: P 6 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.7877 (mt0) REVERT: P 10 GLU cc_start: 0.7200 (pt0) cc_final: 0.6930 (pt0) REVERT: P 60 TYR cc_start: 0.9161 (m-80) cc_final: 0.8656 (m-80) REVERT: Q 46 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8600 (tp) REVERT: Q 211 ASN cc_start: 0.5237 (p0) cc_final: 0.4768 (m-40) outliers start: 103 outliers final: 88 residues processed: 349 average time/residue: 0.1112 time to fit residues: 61.2372 Evaluate side-chains 361 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 264 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 265 MET Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 81 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 135 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 154 ASN Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 58 ASP Chi-restraints excluded: chain g residue 77 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 107 CYS Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain n residue 255 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 199 HIS Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 48 MET Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 9 SER Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 79 GLU Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 195 CYS Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 68 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 151 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 141 optimal weight: 0.0010 chunk 61 optimal weight: 0.0270 chunk 54 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 6 GLN ** R 205 ASN ** 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 = 0.4554 r_free = 0.4554 target = 0.201641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.127385 restraints weight = 26098.295| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.19 r_work: 0.3374 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15986 Z= 0.126 Angle : 0.718 12.701 21707 Z= 0.351 Chirality : 0.043 0.198 2512 Planarity : 0.004 0.085 2683 Dihedral : 5.980 57.135 2202 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 4.62 % Allowed : 27.45 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.05 % Twisted Proline : 1.35 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 1938 helix: 2.37 (0.21), residues: 482 sheet: -0.10 (0.21), residues: 636 loop : -0.88 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 117 TYR 0.013 0.001 TYR Q 141 PHE 0.032 0.001 PHE G 118 TRP 0.017 0.001 TRP g 72 HIS 0.002 0.001 HIS m 255 Details of bonding type rmsd covalent geometry : bond 0.00281 (15962) covalent geometry : angle 0.71581 (21657) SS BOND : bond 0.00274 ( 22) SS BOND : angle 1.35579 ( 44) hydrogen bonds : bond 0.03285 ( 767) hydrogen bonds : angle 4.46041 ( 2103) link_NAG-ASN : bond 0.00389 ( 2) link_NAG-ASN : angle 1.74062 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 285 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 23 LYS cc_start: 0.1089 (OUTLIER) cc_final: -0.2815 (pttt) REVERT: D 93 CYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6759 (p) REVERT: D 111 ASP cc_start: 0.6653 (t0) cc_final: 0.6268 (m-30) REVERT: E 125 MET cc_start: 0.6061 (tpp) cc_final: 0.5699 (tpp) REVERT: F 48 THR cc_start: 0.8611 (m) cc_final: 0.8334 (p) REVERT: F 121 ASN cc_start: 0.7075 (t0) cc_final: 0.6785 (t0) REVERT: G 30 LEU cc_start: 0.7944 (mt) cc_final: 0.7548 (mp) REVERT: G 56 PHE cc_start: 0.7811 (m-80) cc_final: 0.7537 (m-10) REVERT: G 103 MET cc_start: 0.7623 (mmt) cc_final: 0.7253 (mmm) REVERT: M 262 MET cc_start: 0.8487 (tpp) cc_final: 0.7755 (tpp) REVERT: M 269 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8611 (tp) REVERT: N 259 ASN cc_start: 0.9113 (t0) cc_final: 0.8702 (t0) REVERT: e 86 GLU cc_start: 0.8851 (mp0) cc_final: 0.8236 (mp0) REVERT: e 117 ARG cc_start: 0.7965 (ttp80) cc_final: 0.6973 (ttp-110) REVERT: f 47 LEU cc_start: 0.8493 (pp) cc_final: 0.7879 (mt) REVERT: f 52 TYR cc_start: 0.2906 (OUTLIER) cc_final: 0.1181 (p90) REVERT: g 51 LYS cc_start: 0.4096 (tmtt) cc_final: 0.3094 (mmtt) REVERT: g 97 LEU cc_start: 0.4236 (OUTLIER) cc_final: 0.3786 (mp) REVERT: m 260 ASN cc_start: 0.7842 (t0) cc_final: 0.7603 (t0) REVERT: m 271 MET cc_start: 0.8543 (ttt) cc_final: 0.8191 (tpt) REVERT: n 253 LEU cc_start: 0.7858 (pt) cc_final: 0.7614 (mm) REVERT: n 266 TYR cc_start: 0.7839 (m-80) cc_final: 0.7612 (m-80) REVERT: O 176 MET cc_start: 0.7359 (ttt) cc_final: 0.7132 (ttt) REVERT: P 6 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: P 60 TYR cc_start: 0.9075 (m-80) cc_final: 0.8598 (m-80) REVERT: P 84 LEU cc_start: 0.9034 (mt) cc_final: 0.8613 (mp) REVERT: Q 46 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8567 (tp) REVERT: Q 96 TRP cc_start: 0.8640 (m100) cc_final: 0.8206 (m100) REVERT: Q 125 GLN cc_start: 0.3192 (mm110) cc_final: 0.2958 (mm-40) REVERT: Q 211 ASN cc_start: 0.5223 (p0) cc_final: 0.4894 (m-40) outliers start: 81 outliers final: 67 residues processed: 343 average time/residue: 0.1148 time to fit residues: 62.0547 Evaluate side-chains 348 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 274 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 265 MET Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 81 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 135 ILE Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 107 CYS Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain n residue 255 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 48 MET Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 79 GLU Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 195 CYS Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 2 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 183 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 6 GLN ** R 205 ASN ** 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 = 0.4520 r_free = 0.4520 target = 0.198666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.119540 restraints weight = 25963.627| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.05 r_work: 0.3332 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15986 Z= 0.200 Angle : 0.740 11.458 21707 Z= 0.365 Chirality : 0.044 0.205 2512 Planarity : 0.004 0.097 2683 Dihedral : 6.082 63.297 2200 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.64 % Favored : 95.25 % Rotamer: Outliers : 4.51 % Allowed : 27.80 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.05 % Twisted Proline : 1.35 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.19), residues: 1938 helix: 2.44 (0.21), residues: 482 sheet: -0.25 (0.21), residues: 635 loop : -0.89 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 117 TYR 0.024 0.001 TYR f 36 PHE 0.030 0.002 PHE G 118 TRP 0.021 0.002 TRP G 72 HIS 0.003 0.001 HIS P 173 Details of bonding type rmsd covalent geometry : bond 0.00466 (15962) covalent geometry : angle 0.73800 (21657) SS BOND : bond 0.00299 ( 22) SS BOND : angle 1.33980 ( 44) hydrogen bonds : bond 0.03389 ( 767) hydrogen bonds : angle 4.57155 ( 2103) link_NAG-ASN : bond 0.00204 ( 2) link_NAG-ASN : angle 2.00034 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6003.74 seconds wall clock time: 103 minutes 42.72 seconds (6222.72 seconds total)