Starting phenix.real_space_refine on Thu Feb 5 07:25:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jy1_61884/02_2026/9jy1_61884.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jy1_61884/02_2026/9jy1_61884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jy1_61884/02_2026/9jy1_61884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jy1_61884/02_2026/9jy1_61884.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jy1_61884/02_2026/9jy1_61884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jy1_61884/02_2026/9jy1_61884.map" } resolution = 3.08 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= 0.018 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 10042 2.51 5 N 2508 2.21 5 O 2988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15642 Number of models: 1 Model: "" Number of chains: 22 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: "O" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1583 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 6, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 39 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: "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: "Q" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1583 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 39 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: "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 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: 2.89, per 1000 atoms: 0.18 Number of scatterers: 15642 At special positions: 0 Unit cell: (183.752, 137.608, 130.192, 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 2988 8.00 N 2508 7.00 C 10042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 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 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 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=2.04 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 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 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 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=2.04 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 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 " " NAG d 201 " - " ASN d 74 " " NAG d 202 " - " ASN d 38 " Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 646.5 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: 3728 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 36 sheets defined 27.2% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.697A 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 'O' and resid 122 through 129 Processing helix chain 'O' and resid 184 through 189 Processing helix chain 'a' and resid 29 through 54 removed outlier: 4.836A pdb=" N LEU a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP a 36 " --> pdb=" O CYS a 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 55 removed outlier: 3.528A pdb=" N PHE b 55 " --> pdb=" O LEU b 51 " (cutoff:3.500A) 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 126 through 153 Processing helix chain 'f' and resid 126 through 154 removed outlier: 3.779A pdb=" N ASN f 154 " --> pdb=" O TYR f 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 80 removed outlier: 3.656A pdb=" N LYS g 79 " --> pdb=" O SER g 76 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP g 80 " --> pdb=" O ASN g 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 76 through 80' Processing helix chain 'g' and resid 111 through 140 Processing helix chain 'm' and resid 256 through 289 Processing helix chain 'n' and resid 252 through 288 Processing helix chain 'R' and resid 28 through 32 removed outlier: 3.701A pdb=" N TYR R 32 " --> pdb=" O PHE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'Q' and resid 122 through 129 Processing helix chain 'Q' and resid 184 through 189 Processing helix chain 'A' and resid 29 through 54 removed outlier: 4.837A pdb=" N LEU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.728A 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 126 through 153 Processing helix chain 'F' and resid 126 through 154 removed outlier: 3.780A pdb=" N ASN F 154 " --> pdb=" O TYR F 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 80 removed outlier: 3.657A pdb=" N LYS G 79 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP G 80 " --> pdb=" O ASN G 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 76 through 80' Processing helix chain 'G' and resid 111 through 140 Processing helix chain 'M' and resid 256 through 289 Processing helix chain 'N' and resid 252 through 288 Processing sheet with id=AA1, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.544A pdb=" N VAL P 12 " --> pdb=" O THR P 119 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET P 34 " --> pdb=" O LEU P 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.544A pdb=" N VAL P 12 " --> pdb=" O THR P 119 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL P 111 " --> pdb=" O ARG P 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 129 through 133 removed outlier: 4.756A pdb=" N LEU P 150 " --> pdb=" O SER P 188 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER P 188 " --> pdb=" O LEU P 150 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS P 152 " --> pdb=" O LEU P 186 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU P 186 " --> pdb=" O LYS P 152 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR P 154 " --> pdb=" O TYR P 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 160 through 163 Processing sheet with id=AA6, first strand: chain 'O' and resid 4 through 5 removed outlier: 3.528A pdb=" N ASP O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.525A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 118 through 119 removed outlier: 3.662A pdb=" N VAL O 134 " --> pdb=" O PHE O 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 154 through 155 removed outlier: 3.923A pdb=" N CYS O 195 " --> pdb=" O LYS O 208 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS O 208 " --> pdb=" O CYS O 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'd' and resid 26 through 29 removed outlier: 5.979A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) removed outlier: 3.734A 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: 5.527A pdb=" N TRP d 43 " --> pdb=" O ARG d 72 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ARG d 72 " --> pdb=" O TRP d 43 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) removed outlier: 4.074A 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 Processing sheet with id=AB4, first strand: chain 'e' and resid 37 through 41 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: 5.862A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG g 102 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N CYS g 87 " --> pdb=" O SER g 94 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR g 85 " --> pdb=" O PRO g 96 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLN g 98 " --> pdb=" O GLY g 83 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLY g 83 " --> pdb=" O GLN g 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.744A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY g 75 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU g 44 " --> pdb=" O ASN g 73 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASN g 73 " --> pdb=" O LEU g 44 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N CYS g 46 " --> pdb=" O LYS g 71 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS g 71 " --> pdb=" O CYS g 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'g' and resid 55 through 57 removed outlier: 7.036A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'R' and resid 10 through 12 removed outlier: 3.544A pdb=" N VAL R 12 " --> pdb=" O THR R 119 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET R 34 " --> pdb=" O LEU R 50 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU R 50 " --> pdb=" O MET R 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 10 through 12 removed outlier: 3.544A pdb=" N VAL R 12 " --> pdb=" O THR R 119 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL R 111 " --> pdb=" O ARG R 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 129 through 133 removed outlier: 4.757A pdb=" N LEU R 150 " --> pdb=" O SER R 188 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER R 188 " --> pdb=" O LEU R 150 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LYS R 152 " --> pdb=" O LEU R 186 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU R 186 " --> pdb=" O LYS R 152 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR R 154 " --> pdb=" O TYR R 184 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 160 through 163 Processing sheet with id=AC6, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.531A pdb=" N ASP Q 70 " --> pdb=" O SER Q 67 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.532A pdb=" N LEU Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR Q 49 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Q' and resid 118 through 119 removed outlier: 3.659A pdb=" N VAL Q 134 " --> pdb=" O PHE Q 119 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 154 through 155 removed outlier: 3.918A pdb=" N CYS Q 195 " --> pdb=" O LYS Q 208 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS Q 208 " --> pdb=" O CYS Q 195 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 26 through 29 removed outlier: 5.978A pdb=" N VAL D 33 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP D 59 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 42 through 46 removed outlier: 5.587A pdb=" N TRP D 43 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG D 72 " --> pdb=" O TRP D 43 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE E 110 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N CYS E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP E 59 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 96 through 98 Processing sheet with id=AD4, first strand: chain 'E' and resid 37 through 41 Processing sheet with id=AD5, first strand: chain 'F' and resid 37 through 41 Processing sheet with id=AD6, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AD7, first strand: chain 'F' and resid 112 through 116 removed outlier: 5.878A pdb=" N TYR F 113 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ARG G 102 " --> pdb=" O TYR F 113 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG F 115 " --> pdb=" O ARG G 102 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N CYS G 87 " --> pdb=" O SER G 94 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TYR G 85 " --> pdb=" O PRO G 96 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN G 98 " --> pdb=" O GLY G 83 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLY G 83 " --> pdb=" O GLN G 98 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 31 through 34 removed outlier: 3.735A pdb=" N LEU G 43 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY G 75 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU G 44 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASN G 73 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N CYS G 46 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS G 71 " --> pdb=" O CYS G 46 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 55 through 57 removed outlier: 7.036A pdb=" N TRP G 55 " --> pdb=" O ILE G 62 " (cutoff:3.500A) 787 hydrogen bonds defined for protein. 2127 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: 2.41 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4637 1.34 - 1.46: 2963 1.46 - 1.58: 8220 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 15966 Sorted by residual: bond pdb=" C SER Q 204 " pdb=" N PRO Q 205 " ideal model delta sigma weight residual 1.333 1.356 -0.022 1.01e-02 9.80e+03 4.92e+00 bond pdb=" C GLU P 157 " pdb=" N PRO P 158 " ideal model delta sigma weight residual 1.331 1.358 -0.026 1.20e-02 6.94e+03 4.84e+00 bond pdb=" C SER O 204 " pdb=" N PRO O 205 " ideal model delta sigma weight residual 1.333 1.356 -0.022 1.01e-02 9.80e+03 4.83e+00 bond pdb=" C GLU R 157 " pdb=" N PRO R 158 " ideal model delta sigma weight residual 1.331 1.357 -0.025 1.20e-02 6.94e+03 4.49e+00 bond pdb=" CA GLY D 75 " pdb=" C GLY D 75 " ideal model delta sigma weight residual 1.516 1.530 -0.014 8.90e-03 1.26e+04 2.50e+00 ... (remaining 15961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 21361 2.65 - 5.29: 247 5.29 - 7.94: 45 7.94 - 10.58: 4 10.58 - 13.23: 7 Bond angle restraints: 21664 Sorted by residual: angle pdb=" C ARG O 108 " pdb=" N ALA O 110 " pdb=" CA ALA O 110 " ideal model delta sigma weight residual 121.70 133.22 -11.52 1.80e+00 3.09e-01 4.10e+01 angle pdb=" CA ARG O 108 " pdb=" C ARG O 108 " pdb=" N ALA O 110 " ideal model delta sigma weight residual 115.21 122.92 -7.71 1.33e+00 5.65e-01 3.36e+01 angle pdb=" CA ILE Q 151 " pdb=" CB ILE Q 151 " pdb=" CG1 ILE Q 151 " ideal model delta sigma weight residual 110.40 117.94 -7.54 1.70e+00 3.46e-01 1.96e+01 angle pdb=" CA ILE O 151 " pdb=" CB ILE O 151 " pdb=" CG1 ILE O 151 " ideal model delta sigma weight residual 110.40 117.88 -7.48 1.70e+00 3.46e-01 1.94e+01 angle pdb=" CA LEU A 34 " pdb=" CB LEU A 34 " pdb=" CG LEU A 34 " ideal model delta sigma weight residual 116.30 129.53 -13.23 3.50e+00 8.16e-02 1.43e+01 ... (remaining 21659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 8002 17.40 - 34.81: 1150 34.81 - 52.21: 351 52.21 - 69.62: 47 69.62 - 87.02: 20 Dihedral angle restraints: 9570 sinusoidal: 3762 harmonic: 5808 Sorted by residual: dihedral pdb=" CB CYS E 49 " pdb=" SG CYS E 49 " pdb=" SG CYS E 98 " pdb=" CB CYS E 98 " ideal model delta sinusoidal sigma weight residual 93.00 5.98 87.02 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS e 49 " pdb=" SG CYS e 49 " pdb=" SG CYS e 98 " pdb=" CB CYS e 98 " ideal model delta sinusoidal sigma weight residual -86.00 -2.25 -83.75 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CB CYS g 46 " pdb=" SG CYS g 46 " pdb=" SG CYS g 87 " pdb=" CB CYS g 87 " ideal model delta sinusoidal sigma weight residual -86.00 -144.64 58.64 1 1.00e+01 1.00e-02 4.60e+01 ... (remaining 9567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 2502 0.141 - 0.283: 16 0.283 - 0.424: 0 0.424 - 0.566: 1 0.566 - 0.707: 1 Chirality restraints: 2520 Sorted by residual: chirality pdb=" C1 NAG D 201 " pdb=" ND2 ASN D 74 " pdb=" C2 NAG D 201 " pdb=" O5 NAG D 201 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" C1 NAG d 201 " pdb=" ND2 ASN d 74 " pdb=" C2 NAG d 201 " pdb=" O5 NAG d 201 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CB VAL b 44 " pdb=" CA VAL b 44 " pdb=" CG1 VAL b 44 " pdb=" CG2 VAL b 44 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 2517 not shown) Planarity restraints: 2684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 74 " -0.034 2.00e-02 2.50e+03 3.24e-02 1.31e+01 pdb=" CG ASN D 74 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN D 74 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN D 74 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG D 201 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN d 74 " -0.034 2.00e-02 2.50e+03 3.04e-02 1.16e+01 pdb=" CG ASN d 74 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN d 74 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN d 74 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG d 201 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 38 " 0.026 2.00e-02 2.50e+03 2.62e-02 8.56e+00 pdb=" CG ASN D 38 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN D 38 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN D 38 " -0.015 2.00e-02 2.50e+03 pdb=" C1 NAG D 202 " 0.020 2.00e-02 2.50e+03 ... (remaining 2681 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 157 2.58 - 3.16: 12783 3.16 - 3.74: 24675 3.74 - 4.32: 33069 4.32 - 4.90: 55431 Nonbonded interactions: 126115 Sorted by model distance: nonbonded pdb=" O GLU e 89 " pdb=" OG SER e 93 " model vdw 2.004 3.040 nonbonded pdb=" O GLU E 89 " pdb=" OG SER E 93 " model vdw 2.006 3.040 nonbonded pdb=" O THR d 47 " pdb=" OH TYR d 71 " model vdw 2.145 3.040 nonbonded pdb=" O THR D 47 " pdb=" OH TYR D 71 " model vdw 2.149 3.040 nonbonded pdb=" OH TYR R 102 " pdb=" O GLY E 67 " model vdw 2.161 3.040 ... (remaining 126110 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: 0.01 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' } ncs_group { reference = (chain 'E' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'F' and resid 33 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: 12.220 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: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.560 Find NCS groups from input model: 0.250 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 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 : 0.004 0.049 15992 Z= 0.172 Angle : 0.794 13.231 21720 Z= 0.410 Chirality : 0.048 0.707 2520 Planarity : 0.004 0.060 2680 Dihedral : 17.625 84.781 5776 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 6.06 % Allowed : 31.41 % Favored : 62.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.19), residues: 1936 helix: 2.02 (0.22), residues: 506 sheet: -0.30 (0.22), residues: 584 loop : -0.78 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 270 TYR 0.042 0.002 TYR N 266 PHE 0.026 0.002 PHE N 277 TRP 0.011 0.002 TRP g 72 HIS 0.003 0.001 HIS Q 55 Details of bonding type rmsd covalent geometry : bond 0.00352 (15966) covalent geometry : angle 0.77549 (21664) SS BOND : bond 0.00253 ( 22) SS BOND : angle 1.76309 ( 44) hydrogen bonds : bond 0.19166 ( 779) hydrogen bonds : angle 7.08335 ( 2127) link_NAG-ASN : bond 0.00710 ( 4) link_NAG-ASN : angle 6.52499 ( 12) *********************** 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 373 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 267 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 6 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.6233 (mt0) REVERT: P 65 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7620 (pttt) REVERT: P 82 GLU cc_start: 0.8100 (tt0) cc_final: 0.7894 (tt0) REVERT: d 64 ILE cc_start: 0.8943 (tp) cc_final: 0.8487 (mt) REVERT: d 120 LEU cc_start: 0.5467 (OUTLIER) cc_final: 0.4967 (mm) REVERT: e 78 ASP cc_start: 0.7962 (m-30) cc_final: 0.7110 (p0) REVERT: e 79 GLU cc_start: 0.8716 (mp0) cc_final: 0.8250 (mt-10) REVERT: e 117 ARG cc_start: 0.7273 (ttp80) cc_final: 0.6866 (ttm170) REVERT: f 52 TYR cc_start: -0.1786 (OUTLIER) cc_final: -0.2386 (m-10) REVERT: f 125 MET cc_start: 0.4831 (mmt) cc_final: 0.4563 (mmp) REVERT: R 65 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7614 (pttt) REVERT: D 36 ASN cc_start: 0.8146 (t0) cc_final: 0.7603 (t0) REVERT: D 64 ILE cc_start: 0.8939 (tp) cc_final: 0.8477 (mt) REVERT: D 120 LEU cc_start: 0.5442 (OUTLIER) cc_final: 0.4928 (mm) REVERT: E 78 ASP cc_start: 0.7941 (m-30) cc_final: 0.7129 (p0) REVERT: E 79 GLU cc_start: 0.8672 (mp0) cc_final: 0.8236 (mt-10) REVERT: E 117 ARG cc_start: 0.7256 (ttp80) cc_final: 0.6862 (ttm170) REVERT: F 52 TYR cc_start: -0.1626 (OUTLIER) cc_final: -0.2619 (m-10) REVERT: M 288 PHE cc_start: 0.1720 (OUTLIER) cc_final: 0.1481 (t80) outliers start: 106 outliers final: 82 residues processed: 356 average time/residue: 0.1056 time to fit residues: 57.9724 Evaluate side-chains 321 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 231 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 81 MET Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 180 LYS Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 183 THR Chi-restraints excluded: chain O residue 199 HIS Chi-restraints excluded: chain a residue 28 ASP Chi-restraints excluded: chain a residue 38 ILE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 45 GLU Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 41 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 118 VAL Chi-restraints excluded: chain e residue 128 MET Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 280 ASN Chi-restraints excluded: chain m residue 281 PHE Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 MET Chi-restraints excluded: chain R residue 44 ASN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 65 LYS Chi-restraints excluded: chain R residue 81 MET 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 180 LYS Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 34 ASN Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 199 HIS Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 41 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 118 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain M residue 288 PHE Chi-restraints excluded: chain N residue 268 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 44 ASN e 74 ASN ** m 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 35 ASN E 74 ASN F 109 ASN ** N 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.244952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.213149 restraints weight = 21234.736| |-----------------------------------------------------------------------------| r_work (start): 0.4501 rms_B_bonded: 1.87 r_work: 0.3884 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15992 Z= 0.175 Angle : 0.694 12.340 21720 Z= 0.351 Chirality : 0.044 0.233 2520 Planarity : 0.004 0.055 2680 Dihedral : 8.690 58.888 2375 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 7.15 % Allowed : 27.92 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 1936 helix: 2.30 (0.21), residues: 518 sheet: -0.17 (0.21), residues: 600 loop : -0.89 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 270 TYR 0.034 0.002 TYR n 264 PHE 0.018 0.002 PHE O 136 TRP 0.015 0.001 TRP g 72 HIS 0.003 0.001 HIS O 55 Details of bonding type rmsd covalent geometry : bond 0.00390 (15966) covalent geometry : angle 0.68420 (21664) SS BOND : bond 0.00280 ( 22) SS BOND : angle 1.28165 ( 44) hydrogen bonds : bond 0.04232 ( 779) hydrogen bonds : angle 5.16166 ( 2127) link_NAG-ASN : bond 0.00910 ( 4) link_NAG-ASN : angle 4.48617 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 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 367 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 242 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7758 (pttt) REVERT: O 176 MET cc_start: 0.6564 (tpp) cc_final: 0.6259 (tpt) REVERT: O 210 PHE cc_start: 0.4605 (OUTLIER) cc_final: 0.2647 (m-10) REVERT: d 56 THR cc_start: 0.6359 (p) cc_final: 0.6047 (p) REVERT: d 64 ILE cc_start: 0.8904 (tp) cc_final: 0.8471 (mt) REVERT: d 70 ILE cc_start: 0.8298 (mt) cc_final: 0.7996 (mt) REVERT: d 107 ILE cc_start: 0.7339 (mm) cc_final: 0.7003 (tp) REVERT: e 78 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7515 (p0) REVERT: e 79 GLU cc_start: 0.8618 (mp0) cc_final: 0.8366 (mt-10) REVERT: e 117 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7427 (ttm170) REVERT: f 52 TYR cc_start: -0.0884 (OUTLIER) cc_final: -0.2823 (m-10) REVERT: R 65 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7758 (pttt) REVERT: Q 141 TYR cc_start: 0.7169 (t80) cc_final: 0.6849 (t80) REVERT: Q 176 MET cc_start: 0.6445 (tpp) cc_final: 0.6176 (tpt) REVERT: Q 210 PHE cc_start: 0.4599 (OUTLIER) cc_final: 0.2641 (m-10) REVERT: D 36 ASN cc_start: 0.8447 (t0) cc_final: 0.8139 (t0) REVERT: D 64 ILE cc_start: 0.8905 (tp) cc_final: 0.8453 (mt) REVERT: D 70 ILE cc_start: 0.8295 (mt) cc_final: 0.7990 (mt) REVERT: D 107 ILE cc_start: 0.6981 (mm) cc_final: 0.6730 (tp) REVERT: E 78 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7500 (p0) REVERT: E 79 GLU cc_start: 0.8589 (mp0) cc_final: 0.8355 (mt-10) REVERT: E 117 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7607 (ttt-90) REVERT: F 52 TYR cc_start: -0.0914 (OUTLIER) cc_final: -0.2701 (m-10) REVERT: N 265 MET cc_start: 0.7942 (tmm) cc_final: 0.7620 (tmm) REVERT: N 266 TYR cc_start: 0.7730 (m-80) cc_final: 0.7301 (m-80) outliers start: 125 outliers final: 85 residues processed: 350 average time/residue: 0.1120 time to fit residues: 60.7322 Evaluate side-chains 320 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 227 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 44 ASN Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 180 LYS Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 164 TRP Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 183 THR Chi-restraints excluded: chain O residue 199 HIS Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain a residue 36 ASP Chi-restraints excluded: chain a residue 38 ILE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 46 ILE Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 78 ASP Chi-restraints excluded: chain e residue 101 ARG Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 60 LYS Chi-restraints excluded: chain g residue 79 LYS Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 280 ASN Chi-restraints excluded: chain m residue 281 PHE Chi-restraints excluded: chain n residue 284 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 44 ASN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 65 LYS Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 180 LYS 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 48 ILE Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 164 TRP Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 199 HIS Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 284 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 1 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 164 optimal weight: 30.0000 chunk 109 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 chunk 122 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 109 ASN ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 259 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 = 0.4796 r_free = 0.4796 target = 0.245002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.213340 restraints weight = 21261.340| |-----------------------------------------------------------------------------| r_work (start): 0.4554 rms_B_bonded: 1.87 r_work: 0.4203 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.4112 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15992 Z= 0.153 Angle : 0.652 11.944 21720 Z= 0.327 Chirality : 0.043 0.233 2520 Planarity : 0.004 0.046 2680 Dihedral : 7.612 57.791 2303 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 6.81 % Allowed : 28.15 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 1936 helix: 2.46 (0.21), residues: 520 sheet: -0.05 (0.21), residues: 604 loop : -0.87 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 270 TYR 0.032 0.001 TYR n 264 PHE 0.017 0.001 PHE M 288 TRP 0.008 0.001 TRP f 59 HIS 0.003 0.001 HIS O 55 Details of bonding type rmsd covalent geometry : bond 0.00340 (15966) covalent geometry : angle 0.64474 (21664) SS BOND : bond 0.00331 ( 22) SS BOND : angle 1.05521 ( 44) hydrogen bonds : bond 0.03682 ( 779) hydrogen bonds : angle 4.78967 ( 2127) link_NAG-ASN : bond 0.00707 ( 4) link_NAG-ASN : angle 3.89133 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 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 354 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 235 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7638 (pttt) REVERT: O 210 PHE cc_start: 0.3307 (OUTLIER) cc_final: 0.1895 (m-10) REVERT: d 56 THR cc_start: 0.6595 (p) cc_final: 0.6140 (p) REVERT: d 64 ILE cc_start: 0.8799 (tp) cc_final: 0.8458 (mt) REVERT: f 52 TYR cc_start: -0.1851 (OUTLIER) cc_final: -0.2764 (m-10) REVERT: g 61 MET cc_start: -0.0438 (tpt) cc_final: -0.0792 (ttm) REVERT: R 65 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7682 (pttt) REVERT: Q 210 PHE cc_start: 0.3299 (OUTLIER) cc_final: 0.1828 (m-10) REVERT: D 64 ILE cc_start: 0.8809 (tp) cc_final: 0.8460 (mt) REVERT: F 52 TYR cc_start: -0.1595 (OUTLIER) cc_final: -0.2322 (m-10) REVERT: G 61 MET cc_start: -0.0472 (tpt) cc_final: -0.0932 (ttm) outliers start: 119 outliers final: 78 residues processed: 336 average time/residue: 0.1017 time to fit residues: 52.6554 Evaluate side-chains 302 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 218 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 44 ASN Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 180 LYS Chi-restraints excluded: chain P residue 215 VAL Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 164 TRP Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain a residue 36 ASP Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain m residue 280 ASN Chi-restraints excluded: chain m residue 281 PHE Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 65 LYS Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 180 LYS Chi-restraints excluded: chain R residue 215 VAL 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 48 ILE Chi-restraints excluded: chain Q residue 61 LYS Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 284 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 44 ASN ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN G 86 GLN ** N 259 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 = 0.4768 r_free = 0.4768 target = 0.241804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.206002 restraints weight = 21100.551| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 2.05 r_work: 0.4135 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4045 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15992 Z= 0.244 Angle : 0.695 12.088 21720 Z= 0.353 Chirality : 0.045 0.210 2520 Planarity : 0.004 0.052 2680 Dihedral : 7.637 59.781 2287 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 8.35 % Allowed : 26.49 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 1936 helix: 2.54 (0.21), residues: 508 sheet: -0.22 (0.21), residues: 586 loop : -1.01 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 72 TYR 0.038 0.002 TYR N 266 PHE 0.017 0.002 PHE Q 98 TRP 0.010 0.002 TRP P 36 HIS 0.004 0.001 HIS P 41 Details of bonding type rmsd covalent geometry : bond 0.00565 (15966) covalent geometry : angle 0.68917 (21664) SS BOND : bond 0.00623 ( 22) SS BOND : angle 1.19418 ( 44) hydrogen bonds : bond 0.03686 ( 779) hydrogen bonds : angle 4.90560 ( 2127) link_NAG-ASN : bond 0.00555 ( 4) link_NAG-ASN : angle 3.36034 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 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 383 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 237 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 10 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7291 (tt0) REVERT: P 18 MET cc_start: 0.7586 (tpt) cc_final: 0.6994 (tpt) REVERT: P 65 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7730 (pttt) REVERT: O 141 TYR cc_start: 0.7404 (t80) cc_final: 0.7193 (t80) REVERT: O 210 PHE cc_start: 0.3391 (OUTLIER) cc_final: 0.1628 (m-80) REVERT: d 64 ILE cc_start: 0.8848 (tp) cc_final: 0.8501 (mt) REVERT: f 52 TYR cc_start: -0.1645 (OUTLIER) cc_final: -0.2437 (m-10) REVERT: m 283 LEU cc_start: 0.3809 (OUTLIER) cc_final: 0.3467 (tp) REVERT: R 10 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7308 (tt0) REVERT: R 18 MET cc_start: 0.7667 (tpt) cc_final: 0.7077 (tpt) REVERT: R 65 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7753 (pttt) REVERT: Q 126 LEU cc_start: 0.2991 (OUTLIER) cc_final: 0.2765 (mm) REVERT: Q 141 TYR cc_start: 0.7466 (t80) cc_final: 0.7254 (t80) REVERT: Q 210 PHE cc_start: 0.3353 (OUTLIER) cc_final: 0.1584 (m-80) REVERT: D 64 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8477 (mt) REVERT: F 52 TYR cc_start: -0.1683 (OUTLIER) cc_final: -0.2528 (m-10) REVERT: G 61 MET cc_start: -0.0596 (tpt) cc_final: -0.0807 (ttm) outliers start: 146 outliers final: 104 residues processed: 362 average time/residue: 0.1053 time to fit residues: 60.3238 Evaluate side-chains 336 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 223 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 44 ASN Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 180 LYS Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 90 GLN Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain O residue 164 TRP Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain a residue 36 ASP Chi-restraints excluded: chain a residue 38 ILE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 46 ILE Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 78 ASP Chi-restraints excluded: chain e residue 79 GLU Chi-restraints excluded: chain e residue 101 ARG Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 280 ASN Chi-restraints excluded: chain m residue 281 PHE Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain n residue 256 GLN Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 65 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 180 LYS 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 48 ILE Chi-restraints excluded: chain Q residue 61 LYS Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 164 TRP Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 284 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 152 optimal weight: 0.1980 chunk 65 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.244293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.209420 restraints weight = 21165.352| |-----------------------------------------------------------------------------| r_work (start): 0.4519 rms_B_bonded: 2.00 r_work: 0.4142 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15992 Z= 0.145 Angle : 0.637 11.627 21720 Z= 0.316 Chirality : 0.042 0.241 2520 Planarity : 0.004 0.049 2680 Dihedral : 7.236 58.982 2287 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 6.98 % Allowed : 28.20 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 1936 helix: 2.63 (0.21), residues: 510 sheet: -0.13 (0.22), residues: 568 loop : -1.00 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG m 270 TYR 0.033 0.001 TYR n 264 PHE 0.010 0.001 PHE O 98 TRP 0.008 0.001 TRP P 36 HIS 0.003 0.001 HIS R 173 Details of bonding type rmsd covalent geometry : bond 0.00324 (15966) covalent geometry : angle 0.63117 (21664) SS BOND : bond 0.00331 ( 22) SS BOND : angle 1.10300 ( 44) hydrogen bonds : bond 0.03316 ( 779) hydrogen bonds : angle 4.65143 ( 2127) link_NAG-ASN : bond 0.00570 ( 4) link_NAG-ASN : angle 3.13915 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 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 351 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 229 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 10 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7141 (tt0) REVERT: P 18 MET cc_start: 0.7226 (tpt) cc_final: 0.6656 (tpt) REVERT: P 65 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7773 (pttt) REVERT: O 210 PHE cc_start: 0.3381 (OUTLIER) cc_final: 0.1631 (m-80) REVERT: d 64 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8439 (mt) REVERT: d 71 TYR cc_start: 0.7753 (m-80) cc_final: 0.7531 (m-80) REVERT: f 52 TYR cc_start: -0.1839 (OUTLIER) cc_final: -0.2521 (m-10) REVERT: m 283 LEU cc_start: 0.3933 (OUTLIER) cc_final: 0.3581 (tp) REVERT: n 266 TYR cc_start: 0.7429 (m-80) cc_final: 0.7124 (m-80) REVERT: R 10 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7210 (tt0) REVERT: R 18 MET cc_start: 0.7358 (tpt) cc_final: 0.6798 (tpt) REVERT: R 65 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7792 (pttt) REVERT: Q 126 LEU cc_start: 0.2948 (OUTLIER) cc_final: 0.2702 (mm) REVERT: Q 210 PHE cc_start: 0.3359 (OUTLIER) cc_final: 0.1585 (m-80) REVERT: D 64 ILE cc_start: 0.8781 (tp) cc_final: 0.8427 (mt) REVERT: D 71 TYR cc_start: 0.7781 (m-80) cc_final: 0.7412 (m-80) REVERT: F 52 TYR cc_start: -0.1819 (OUTLIER) cc_final: -0.2491 (m-10) outliers start: 122 outliers final: 90 residues processed: 333 average time/residue: 0.0947 time to fit residues: 50.3995 Evaluate side-chains 316 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 217 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 44 ASN Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 180 LYS Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 61 LYS Chi-restraints excluded: chain O residue 90 GLN Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 195 CYS Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain a residue 36 ASP Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 79 GLU Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 280 ASN Chi-restraints excluded: chain m residue 281 PHE Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 44 ASN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 65 LYS Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 180 LYS 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 48 ILE Chi-restraints excluded: chain Q residue 61 LYS Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 195 CYS Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 284 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN ** N 259 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 = 0.4802 r_free = 0.4802 target = 0.244498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.195137 restraints weight = 20659.126| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 2.89 r_work: 0.3865 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15992 Z= 0.245 Angle : 0.713 11.640 21720 Z= 0.355 Chirality : 0.045 0.217 2520 Planarity : 0.004 0.043 2680 Dihedral : 7.531 59.722 2287 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 7.89 % Allowed : 27.69 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 1936 helix: 2.55 (0.21), residues: 516 sheet: -0.38 (0.21), residues: 594 loop : -1.07 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG m 270 TYR 0.036 0.002 TYR N 266 PHE 0.018 0.002 PHE Q 98 TRP 0.010 0.002 TRP R 36 HIS 0.004 0.001 HIS Q 55 Details of bonding type rmsd covalent geometry : bond 0.00569 (15966) covalent geometry : angle 0.70839 (21664) SS BOND : bond 0.00428 ( 22) SS BOND : angle 1.19226 ( 44) hydrogen bonds : bond 0.03497 ( 779) hydrogen bonds : angle 4.86745 ( 2127) link_NAG-ASN : bond 0.00536 ( 4) link_NAG-ASN : angle 3.00681 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 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 363 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 225 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 10 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7805 (mt-10) REVERT: P 18 MET cc_start: 0.7697 (tpt) cc_final: 0.7443 (tpt) REVERT: P 65 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7865 (pttt) REVERT: P 144 MET cc_start: 0.2446 (ptp) cc_final: 0.2184 (ttp) REVERT: O 141 TYR cc_start: 0.7383 (t80) cc_final: 0.7174 (t80) REVERT: O 210 PHE cc_start: 0.3766 (OUTLIER) cc_final: 0.1597 (m-80) REVERT: d 64 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8437 (mt) REVERT: d 71 TYR cc_start: 0.7951 (m-80) cc_final: 0.7650 (m-80) REVERT: f 52 TYR cc_start: -0.1676 (OUTLIER) cc_final: -0.2859 (m-10) REVERT: g 61 MET cc_start: 0.1273 (tpp) cc_final: 0.0604 (ttm) REVERT: m 283 LEU cc_start: 0.4410 (OUTLIER) cc_final: 0.3839 (tp) REVERT: n 266 TYR cc_start: 0.7672 (m-80) cc_final: 0.7391 (m-80) REVERT: R 18 MET cc_start: 0.7780 (tpt) cc_final: 0.7537 (tpt) REVERT: R 65 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7886 (pttt) REVERT: R 144 MET cc_start: 0.2458 (ptp) cc_final: 0.2180 (ttp) REVERT: Q 126 LEU cc_start: 0.2600 (OUTLIER) cc_final: 0.2332 (mm) REVERT: Q 210 PHE cc_start: 0.3711 (OUTLIER) cc_final: 0.1598 (m-80) REVERT: A 41 ILE cc_start: 0.5076 (OUTLIER) cc_final: 0.4769 (tp) REVERT: D 64 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8462 (mt) REVERT: D 71 TYR cc_start: 0.7981 (m-80) cc_final: 0.7645 (m-80) REVERT: F 52 TYR cc_start: -0.1652 (OUTLIER) cc_final: -0.2739 (m-10) outliers start: 138 outliers final: 110 residues processed: 340 average time/residue: 0.1007 time to fit residues: 53.6094 Evaluate side-chains 338 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 217 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 180 LYS Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 34 ASN 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 61 LYS Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 90 GLN Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain O residue 164 TRP Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 195 CYS Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain a residue 36 ASP Chi-restraints excluded: chain a residue 38 ILE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 46 ILE Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 79 GLU Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain e residue 101 ARG Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 280 ASN Chi-restraints excluded: chain m residue 281 PHE Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 34 MET Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 44 ASN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 65 LYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 180 LYS 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 48 ILE Chi-restraints excluded: chain Q residue 61 LYS Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 90 GLN Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 164 TRP Chi-restraints excluded: chain Q residue 178 SER Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 195 CYS Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 284 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 28 optimal weight: 0.8980 chunk 172 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 81 optimal weight: 0.0000 chunk 20 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 177 optimal weight: 20.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 HIS ** N 259 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 = 0.4798 r_free = 0.4798 target = 0.245156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.211190 restraints weight = 20968.290| |-----------------------------------------------------------------------------| r_work (start): 0.4543 rms_B_bonded: 2.00 r_work: 0.4187 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.4073 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15992 Z= 0.129 Angle : 0.656 11.962 21720 Z= 0.321 Chirality : 0.042 0.239 2520 Planarity : 0.004 0.046 2680 Dihedral : 7.034 59.583 2287 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 6.01 % Allowed : 29.92 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.19), residues: 1936 helix: 2.68 (0.21), residues: 510 sheet: -0.24 (0.21), residues: 590 loop : -1.10 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG m 270 TYR 0.035 0.001 TYR n 264 PHE 0.014 0.001 PHE Q 140 TRP 0.006 0.001 TRP O 96 HIS 0.002 0.001 HIS P 173 Details of bonding type rmsd covalent geometry : bond 0.00282 (15966) covalent geometry : angle 0.65183 (21664) SS BOND : bond 0.00334 ( 22) SS BOND : angle 1.14263 ( 44) hydrogen bonds : bond 0.03214 ( 779) hydrogen bonds : angle 4.59840 ( 2127) link_NAG-ASN : bond 0.00516 ( 4) link_NAG-ASN : angle 2.74722 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 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 327 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 222 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7779 (pttt) REVERT: P 144 MET cc_start: 0.2913 (ptp) cc_final: 0.2683 (ttp) REVERT: O 210 PHE cc_start: 0.3208 (OUTLIER) cc_final: 0.1248 (m-80) REVERT: d 64 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8430 (mt) REVERT: e 70 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7391 (mt-10) REVERT: f 52 TYR cc_start: -0.1871 (OUTLIER) cc_final: -0.2576 (m-10) REVERT: g 61 MET cc_start: 0.1167 (tpp) cc_final: 0.0564 (ttm) REVERT: m 283 LEU cc_start: 0.4097 (OUTLIER) cc_final: 0.3677 (tp) REVERT: R 10 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7633 (tt0) REVERT: R 18 MET cc_start: 0.7706 (tpt) cc_final: 0.7305 (tpt) REVERT: R 65 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7759 (pttt) REVERT: R 144 MET cc_start: 0.2956 (ptp) cc_final: 0.2673 (ttp) REVERT: Q 210 PHE cc_start: 0.3189 (OUTLIER) cc_final: 0.1216 (m-80) REVERT: D 64 ILE cc_start: 0.8768 (tp) cc_final: 0.8496 (mt) REVERT: E 70 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7396 (mt-10) REVERT: E 128 MET cc_start: 0.7688 (mmt) cc_final: 0.7030 (ptm) REVERT: F 52 TYR cc_start: -0.1846 (OUTLIER) cc_final: -0.2523 (m-10) REVERT: F 58 LEU cc_start: 0.2160 (OUTLIER) cc_final: 0.1704 (mp) REVERT: F 110 PHE cc_start: 0.1300 (m-10) cc_final: 0.0928 (m-10) REVERT: G 61 MET cc_start: 0.1023 (tpp) cc_final: 0.0502 (ttm) REVERT: M 270 ARG cc_start: 0.7359 (mmp80) cc_final: 0.6036 (mmt-90) REVERT: N 266 TYR cc_start: 0.6657 (m-80) cc_final: 0.6426 (m-80) outliers start: 105 outliers final: 88 residues processed: 310 average time/residue: 0.0910 time to fit residues: 44.9421 Evaluate side-chains 313 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 216 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 180 LYS Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 61 LYS Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 90 GLN Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 195 CYS Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain a residue 36 ASP Chi-restraints excluded: chain a residue 38 ILE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 79 GLU Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 280 ASN Chi-restraints excluded: chain m residue 281 PHE Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain n residue 270 LEU Chi-restraints excluded: chain n residue 282 CYS Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 65 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 180 LYS 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 48 ILE Chi-restraints excluded: chain Q residue 61 LYS Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 90 GLN Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 195 CYS Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 284 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 17 optimal weight: 0.0040 chunk 72 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 109 ASN ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 259 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 = 0.4795 r_free = 0.4795 target = 0.244753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.209747 restraints weight = 20981.895| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 2.03 r_work: 0.4184 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.4073 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15992 Z= 0.141 Angle : 0.672 12.109 21720 Z= 0.325 Chirality : 0.042 0.265 2520 Planarity : 0.004 0.044 2680 Dihedral : 6.996 59.613 2285 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 6.24 % Allowed : 29.86 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 1936 helix: 2.70 (0.21), residues: 510 sheet: -0.18 (0.22), residues: 588 loop : -1.01 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 270 TYR 0.039 0.001 TYR n 264 PHE 0.010 0.001 PHE O 98 TRP 0.007 0.001 TRP R 36 HIS 0.002 0.001 HIS Q 55 Details of bonding type rmsd covalent geometry : bond 0.00315 (15966) covalent geometry : angle 0.66581 (21664) SS BOND : bond 0.00329 ( 22) SS BOND : angle 1.64909 ( 44) hydrogen bonds : bond 0.03204 ( 779) hydrogen bonds : angle 4.58382 ( 2127) link_NAG-ASN : bond 0.00470 ( 4) link_NAG-ASN : angle 2.72731 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 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 331 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 222 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 18 MET cc_start: 0.7651 (tpt) cc_final: 0.7335 (tpt) REVERT: P 65 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7783 (pttt) REVERT: P 144 MET cc_start: 0.3016 (ptp) cc_final: 0.2751 (ttp) REVERT: O 210 PHE cc_start: 0.2887 (OUTLIER) cc_final: 0.0936 (m-80) REVERT: d 51 LEU cc_start: 0.8342 (tp) cc_final: 0.8089 (tp) REVERT: d 56 THR cc_start: 0.6636 (p) cc_final: 0.6183 (p) REVERT: d 64 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8467 (mt) REVERT: e 66 ILE cc_start: 0.8481 (tt) cc_final: 0.8204 (pt) REVERT: e 128 MET cc_start: 0.7607 (mmt) cc_final: 0.7020 (ptm) REVERT: f 52 TYR cc_start: -0.1838 (OUTLIER) cc_final: -0.2535 (m-10) REVERT: f 58 LEU cc_start: 0.1918 (OUTLIER) cc_final: 0.1566 (mp) REVERT: g 61 MET cc_start: 0.1140 (tpp) cc_final: 0.0538 (ttm) REVERT: m 283 LEU cc_start: 0.4111 (OUTLIER) cc_final: 0.3645 (tp) REVERT: R 10 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7532 (tt0) REVERT: R 18 MET cc_start: 0.7684 (tpt) cc_final: 0.7193 (tpt) REVERT: R 65 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7770 (pttt) REVERT: R 144 MET cc_start: 0.3037 (ptp) cc_final: 0.2750 (ttp) REVERT: Q 210 PHE cc_start: 0.2712 (OUTLIER) cc_final: 0.0859 (m-80) REVERT: E 66 ILE cc_start: 0.8472 (tt) cc_final: 0.8209 (pt) REVERT: F 52 TYR cc_start: -0.1993 (OUTLIER) cc_final: -0.2614 (m-10) REVERT: F 58 LEU cc_start: 0.1885 (OUTLIER) cc_final: 0.1543 (mp) REVERT: G 61 MET cc_start: 0.1123 (tpp) cc_final: 0.0856 (ttm) REVERT: M 270 ARG cc_start: 0.7431 (mmp80) cc_final: 0.6106 (mmt-90) outliers start: 109 outliers final: 93 residues processed: 312 average time/residue: 0.0905 time to fit residues: 45.2402 Evaluate side-chains 321 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 218 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 180 LYS Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 61 LYS Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 90 GLN Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 195 CYS Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain a residue 36 ASP Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 79 GLU Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 280 ASN Chi-restraints excluded: chain m residue 281 PHE Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain n residue 270 LEU Chi-restraints excluded: chain n residue 282 CYS Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 44 ASN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 65 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 180 LYS Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 34 ASN Chi-restraints excluded: chain Q residue 37 GLN Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 61 LYS Chi-restraints excluded: chain Q residue 90 GLN Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 168 ASP Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 195 CYS Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 284 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 68 optimal weight: 0.0070 chunk 14 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 38 GLN e 51 GLN g 29 HIS m 260 ASN ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.244482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.212912 restraints weight = 21144.006| |-----------------------------------------------------------------------------| r_work (start): 0.4514 rms_B_bonded: 1.82 r_work: 0.4161 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15992 Z= 0.226 Angle : 0.723 12.778 21720 Z= 0.356 Chirality : 0.044 0.236 2520 Planarity : 0.004 0.048 2680 Dihedral : 7.423 59.641 2285 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 6.86 % Allowed : 28.83 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.19), residues: 1936 helix: 2.65 (0.21), residues: 508 sheet: -0.35 (0.22), residues: 584 loop : -1.01 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG m 270 TYR 0.039 0.002 TYR n 264 PHE 0.020 0.002 PHE F 110 TRP 0.010 0.001 TRP R 36 HIS 0.003 0.001 HIS O 55 Details of bonding type rmsd covalent geometry : bond 0.00523 (15966) covalent geometry : angle 0.71632 (21664) SS BOND : bond 0.00437 ( 22) SS BOND : angle 1.75120 ( 44) hydrogen bonds : bond 0.03429 ( 779) hydrogen bonds : angle 4.79374 ( 2127) link_NAG-ASN : bond 0.00451 ( 4) link_NAG-ASN : angle 2.86157 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 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 344 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 224 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7624 (pttt) REVERT: P 144 MET cc_start: 0.3304 (ptp) cc_final: 0.2885 (ttp) REVERT: O 210 PHE cc_start: 0.2858 (OUTLIER) cc_final: 0.0830 (m-80) REVERT: d 51 LEU cc_start: 0.8338 (tp) cc_final: 0.8067 (tp) REVERT: d 64 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8435 (mt) REVERT: f 52 TYR cc_start: -0.1788 (OUTLIER) cc_final: -0.2582 (m-10) REVERT: f 58 LEU cc_start: 0.1802 (OUTLIER) cc_final: 0.1491 (mp) REVERT: g 61 MET cc_start: 0.1151 (tpp) cc_final: 0.0637 (ttm) REVERT: m 283 LEU cc_start: 0.4022 (OUTLIER) cc_final: 0.3574 (tp) REVERT: R 10 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7542 (tt0) REVERT: R 65 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7645 (pttt) REVERT: R 144 MET cc_start: 0.3216 (ptp) cc_final: 0.2786 (ttp) REVERT: Q 210 PHE cc_start: 0.2802 (OUTLIER) cc_final: 0.0944 (m-80) REVERT: D 51 LEU cc_start: 0.8349 (tp) cc_final: 0.8040 (tp) REVERT: E 128 MET cc_start: 0.7615 (mmt) cc_final: 0.7196 (ptm) REVERT: F 52 TYR cc_start: -0.1739 (OUTLIER) cc_final: -0.2481 (m-10) REVERT: F 58 LEU cc_start: 0.1802 (OUTLIER) cc_final: 0.1486 (mp) REVERT: G 61 MET cc_start: 0.1030 (tpp) cc_final: 0.0583 (ttm) outliers start: 120 outliers final: 97 residues processed: 322 average time/residue: 0.0834 time to fit residues: 43.2025 Evaluate side-chains 323 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 216 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 65 LYS 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 180 LYS Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 34 ASN 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 61 LYS Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 90 GLN Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 195 CYS Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain a residue 36 ASP Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 79 GLU Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 280 ASN Chi-restraints excluded: chain m residue 281 PHE Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain n residue 270 LEU Chi-restraints excluded: chain n residue 282 CYS Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 34 MET Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 65 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 180 LYS Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 34 ASN Chi-restraints excluded: chain Q residue 37 GLN Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 61 LYS Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 90 GLN Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 168 ASP Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 195 CYS Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 38 GLN ** m 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 259 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 = 0.4812 r_free = 0.4812 target = 0.244890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.212009 restraints weight = 21008.924| |-----------------------------------------------------------------------------| r_work (start): 0.4534 rms_B_bonded: 1.92 r_work: 0.4206 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4092 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15992 Z= 0.160 Angle : 0.697 13.142 21720 Z= 0.338 Chirality : 0.043 0.236 2520 Planarity : 0.004 0.053 2680 Dihedral : 7.150 59.963 2285 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 6.12 % Allowed : 30.15 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 1936 helix: 2.68 (0.21), residues: 508 sheet: -0.35 (0.22), residues: 558 loop : -0.95 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG m 270 TYR 0.044 0.001 TYR N 264 PHE 0.015 0.001 PHE F 110 TRP 0.007 0.001 TRP R 36 HIS 0.003 0.001 HIS Q 55 Details of bonding type rmsd covalent geometry : bond 0.00362 (15966) covalent geometry : angle 0.69127 (21664) SS BOND : bond 0.00336 ( 22) SS BOND : angle 1.55389 ( 44) hydrogen bonds : bond 0.03235 ( 779) hydrogen bonds : angle 4.67593 ( 2127) link_NAG-ASN : bond 0.00456 ( 4) link_NAG-ASN : angle 2.73515 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 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 328 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 221 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7730 (pttt) REVERT: P 144 MET cc_start: 0.3269 (ptp) cc_final: 0.2819 (ttp) REVERT: O 210 PHE cc_start: 0.2734 (OUTLIER) cc_final: 0.0726 (m-80) REVERT: d 51 LEU cc_start: 0.8322 (tp) cc_final: 0.8012 (tp) REVERT: d 64 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8487 (mt) REVERT: f 52 TYR cc_start: -0.1515 (OUTLIER) cc_final: -0.2385 (m-10) REVERT: f 58 LEU cc_start: 0.1873 (OUTLIER) cc_final: 0.1591 (mp) REVERT: g 61 MET cc_start: 0.1224 (tpp) cc_final: 0.0707 (ttm) REVERT: m 283 LEU cc_start: 0.3996 (OUTLIER) cc_final: 0.3559 (tp) REVERT: R 10 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7454 (tt0) REVERT: R 18 MET cc_start: 0.7658 (tpt) cc_final: 0.7136 (tpt) REVERT: R 65 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7763 (pttt) REVERT: R 144 MET cc_start: 0.3254 (ptp) cc_final: 0.2765 (ttp) REVERT: Q 210 PHE cc_start: 0.2640 (OUTLIER) cc_final: 0.0759 (m-80) REVERT: E 128 MET cc_start: 0.7549 (mmt) cc_final: 0.7127 (ptm) REVERT: F 52 TYR cc_start: -0.1883 (OUTLIER) cc_final: -0.2543 (m-10) REVERT: G 61 MET cc_start: 0.1032 (tpp) cc_final: 0.0661 (ttm) REVERT: M 270 ARG cc_start: 0.7395 (mmp80) cc_final: 0.6089 (mmt90) outliers start: 107 outliers final: 95 residues processed: 308 average time/residue: 0.1056 time to fit residues: 52.2269 Evaluate side-chains 320 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 216 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 180 LYS Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 34 ASN 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 61 LYS Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 90 GLN Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 195 CYS Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain a residue 36 ASP Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 79 GLU Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 280 ASN Chi-restraints excluded: chain m residue 281 PHE Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain n residue 270 LEU Chi-restraints excluded: chain n residue 282 CYS Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 34 MET Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 65 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 180 LYS Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 34 ASN Chi-restraints excluded: chain Q residue 37 GLN Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 61 LYS Chi-restraints excluded: chain Q residue 90 GLN Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 168 ASP Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 195 CYS Chi-restraints excluded: chain Q residue 210 PHE Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 139 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 101 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 38 GLN ** m 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 259 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 = 0.4794 r_free = 0.4794 target = 0.244280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.212383 restraints weight = 20991.800| |-----------------------------------------------------------------------------| r_work (start): 0.4563 rms_B_bonded: 1.85 r_work: 0.4113 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15992 Z= 0.143 Angle : 0.675 12.992 21720 Z= 0.328 Chirality : 0.042 0.221 2520 Planarity : 0.004 0.053 2680 Dihedral : 6.936 59.933 2285 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 6.75 % Allowed : 29.52 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 1936 helix: 2.61 (0.21), residues: 512 sheet: -0.29 (0.22), residues: 576 loop : -0.90 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 115 TYR 0.039 0.001 TYR N 264 PHE 0.015 0.001 PHE F 110 TRP 0.008 0.001 TRP F 59 HIS 0.003 0.001 HIS O 55 Details of bonding type rmsd covalent geometry : bond 0.00320 (15966) covalent geometry : angle 0.66991 (21664) SS BOND : bond 0.00315 ( 22) SS BOND : angle 1.39345 ( 44) hydrogen bonds : bond 0.03162 ( 779) hydrogen bonds : angle 4.58485 ( 2127) link_NAG-ASN : bond 0.00440 ( 4) link_NAG-ASN : angle 2.70507 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4711.01 seconds wall clock time: 81 minutes 25.63 seconds (4885.63 seconds total)